Test project /home/labhhc/gromacs/build Start 63: MdrunIOTests 1/1 Test #63: MdrunIOTests .....................***Failed 4.48 sec [==========] Running 68 tests from 12 test suites. [----------] Global test environment set-up. [----------] 8 tests from GromppTest [ RUN ] GromppTest.EmptyMdpFileWorks NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Number of degrees of freedom in T-Coupling group rest is 12.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Setting the LD random seed to -34096461 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.EmptyMdpFileWorks (2 ms) [ RUN ] GromppTest.SimulatedAnnealingWorks NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Simulated annealing for group rest: Periodic, 4 timepoints Time (ps) Temperature (K) 0.0 298.0 2.0 320.0 4.0 320.0 6.0 298.0 Number of degrees of freedom in T-Coupling group rest is 12.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Setting the LD random seed to -1493835794 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.SimulatedAnnealingWorks (1 ms) [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Simulated annealing for group Methanol: Single, 3 timepoints Time (ps) Temperature (K) 0.0 298.0 3.0 280.0 6.0- 270.0 Simulated annealing for group SOL: Periodic, 4 timepoints Time (ps) Temperature (K) 0.0 298.0 2.0 320.0 4.0 320.0 6.0 298.0 Number of degrees of freedom in T-Coupling group Methanol is 7.20 Number of degrees of freedom in T-Coupling group SOL is 4.80 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Setting the LD random seed to -23072810 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (1 ms) [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError [WARNING] /home/labhhc/gromacs/src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 6 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. Setting the LD random seed to 2145186781 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (7 ms) [ RUN ] GromppTest.HandlesMaxwarn NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs There was 1 WARNING Setting the LD random seed to -1208670209 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.HandlesMaxwarn (1 ms) [ RUN ] GromppTest.MaxwarnShouldBePositive [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) [ RUN ] GromppTest.ValidTransformationCoord NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Pull group 1 'SOL' has 3 atoms Pull group 2 'Methanol' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 12.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 3 5 2 3 2 0.613 nm 0.000 nm 1 3 5 2 3 2 0.613 nm 0.000 nm There were 3 NOTEs Setting the LD random seed to -1213694021 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.ValidTransformationCoord (5 ms) [ RUN ] GromppTest.InvalidTransformationCoord NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Pull group 1 'SOL' has 3 atoms Pull group 2 'Methanol' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 12.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 3 5 2 3 2 0.613 nm 0.000 nm 1 3 5 2 3 2 Setting the LD random seed to -77692931 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup [ OK ] GromppTest.InvalidTransformationCoord (4 ms) [----------] 8 tests from GromppTest (24 ms total) [----------] 6 tests from MdrunTerminationTest [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1881441281 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.046 0.023 199.7 (ns/day) (hour/ns) Performance: 11.219 2.139 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 4 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 29 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.006 0.003 198.9 (ns/day) (hour/ns) Performance: 84.571 0.284 [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (33 ms) [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 1, rlist from 1.032 to 1 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 100 steps, 0.1 ps. Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps Setting the LD random seed to 2139537395 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Core t (s) Wall t (s) (%) Time: 0.023 0.011 199.7 (ns/day) (hour/ns) Performance: 15.042 1.596 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 102 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 100 Runtime for the run 0.1 ps Run end step 100 Run end time 0.1 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 102 Runtime for the run 0.102 ps Run end step 102 Run end time 0.102 ps Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.039 0.019 199.8 (ns/day) (hour/ns) Performance: 453.841 0.053 [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (36 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1614854701 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 21 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.2 (ns/day) (hour/ns) Performance: 62.377 0.385 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 4 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.5 (ns/day) (hour/ns) Performance: 65.650 0.366 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 6 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 6 Runtime for the run 0.006 ps Run end step 6 Run end time 0.006 ps Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.6 (ns/day) (hour/ns) Performance: 65.229 0.368 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 8 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 6 Runtime for the run 0.006 ps Run end step 6 Run end time 0.006 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 8 Runtime for the run 0.008 ps Run end step 8 Run end time 0.008 ps Writing final coordinates. NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.5 (ns/day) (hour/ns) Performance: 64.995 0.369 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). NOTE: 61 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.003 0.001 198.7 (ns/day) (hour/ns) Performance: 59.379 0.404 [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (30 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1619576929 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 21 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.1 (ns/day) (hour/ns) Performance: 62.427 0.384 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 4 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 4 steps, 0.0 ps. Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 20 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.009 0.004 199.2 (ns/day) (hour/ns) Performance: 97.826 0.245 [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (14 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to 781121405 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.2 (ns/day) (hour/ns) Performance: 63.207 0.380 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 4 Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (7 ms) [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 NOTE Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -2299923 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 26 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.009 0.004 199.1 (ns/day) (hour/ns) Performance: 58.371 0.411 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Setting nsteps to 4 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 24 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.5 (ns/day) (hour/ns) Performance: 67.526 0.355 [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (14 ms) [----------] 6 tests from MdrunTerminationTest (137 ms total) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.012 199.6 (ns/day) (hour/ns) Performance: 126.376 0.190 trr version: GMX_trn_file (single precision) [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (16 ms) [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.0 (ns/day) (hour/ns) Performance: 166.945 0.144 [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (14 ms) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (31 ms total) [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.5 (ns/day) (hour/ns) Performance: 170.942 0.140 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.2 (ns/day) (hour/ns) Performance: 122.103 0.197 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.3 (ns/day) (hour/ns) Performance: 114.651 0.209 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (32 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.9 (ns/day) (hour/ns) Performance: 172.002 0.140 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.0 (ns/day) (hour/ns) Performance: 111.226 0.216 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 198.7 (ns/day) (hour/ns) Performance: 115.598 0.208 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (34 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.6 (ns/day) (hour/ns) Performance: 176.329 0.136 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.5 (ns/day) (hour/ns) Performance: 118.089 0.203 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.1 (ns/day) (hour/ns) Performance: 115.738 0.207 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (31 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.5 (ns/day) (hour/ns) Performance: 176.208 0.136 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.5 (ns/day) (hour/ns) Performance: 116.904 0.205 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.012 0.006 199.3 (ns/day) (hour/ns) Performance: 124.584 0.193 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (35 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.3 (ns/day) (hour/ns) Performance: 176.699 0.136 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.007 199.2 (ns/day) (hour/ns) Performance: 104.757 0.229 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 19 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.2 (ns/day) (hour/ns) Performance: 109.914 0.218 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (36 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm Set rlist, assuming 4x4 atom pair-list, to 0.893 nm, buffer size 0.193 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.0 (ns/day) (hour/ns) Performance: 169.985 0.141 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.008 198.0 (ns/day) (hour/ns) Performance: 102.941 0.233 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.007 198.7 (ns/day) (hour/ns) Performance: 105.067 0.228 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (37 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.6 (ns/day) (hour/ns) Performance: 180.997 0.133 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.5 (ns/day) (hour/ns) Performance: 112.968 0.212 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.2 (ns/day) (hour/ns) Performance: 122.640 0.196 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (32 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.4 (ns/day) (hour/ns) Performance: 162.531 0.148 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.76 to 0.915 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.4 (ns/day) (hour/ns) Performance: 113.230 0.212 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.76 to 0.915 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.2 (ns/day) (hour/ns) Performance: 119.846 0.200 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (36 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.009 199.3 (ns/day) (hour/ns) Performance: 156.309 0.154 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.3 (ns/day) (hour/ns) Performance: 108.782 0.221 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.0 (ns/day) (hour/ns) Performance: 108.280 0.222 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:116: Failure Value of: energyValueInTest Actual: 46.601699829101562 Expected: energyValueInReference Which is: 46.601490020751953 Difference: 0.000209808 (55 single-prec. ULPs, rel. 4.5e-06) Tolerance: abs. 3.8147e-05, 32 ULPs Google Test trace: /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:109: Comparing Kinetic En. between frames /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:105: Comparing energy reference frame Time 0.012000 Step 12 and test frame Time 0.012000 Step 12 /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:199: Comparing frames from two runs 'Time 0.012000 Step 12' and 'Time 0.012000 Step 12' /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:391: Comparing normal and two-part run of simulation 'alanine_vsite_vacuo' with integrator 'md' Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:116: Failure Value of: energyValueInTest Actual: 49.859718322753906 Expected: energyValueInReference Which is: 49.858860015869141 Difference: 0.000858307 (225 single-prec. ULPs, rel. 1.72e-05) Tolerance: abs. 3.8147e-05, 32 ULPs Google Test trace: /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:109: Comparing Kinetic En. between frames /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:105: Comparing energy reference frame Time 0.016000 Step 16 and test frame Time 0.016000 Step 16 /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:199: Comparing frames from two runs 'Time 0.016000 Step 16' and 'Time 0.016000 Step 16' /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:391: Comparing normal and two-part run of simulation 'alanine_vsite_vacuo' with integrator 'md' /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:116: Failure Value of: energyValueInTest Actual: -142.494384765625 Expected: energyValueInReference Which is: -142.49310302734375 Difference: 0.00128174 (84 single-prec. ULPs, rel. 9e-06) Tolerance: abs. 3.8147e-05, 32 ULPs Google Test trace: /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:109: Comparing Potential between frames /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:105: Comparing energy reference frame Time 0.016000 Step 16 and test frame Time 0.016000 Step 16 /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:199: Comparing frames from two runs 'Time 0.016000 Step 16' and 'Time 0.016000 Step 16' /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:391: Comparing normal and two-part run of simulation 'alanine_vsite_vacuo' with integrator 'md' Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ FAILED ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8, where GetParam() = ("alanine_vsite_vacuo", "md", "no", "no", 4-byte object <00-00 00-00>) (41 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 199.5 (ns/day) (hour/ns) Performance: 154.409 0.155 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.007 199.4 (ns/day) (hour/ns) Performance: 106.334 0.226 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.4 (ns/day) (hour/ns) Performance: 111.162 0.216 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:116: Failure Value of: energyValueInTest Actual: 49.294483184814453 Expected: energyValueInReference Which is: 49.294204711914062 Difference: 0.000278473 (73 single-prec. ULPs, rel. 5.65e-06) Tolerance: abs. 3.8147e-05, 32 ULPs Google Test trace: /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:109: Comparing Kinetic En. between frames /home/labhhc/gromacs/src/programs/mdrun/tests/energycomparison.cpp:105: Comparing energy reference frame Time 0.016000 Step 16 and test frame Time 0.016000 Step 16 /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:199: Comparing frames from two runs 'Time 0.016000 Step 16' and 'Time 0.016000 Step 16' /home/labhhc/gromacs/src/programs/mdrun/tests/exactcontinuation.cpp:391: Comparing normal and two-part run of simulation 'alanine_vsite_vacuo' with integrator 'md-vv' Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ FAILED ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9, where GetParam() = ("alanine_vsite_vacuo", "md-vv", "no", "no", 4-byte object <00-00 00-00>) (40 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.009 199.6 (ns/day) (hour/ns) Performance: 154.820 0.155 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.748 to 0.885 Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.4 (ns/day) (hour/ns) Performance: 119.934 0.200 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.748 to 0.885 Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.4 (ns/day) (hour/ns) Performance: 118.859 0.202 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (46 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.009 199.6 (ns/day) (hour/ns) Performance: 157.600 0.152 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 40, rlist from 0.729 to 0.887 Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.4 (ns/day) (hour/ns) Performance: 116.657 0.206 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 40, rlist from 0.729 to 0.887 Update groups can not be used for this system because an incompatible virtual site type is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 198.9 (ns/day) (hour/ns) Performance: 111.837 0.215 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (43 ms) [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (449 ms total) [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps. Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 18 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.022 0.011 199.5 (ns/day) (hour/ns) Performance: 134.177 0.179 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 198.8 (ns/day) (hour/ns) Performance: 85.811 0.280 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 24 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.2 (ns/day) (hour/ns) Performance: 87.923 0.273 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (45 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps. Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.025 0.012 199.1 (ns/day) (hour/ns) Performance: 117.506 0.204 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.020 0.010 199.3 (ns/day) (hour/ns) Performance: 79.407 0.302 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.021 0.010 198.6 (ns/day) (hour/ns) Performance: 74.380 0.323 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (49 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps. Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 19 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.021 0.011 199.5 (ns/day) (hour/ns) Performance: 136.948 0.175 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.732 to 0.821 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.8 (ns/day) (hour/ns) Performance: 89.461 0.268 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.732 to 0.821 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 19 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.0 (ns/day) (hour/ns) Performance: 94.874 0.253 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (58 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps. Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 19 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.022 0.011 199.5 (ns/day) (hour/ns) Performance: 130.737 0.184 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.757 to 0.908 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.1 (ns/day) (hour/ns) Performance: 85.890 0.279 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.757 to 0.909 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 23 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.1 (ns/day) (hour/ns) Performance: 89.353 0.269 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (50 ms) [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (204 ms total) [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.6 (ns/day) (hour/ns) Performance: 166.976 0.144 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.2 (ns/day) (hour/ns) Performance: 118.204 0.203 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 20 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.2 (ns/day) (hour/ns) Performance: 112.407 0.214 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (33 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.6 (ns/day) (hour/ns) Performance: 175.666 0.137 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.2 (ns/day) (hour/ns) Performance: 120.062 0.200 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 18 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.2 (ns/day) (hour/ns) Performance: 110.735 0.217 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (33 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.6 (ns/day) (hour/ns) Performance: 177.759 0.135 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.1 (ns/day) (hour/ns) Performance: 118.397 0.203 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.1 (ns/day) (hour/ns) Performance: 115.639 0.208 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (32 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 198.8 (ns/day) (hour/ns) Performance: 173.469 0.138 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 198.9 (ns/day) (hour/ns) Performance: 114.178 0.210 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 198.1 (ns/day) (hour/ns) Performance: 121.367 0.198 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (34 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.2 (ns/day) (hour/ns) Performance: 176.430 0.136 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 198.8 (ns/day) (hour/ns) Performance: 115.787 0.207 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 197.7 (ns/day) (hour/ns) Performance: 113.665 0.211 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (34 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 199.1 (ns/day) (hour/ns) Performance: 154.536 0.155 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.2 (ns/day) (hour/ns) Performance: 88.599 0.271 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.007 198.8 (ns/day) (hour/ns) Performance: 105.772 0.227 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (43 ms) [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (212 ms total) [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.6 (ns/day) (hour/ns) Performance: 161.247 0.149 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.007 199.2 (ns/day) (hour/ns) Performance: 106.079 0.226 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.5 (ns/day) (hour/ns) Performance: 110.578 0.217 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (34 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.3 (ns/day) (hour/ns) Performance: 165.053 0.145 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.5 (ns/day) (hour/ns) Performance: 109.527 0.219 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.1 (ns/day) (hour/ns) Performance: 111.466 0.215 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (33 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.022 0.011 198.8 (ns/day) (hour/ns) Performance: 134.326 0.179 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 199.2 (ns/day) (hour/ns) Performance: 92.422 0.260 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 198.5 (ns/day) (hour/ns) Performance: 91.705 0.262 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (41 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.010 199.0 (ns/day) (hour/ns) Performance: 140.179 0.171 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.2 (ns/day) (hour/ns) Performance: 88.567 0.271 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.4 (ns/day) (hour/ns) Performance: 94.907 0.253 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (40 ms) [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (149 ms total) [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. WARNING 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There were 2 WARNINGs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. WARNING 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There were 2 WARNINGs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.009 199.6 (ns/day) (hour/ns) Performance: 156.690 0.153 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 20 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.008 199.2 (ns/day) (hour/ns) Performance: 100.110 0.240 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.5 (ns/day) (hour/ns) Performance: 110.182 0.218 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (35 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.6 (ns/day) (hour/ns) Performance: 169.247 0.142 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.1 (ns/day) (hour/ns) Performance: 115.791 0.207 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.4 (ns/day) (hour/ns) Performance: 115.521 0.208 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (32 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.6 (ns/day) (hour/ns) Performance: 162.506 0.148 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.4 (ns/day) (hour/ns) Performance: 123.182 0.195 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.0 (ns/day) (hour/ns) Performance: 115.390 0.208 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (32 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.3 (ns/day) (hour/ns) Performance: 171.337 0.140 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.4 (ns/day) (hour/ns) Performance: 115.447 0.208 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.1 (ns/day) (hour/ns) Performance: 120.872 0.199 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (35 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 199.3 (ns/day) (hour/ns) Performance: 151.321 0.159 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.3 (ns/day) (hour/ns) Performance: 114.631 0.209 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.0 (ns/day) (hour/ns) Performance: 118.889 0.202 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (35 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.3 (ns/day) (hour/ns) Performance: 168.700 0.142 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.4 (ns/day) (hour/ns) Performance: 114.386 0.210 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 198.8 (ns/day) (hour/ns) Performance: 120.031 0.200 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (34 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.6 (ns/day) (hour/ns) Performance: 169.587 0.142 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.006 199.0 (ns/day) (hour/ns) Performance: 119.842 0.200 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.4 (ns/day) (hour/ns) Performance: 116.690 0.206 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (33 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.3 (ns/day) (hour/ns) Performance: 169.957 0.141 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.4 (ns/day) (hour/ns) Performance: 113.994 0.211 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.0 (ns/day) (hour/ns) Performance: 118.243 0.203 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (32 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 199.6 (ns/day) (hour/ns) Performance: 171.471 0.140 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.013 0.007 199.0 (ns/day) (hour/ns) Performance: 119.600 0.201 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.014 0.007 199.4 (ns/day) (hour/ns) Performance: 113.939 0.211 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (34 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. WARNING 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There were 2 WARNINGs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. WARNING 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There were 2 WARNINGs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 198.9 (ns/day) (hour/ns) Performance: 144.256 0.166 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.1 (ns/day) (hour/ns) Performance: 94.252 0.255 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.3 (ns/day) (hour/ns) Performance: 99.242 0.242 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (37 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 199.3 (ns/day) (hour/ns) Performance: 145.623 0.165 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.6 (ns/day) (hour/ns) Performance: 96.380 0.249 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.2 (ns/day) (hour/ns) Performance: 94.067 0.255 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (38 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.021 0.011 199.2 (ns/day) (hour/ns) Performance: 138.893 0.173 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.1 (ns/day) (hour/ns) Performance: 96.766 0.248 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.4 (ns/day) (hour/ns) Performance: 98.401 0.244 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (41 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs There was 1 WARNING Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 199.2 (ns/day) (hour/ns) Performance: 145.232 0.165 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.008 199.0 (ns/day) (hour/ns) Performance: 100.502 0.239 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.5 (ns/day) (hour/ns) Performance: 96.130 0.250 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (38 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 199.3 (ns/day) (hour/ns) Performance: 143.798 0.167 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.1 (ns/day) (hour/ns) Performance: 99.670 0.241 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.6 (ns/day) (hour/ns) Performance: 89.214 0.269 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (38 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.010 199.1 (ns/day) (hour/ns) Performance: 142.192 0.169 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.6 (ns/day) (hour/ns) Performance: 93.667 0.256 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 199.0 (ns/day) (hour/ns) Performance: 97.320 0.247 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (39 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.010 199.4 (ns/day) (hour/ns) Performance: 141.995 0.169 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.016 0.008 198.8 (ns/day) (hour/ns) Performance: 98.279 0.244 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.008 198.6 (ns/day) (hour/ns) Performance: 91.702 0.262 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (37 ms) [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (578 ms total) [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.011 199.2 (ns/day) (hour/ns) Performance: 130.726 0.184 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.7 (ns/day) (hour/ns) Performance: 90.039 0.267 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 100, rlist from 0.703 to 0.75 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.7 (ns/day) (hour/ns) Performance: 90.278 0.266 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (40 ms) [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (40 ms total) [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm Set rlist, assuming 4x4 atom pair-list, to 0.863 nm, buffer size 0.163 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm Set rlist, assuming 4x4 atom pair-list, to 0.863 nm, buffer size 0.163 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.011 199.3 (ns/day) (hour/ns) Performance: 135.030 0.178 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.018 0.009 199.5 (ns/day) (hour/ns) Performance: 87.306 0.275 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.011 199.4 (ns/day) (hour/ns) Performance: 69.890 0.343 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (43 ms) [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm There were 3 NOTEs NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm Set rlist, assuming 4x4 atom pair-list, to 0.863 nm, buffer size 0.163 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm Set rlist, assuming 4x4 atom pair-list, to 0.863 nm, buffer size 0.163 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 198.8 (ns/day) (hour/ns) Performance: 143.223 0.168 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.7 (ns/day) (hour/ns) Performance: 89.031 0.270 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.017 0.009 198.9 (ns/day) (hour/ns) Performance: 89.987 0.267 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (42 ms) [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (86 ms total) [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 Setting the AWH bias MC random seed to -405045258 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 NOTEs Setting the AWH bias MC random seed to -1152389121 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.012 199.1 (ns/day) (hour/ns) Performance: 125.670 0.191 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.754 to 0.899 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 199.3 (ns/day) (hour/ns) Performance: 81.707 0.294 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.754 to 0.899 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 198.7 (ns/day) (hour/ns) Performance: 80.413 0.298 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (51 ms) [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 Setting the AWH bias MC random seed to -2114085143 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 NOTEs Setting the AWH bias MC random seed to -109097153 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.012 199.3 (ns/day) (hour/ns) Performance: 127.298 0.189 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.754 to 0.899 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.020 0.010 198.9 (ns/day) (hour/ns) Performance: 79.118 0.303 Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Changing nstlist from 8 to 25, rlist from 0.754 to 0.899 NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.019 0.010 199.0 (ns/day) (hour/ns) Performance: 81.697 0.294 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (53 ms) [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (105 ms total) [----------] 3 tests from Checking/InitialConstraintsTest [ RUN ] Checking/InitialConstraintsTest.Works/0 Number of degrees of freedom in T-Coupling group rest is 11.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -1073159 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.015 0.008 199.5 (ns/day) (hour/ns) Performance: 22.775 1.054 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (12 ms) [ RUN ] Checking/InitialConstraintsTest.Works/1 Number of degrees of freedom in T-Coupling group rest is 11.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -1079148625 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 28 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.010 0.005 198.2 (ns/day) (hour/ns) Performance: 35.269 0.680 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (10 ms) [ RUN ] Checking/InitialConstraintsTest.Works/2 NOTE 1 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: Integrator method md-vv-avek is implemented primarily for validation purposes; for molecular dynamics, you should probably be using md or md-vv Number of degrees of freedom in T-Coupling group rest is 11.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 3 [file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2023-beta-dev-20221122-83a4eb6163-dirty (single precision) Can not increase nstlist because an NVE ensemble is used NOTE: SYCL GPU support in GROMACS is still new and less tested than other backends. Please, pay extra attention to the correctness of your results. 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU Using 1 MPI thread Using 2 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cpus and the -pin option is set to auto: will not pin threads to cpus. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -271784593 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 21 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.008 0.004 199.1 (ns/day) (hour/ns) Performance: 41.764 0.575 Opened /home/labhhc/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (8 ms) [----------] 3 tests from Checking/InitialConstraintsTest (32 ms total) [----------] Global test environment tear-down [==========] 68 tests from 12 test suites ran. (4419 ms total) [ PASSED ] 66 tests. [ FAILED ] 2 tests, listed below: [ FAILED ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8, where GetParam() = ("alanine_vsite_vacuo", "md", "no", "no", 4-byte object <00-00 00-00>) [ FAILED ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9, where GetParam() = ("alanine_vsite_vacuo", "md-vv", "no", "no", 4-byte object <00-00 00-00>) 2 FAILED TESTS 0% tests passed, 1 tests failed out of 1 Label Time Summary: GTest = 4.48 sec*proc (1 test) IntegrationTest = 4.48 sec*proc (1 test) SlowGpuTest = 4.48 sec*proc (1 test) Total Test time (real) = 4.49 sec The following tests FAILED: 63 - MdrunIOTests (Failed) Errors while running CTest