# Gromacs 2021.1 installation, make check fails at Mdrun Mpi Coordination Tests and regression tests **URL:** \ **Category:** User discussions\ **Tags:** installation-error\ **Created:** [March 12, 2021, 3:56pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743 "2021-03-12T15:56:32Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 12, 2021, 3:56pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/1 "2021-03-12T15:56:32Z")
GROMACS version: 2021.1 GROMACS modification: No Hi, could I get some advise on instalation please? I am installing gromacs 2021 on the local HPC. I have logged into an interactive node with GPUs to stay off the way. The node info: num\_proc=20 gputype=TITAN-X gpus=4 I am using (via loded modules): - cmake 3.18.0 - gcc 8.4.0 - openmpi 4.0.0 - cuda 10.1.105 - python 3.7.3 My flags are: `cmake ../ -DCMAKE_C_COMPILER=gcc -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=$prefix -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DBUILD_SHARED_LIBS=yes` when i run `make check` I get the following failed/timed out tests: ``` 63 - MdrunMpiCoordinationTestsTwoRanks (Timeout) 68 - regressiontests/complex (Failed) 69 - regressiontests/freeenergy (Timeout) 71 - regressiontests/essentialdynamics (Failed) ``` I am not sure what these test actually mean - please advise - Have I done something wrong? - Are these failuars something I _should expect_ if doing tests of a single node? Should I be testing somehow else? Thank you! V ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [March 12, 2021, 5:07pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/2 "2021-03-12T17:07:09Z")
> [@Valentina](#): > > Have I done something wrong? No. > [@Valentina](#): > > Are these failuars something I _should expect_ if doing tests of a single node? Should I be testing somehow else? No. Can you please: - share the entire output (all errors the complex and essentialdynamics tests) - try to run with a single GPU, some of the test scripts can run into hiccups on multi-GPU nodes; e.g. run `CUDA_VISIBLE_DEVICES=0 make check` Cheers, Szilárd ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 12, 2021, 7:52pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/3 "2021-03-12T19:52:16Z")
Thank you Szilárd. Below is the last part of the make check, from where it times out at mdrun mpi coordinatioon tests two ranks. It is fine for one rank. As you sugested, I am also now trying `CUDA_VISIBLE_DEVICES=0 make check` Thanks again! V > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 48 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.701 1.883 196.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.780 30.767 > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_reference.edr as single precision energy file > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21.edr as single precision energy file > > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 48 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.751 1.908 196.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.770 31.176 > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_reference.edr as single precision energy file > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21.edr as single precision energy file > > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 48 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.699 1.882 196.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.780 30.751 > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21\_reference.edr as single precision energy file > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_21.edr as single precision energy file > [OK] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (22091 ms) > [RUN] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 > > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 48 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.715 1.899 195.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.773 31.029 > > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 47 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.708 1.886 196.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.779 30.824 > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_reference.edr as single precision energy file > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.edr as single precision energy file > Last energy frame read 4 time 0.016 > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > 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 0.701 nm, buffer size 0.001 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 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: 48 % of the run time was spent communicating energies, > you might want to increase some nst\* mdp options > > ``` > Core t (s) Wall t (s) (%) > Time: 3.777 1.921 196.6 > (ns/day) (hour/ns) > > ``` > > Performance: 0.765 31.388 > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_reference.edr as single precision energy file > Opened /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.edr as single precision energy file > Last energy frame read 4 time 0.016 > NOTE 1 [file /home/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22\_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/verastov/group/SOFTWARE/gromacs-2021.1/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling\_PeriodicActionsTest\_PeriodicActionsAgreeWithReference\_22.tpr, VERSION 2021.1 (single precision) > Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 > > Using 2 MPI threads > > Non-default thread affinity set, disabling internal thread affinity > > Using 1 OpenMP thread per tMPI thread > > ``` > Start 64: MdrunFEPTests > > ``` > > 64/71 Test #64: MdrunFEPTests … Passed 14.10 sec > Start 65: MdrunSimulatorComparison > 65/71 Test #65: MdrunSimulatorComparison … Passed 0.04 sec > Start 66: GmxapiExternalInterfaceTests > 66/71 Test #66: GmxapiExternalInterfaceTests … Passed 14.25 sec > Start 67: GmxapiInternalInterfaceTests > 67/71 Test #67: GmxapiInternalInterfaceTests … Passed 12.77 sec > Start 68: regressiontests/complex > 68/71 Test #68: regressiontests/complex …\*\*\*Timeout 1500.09 sec > sh: line 1: 196107 Aborted (core dumped) gmx mdrun -notunepme \> mdrun.out 2\>&1 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric > sh: line 1: 196198 Aborted (core dumped) gmx mdrun -notunepme \> mdrun.out 2\>&1 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB > sh: line 1: 196326 Aborted (core dumped) gmx mdrun -notunepme \> mdrun.out 2\>&1 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch > sh: line 1: 1000 Aborted (core dumped) gmx mdrun -notunepme \> mdrun.out 2\>&1 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn\_pme\_order6 for nbnxn\_pme\_order6 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron > sh: line 1: 2027 Aborted (core dumped) gmx mdrun -notunepme \> mdrun.out 2\>&1 > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in pr-vrescale for pr-vrescale > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_x for swap\_x > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_y for swap\_y > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in swap\_z for swap\_z > > ``` > Start 69: regressiontests/freeenergy > > ``` > > 69/71 Test #69: regressiontests/freeenergy …\*\*\*Failed 471.37 sec > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential\_coul for coulandvdwsequential\_coul > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential\_vdw for coulandvdwsequential\_vdw > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in coulandvdwtogether for coulandvdwtogether > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in restraints for restraints > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in simtemp for simtemp > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was -1 > FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -notunepme \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > 6 out of 10 freeenergy tests FAILED > > ``` > Start 70: regressiontests/rotation > > ``` > > 70/71 Test #70: regressiontests/rotation … Passed 152.30 sec > Start 71: regressiontests/essentialdynamics > 71/71 Test #71: regressiontests/essentialdynamics …\*\*\*Failed 90.87 sec > > Abnormal return value for ’ gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg \>mdrun.out 2\>&1’ was -1 > > Abnormal return value for ’ gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg \>mdrun.out 2\>&1’ was -1 > Essential dynamics tests FAILED with 2 errors! > > 94% tests passed, 4 tests failed out of 71 > > Label Time Summary: > GTest = 856.49 sec_proc (65 tests) > IntegrationTest = 242.72 sec_proc (18 tests) > MpiTest = 633.83 sec_proc (8 tests) > SlowTest = 540.68 sec_proc (8 tests) > UnitTest = 73.09 sec\*proc (39 tests) > > Total Test time (real) = 3072.04 sec > > The following tests FAILED: > 63 - MdrunMpiCoordinationTestsTwoRanks (Timeout) > 68 - regressiontests/complex (Timeout) > 69 - regressiontests/freeenergy (Failed) > 71 - regressiontests/essentialdynamics (Failed) > Errors while running CTest > make[3]: \*\*\* [CMakeFiles/run-ctest-nophys] Error 8 > make[2]: \*\*\* [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > make[1]: \*\*\* [CMakeFiles/check.dir/rule] Error 2 > make: \*\*\* [check] Error 2 ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 13, 2021, 2:51pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/4 "2021-03-13T14:51:26Z")
Thank you Szilárd! Also done `CUDA_VISIBLE_DEVICES=0 make check` and same as on multi-GPU (see below) Do you have any insights on what is happening or what am I missing? Thank you again V > ``` > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 > FAILED. Check mdrun.out, md.log file(s) in simtemp for simtemp > sh: line 1: 18452 Aborted (core dumped) gmx mdrun -notunepme > mdrun.out 2>&1 > > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 > FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was 1 > Retrying mdrun with better settings... > 6 out of 10 freeenergy tests FAILED > > Start 70: regressiontests/rotation > 70/71 Test #70: regressiontests/rotation .............. Passed 149.20 sec > Start 71: regressiontests/essentialdynamics > 71/71 Test #71: regressiontests/essentialdynamics .....***Failed 89.07 sec > > Abnormal return value for ' gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1' was -1 > > Abnormal return value for ' gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1' was -1 > Essential dynamics tests FAILED with 2 errors! > > 94% tests passed, 4 tests failed out of 71 > > Label Time Summary: > GTest = 855.12 sec*proc (65 tests) > IntegrationTest = 241.89 sec*proc (18 tests) > MpiTest = 633.67 sec*proc (8 tests) > SlowTest = 542.76 sec*proc (8 tests) > UnitTest = 70.46 sec*proc (39 tests) > > Total Test time (real) = 3063.27 sec > > The following tests FAILED: > 63 - MdrunMpiCoordinationTestsTwoRanks (Timeout) > 68 - regressiontests/complex (Timeout) > 69 - regressiontests/freeenergy (Failed) > 71 - regressiontests/essentialdynamics (Failed) > Errors while running CTest > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > make: *** [check] Error 2 > > ``` ---
**Author:** ![vasyl](https://avatars.discourse-cdn.com/v4/letter/v/b5a626/32.png) [@vasyl](https://gromacs.bioexcel.eu/u/vasyl)\ **Post date:** [March 16, 2021, 5:37pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/5 "2021-03-16T17:37:01Z")
Hi Valentina, Have you tried to compile with MPI? On my computer it passed 100% tests. You would need the following flags for cmake: -DGMX\_MPI=ON -DCMAKE\_C\_COMPILER=mpicc -DCMAKE\_CXX\_COMPILER=mpicxx ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 16, 2021, 6:44pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/6 "2021-03-16T18:44:57Z")
Hi, Not yet, trying but atm have this error: ``` CMake Error in /home/verastov/group/SOFTWARE/gromacs-2021.1/build-mpi/CMakeFiles/CMakeTmp/CMakeLists.txt: Target "cmTC_9d91c" requires the language dialect "CXX17" , but CMake does not know the compile flags to use to enable it. ``` I am using: `parallel_studio_xe_2017_update4/compilers_and_libraries/linux/mpi/intel64/bin/mpicxx` and `mpicc` ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [March 16, 2021, 6:55pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/7 "2021-03-16T18:55:15Z")
There are at least two issues here, neither of which is expected (timeouts and failing tests); let’s try to diagnose them I suggest. First, please try to run `GMX_DISABLE_GPU_DETECTION=1 make check` which will test your GROMACS build only using a CPU, I assume this will resolve at least the timeout (or both issues). I am not sure why are you getting timeouts with the GPU-enabled test, is there anything else running on the machine? Last, can you please attach the output files of the failing tests? ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 16, 2021, 7:10pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/8 "2021-03-16T19:10:41Z")
Thank you, trying `GMX_DISABLE_GPU_DETECTION=1 make check` Where are the errors written out to? There may be stuff running on the node, I am not sure I can get whole node to myself TBH, will check. Still, independent on what node I get and resources I get - same errors. ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [March 16, 2021, 7:57pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/9 "2021-03-16T19:57:51Z")
Hi, Same w/o GPUs. ``` ... Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in restraints for restraints Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in simtemp for simtemp sh: line 1: 173807 Aborted (core dumped) gmx mdrun -notunepme > mdrun.out 2>&1 Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1 FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... 6 out of 10 freeenergy tests FAILED Start 70: regressiontests/rotation 70/71 Test #70: regressiontests/rotation .............. Passed 24.38 sec Start 71: regressiontests/essentialdynamics 71/71 Test #71: regressiontests/essentialdynamics .....***Failed 16.96 sec Abnormal return value for ' gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1' was -1 Abnormal return value for ' gmx mdrun -ei /home/verastov/group/SOFTWARE/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1' was -1 Essential dynamics tests FAILED with 2 errors! 94% tests passed, 4 tests failed out of 71 Label Time Summary: GTest = 660.78 sec*proc (65 tests) IntegrationTest = 119.39 sec*proc (18 tests) MpiTest = 592.61 sec*proc (8 tests) SlowTest = 530.32 sec*proc (8 tests) UnitTest = 11.07 sec*proc (39 tests) Total Test time (real) = 2179.85 sec The following tests FAILED: 63 - MdrunMpiCoordinationTestsTwoRanks (Timeout) 68 - regressiontests/complex (Failed) 69 - regressiontests/freeenergy (Failed) 71 - regressiontests/essentialdynamics (Failed) Errors while running CTest make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[1]: *** [CMakeFiles/check.dir/rule] Error 2 make: *** [check] Error 2 ``` ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [March 29, 2021, 3:19pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/10 "2021-03-29T15:19:39Z")
> [@Valentina](#): > > Where are the errors written out to? In your build directory where you run `make check` from, in `tests/regressiontests-2021`. From there, grab the `freeenergy` and `essentialdynamics` directories and please file an issue on [Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/issues) > [@Valentina](#): > > There may be stuff running on the node, I am not sure I can get whole node to myself TBH, will check. Still, independent on what node I get and resources I get - same errors. The timeouts are most likely related to the resources you are trying to run the tests on being oversubscribed, e.g. the CPU cores or GPUs assigned to `make check` already running something else which makes some of the slower test not complete in time. If your CPU-only tests are not timing out, it is more likely that you are running on GPUs which are already busy. ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [April 1, 2021, 11:01am UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/11 "2021-04-01T11:01:17Z")
Hi, it seems I need a new[er than 2019] intel on the HPC, so getting IT to compile it, then will retry. Thank you for replying. I will update when I try with the new compilers/libraries. ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [April 12, 2021, 4:05pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/12 "2021-04-12T16:05:23Z")
I suggest trying GNU gcc, typically there is no advantage to using the Intel compilers over GNU. ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [April 29, 2021, 5:28pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/13 "2021-04-29T17:28:48Z")
Hi! Thank you for continuous advise! We had some updates on the HPC, so only now got again onto the install. I only have gcc working. which should be OK. I have logged into a node to install, got 6 GPUs and 6CPUs on it. I am doing `make check` and the following fail: > ``` > 97% tests passed, 2 tests failed out of 71 > > Label Time Summary: > GTest = 1190.84 sec*proc (65 tests) > IntegrationTest = 511.62 sec*proc (18 tests) > MpiTest = 640.24 sec*proc (8 tests) > SlowTest = 575.70 sec*proc (8 tests) > UnitTest = 103.51 sec*proc (39 tests) > > Total Test time (real) = 3050.20 sec > > The following tests FAILED: > 55 - MdrunIOTests (Timeout) > 71 - regressiontests/essentialdynamics (Failed) > Errors while running CTest > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > make: *** [check] Error 2 > > ``` I am not sure what sis with the `timeout` one. and the regression is: > Start 71: regressiontests/essentialdynamics > 71/71 Test #71: regressiontests/essentialdynamics …\*\*\*Failed 185.82 sec > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -ei /home/verastov/group/SOFTWARE/GROMACS-2021.1/install\_gmx/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > > Abnormal return value for ’ gmx mdrun -ntmpi 8 -ei /home/verastov/group/SOFTWARE/GROMACS-2021.1/install\_gmx/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg \>mdrun.out 2\>&1’ was -1 > Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. > > Abnormal return value for ’ gmx mdrun -ei /home/verastov/group/SOFTWARE/GROMACS-2021.1/install\_gmx/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg \>mdrun.out 2\>&1’ was 1 > Retrying mdrun with better settings… > > Abnormal return value for ’ gmx mdrun -ntmpi 8 -ei /home/verastov/group/SOFTWARE/GROMACS-2021.1/install\_gmx/gromacs-2021.1/build/tests/regressiontests-2021.1/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg \>mdrun.out 2\>&1’ was -1 > Essential dynamics tests FAILED with 2 errors! How can I get more insights to what is going wrong? Thank you Valentina ---
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [April 29, 2021, 5:32pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/14 "2021-04-29T17:32:00Z")
> [@pszilard](#): > > The timeouts are most likely related to the resources you are trying to run the tests on being oversubscribed, e.g. the CPU cores or GPUs assigned to `make check` already running something else which makes some of the slower test not complete in time. If your CPU-only tests are not timing out, it is more likely that you are running on GPUs which are already busy. This answers my question just posted above on the time out. There shouldn’t be any problem with the resources, but I am suspicious on the cluster things… I think the regression is also related to seeing or not the resources. I am going back to the cluster management team :( Thank you! ---
**Author:** ![pbhatta3](https://avatars.discourse-cdn.com/v4/letter/p/d07c76/32.png) [@pbhatta3](https://gromacs.bioexcel.eu/u/pbhatta3)\ **Post date:** [January 9, 2024, 5:04pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/15 "2024-01-09T17:04:53Z")
Hi Valentina, I am facing the similar problem with 2023.3 with Test #74:regressiontests/complex only, 99% passed in my case. Were you able to fix the error? Please let me know. Thanks ---
**Author:** ![rcrehuet](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rcrehuet/32/340_2.png) [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\ **Post date:** [January 17, 2024, 11:21am UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/16 "2024-01-17T11:21:09Z")
Hi @pbhatta3, I also encountered a failed test with gromacs 2023.3 It was regressiontests/complex, but in my case this test is #84. My machine has 8 GPUs and automatic assignment of tasks to these 8 GPUs failed. Following @pszilard suggestion `CUDA_VISIBLE_DEVICES=0 make check`allowed to pass all tests. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [January 17, 2024, 1:59pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/17 "2024-01-17T13:59:30Z")
But are the tests also failing due to timeouts or is some output not within the tolerance? ---
**Author:** ![pbhatta3](https://avatars.discourse-cdn.com/v4/letter/p/d07c76/32.png) [@pbhatta3](https://gromacs.bioexcel.eu/u/pbhatta3)\ **Post date:** [January 17, 2024, 4:12pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/18 "2024-01-17T16:12:36Z")
Hi @rcrehuet , Thank you for your suggestions. Our computer also has 8 GPUs. I will try your and @pszilard 's suggestions and see if they work in my case too. One more thing, I was not able to build GROMACS with MPI support, as many tests failed (71% tests passed, 17 tests failed out of 58). In contrast, when building GROMACS without MPI support, only one test (regressiontests/complex) failed. Do you or @pszilard know how to fix this issue and successfully build GROMACS with MPI support? I have attached the log files for all three steps (cmake, make, make check ) and the CPU information “lscpu” of my computer below (if needed). Any suggestions will be helpful. Thanks [cmake\_output2.log](https://gromacs.bioexcel.eu/uploads/short-url/bHca6Kk7SeyuECJZ23bdfYYfdyQ.log) (16.0 KB) [make\_check\_output.log](https://gromacs.bioexcel.eu/uploads/short-url/vbPlm3ssyiJWWJRDDZGDGNhzB2K.log) (1.2 MB) [make\_output.log](https://gromacs.bioexcel.eu/uploads/short-url/9UNfRF7h3SZAadp2s1myB0cEAYL.log) (6.1 MB) Architecture: x86\_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 96 On-line CPU(s) list: 0-95 Thread(s) per core: 2 Core(s) per socket: 24 Socket(s): 2 NUMA node(s): 2 Vendor ID: AuthenticAMD CPU family: 23 Model: 49 Model name: AMD EPYC 7352 24-Core Processor Stepping: 0 CPU MHz: 3148.522 CPU max MHz: 2300.0000 CPU min MHz: 1500.0000 BogoMIPS: 4599.92 Virtualization: AMD-V L1d cache: 32K L1i cache: 32K L2 cache: 512K L3 cache: 16384K NUMA node0 CPU(s): 0-23,48-71 NUMA node1 CPU(s): 24-47,72-95 ---
**Author:** ![rcrehuet](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rcrehuet/32/340_2.png) [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\ **Post date:** [January 18, 2024, 3:07pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/19 "2024-01-18T15:07:21Z")
It fails with the following error: ```auto ------------------------------------------------------- Program: gmx mdrun, version 2023.3 Source file: src/gromacs/taskassignment/taskassignment.cpp (line 330) Function: static gmx::GpuTaskAssignments gmx::GpuTaskAssignmentsBuilder::build(gmx::ArrayRef, gmx::ArrayRef, const gmx_hw_info_t&, MPI_Comm, const gmx::PhysicalNodeCommunicator&, gmx::TaskTarget, gmx::TaskTarget, gmx::TaskTarget, gmx::TaskTarget, bool, bool, bool, bool) MPI rank: 0 (out of 12) Inconsistency in user input: There were 12 GPU tasks found on node nodo01, but 8 GPUs were available. If the GPUs are equivalent, then it is usually best to have a number of tasks that is a multiple of the number of GPUs. You should reconsider your GPU task assignment, number of ranks, or your use of the -nb, -pme, and -npme options, perhaps after measuring the performance you can get. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` So it is not a problem with tolerance, but with default task assignment to GPUs ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [January 18, 2024, 4:07pm UTC](https://gromacs.bioexcel.eu/t/gromacs-2021-1-installation-make-check-fails-at-mdrun-mpi-coordination-tests-and-regression-tests/1743/20 "2024-01-18T16:07:05Z")
@mabraham is this related with the known GPU/task assignment issue? > **[task assignment issue in PME decomposition (#4684) · Issues · GROMACS /...](https://gitlab.com/gromacs/gromacs/-/issues/4684)** > > The following discussion from !3313 should be addressed: It looks like a different issue.