----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - gmx mdrun, 2023 (-: Executable: /usr/local/gromacs-2023/bin/gmx Data prefix: /usr/local/gromacs-2023 Working dir: /media/data/Egor/m1_new/prod_re Process ID: 51238 Command line: gmx mdrun -deffnm prod_re -v -nsteps -1 -notunepme -nb gpu -bonded gpu -update gpu -cpi prod_re.cpt GROMACS version: 2023 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: CUDA NB cluster size: 8 SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128 GPU FFT library: cuFFT Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 11.3.0 C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 11.3.0 C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG BLAS library: LAPACK library: CUDA compiler: /usr/local/cuda-12.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2023 NVIDIA Corporation;Built on Tue_Feb__7_19:32:13_PST_2023;Cuda compilation tools, release 12.1, V12.1.66;Build cuda_12.1.r12.1/compiler.32415258_0 CUDA compiler flags:-std=c++17;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;--generate-code=arch=compute_89,code=sm_89;--generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG CUDA driver: 12.10 CUDA runtime: 12.10 The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field. Overriding nsteps with value passed on the command line: -1 steps Changing nstlist from 20 to 100, rlist from 1.2 to 1.307 When checking whether update groups are usable: Domain decomposition is not active, so there is no need for update groups 1 GPU selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU PP task will update and constrain coordinates on the GPU PME tasks will do all aspects on the GPU Using 1 MPI thread Using 12 OpenMP threads System total charge: 0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1153 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1153 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1153 data points for 1-4 LJ12. Tabscale = 500 points/nm Using GPU 8x8 nonbonded short-range kernels Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning: outer list: updated every 100 steps, buffer 0.107 nm, rlist 1.307 nm inner list: updated every 22 steps, buffer 0.003 nm, rlist 1.203 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 100 steps, buffer 0.267 nm, rlist 1.467 nm inner list: updated every 22 steps, buffer 0.088 nm, rlist 1.288 nm Pinning threads with an auto-selected logical cpu stride of 2 Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- The number of constraints is 31470 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- There are: 96907 Atoms Updating coordinates and applying constraints on the GPU. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: MEMB 1: SOLV 2: SOLU Started mdrun on rank 0 Fri Mar 31 16:33:46 2023 Received the INT signal, stopping within 100 steps Step Time 2954100 5908.20000 Writing checkpoint, step 2954100 at Fri Mar 31 16:33:52 2023 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.89551e+04 1.30248e+05 1.02122e+05 2.79163e+03 -1.66620e+03 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 2.19840e+04 1.45950e+05 -3.21056e+04 -1.19681e+06 5.08301e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -7.93444e+05 2.69975e+05 -5.23470e+05 -1.31322e+05 2.99360e+02 Pressure (bar) Constr. rmsd 2.13728e+00 0.00000e+00 Energy conservation over simulation part #19 of length 8.2 ps, time 5900 to 5908.2 ps Conserved energy drift: 7.41e-04 kJ/mol/ps per atom <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 2954101 steps using 60 frames Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.93933e+04 1.30527e+05 1.02927e+05 2.81913e+03 -1.53931e+03 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 2.20074e+04 1.44676e+05 -3.07571e+04 -1.19509e+06 5.12948e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -7.89908e+05 2.70839e+05 -5.19069e+05 -3.17989e+05 3.00318e+02 Pressure (bar) Constr. rmsd 2.04055e+01 0.00000e+00 Box-X Box-Y Box-Z 1.14346e+01 8.35528e+00 9.65653e+00 Total Virial (kJ/mol) 8.82091e+04 1.29420e+02 -1.98273e+02 1.29363e+02 8.76408e+04 1.57705e+02 -1.98277e+02 1.57721e+02 9.32926e+04 Pressure (bar) 3.70487e+01 -3.05412e+00 7.19968e+00 -3.05208e+00 3.46346e+01 -8.69424e+00 7.19982e+00 -8.69483e+00 -1.04667e+01 T-MEMB T-SOLV T-SOLU 3.00552e+02 2.99744e+02 3.01050e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 729.395536 6564.560 0.0 NxN Ewald Elec. + LJ [F] 739552.807360 57685118.974 99.2 NxN Ewald Elec. + LJ [V&F] 246.204800 31760.419 0.1 1,4 nonbonded interactions 862.991808 77669.263 0.1 Shift-X 5.911327 35.468 0.0 Bonds 136.030668 8025.809 0.0 Propers 1004.207340 229963.481 0.4 Impropers 18.039006 3752.113 0.0 Virial 58.268152 1048.827 0.0 Stop-CM 0.096907 0.969 0.0 Calc-Ekin 116.385307 3142.403 0.0 CMAP 5.580930 9487.581 0.0 Urey-Bradley 614.694432 112489.081 0.2 ----------------------------------------------------------------------------- Total 58169058.948 100.0 ----------------------------------------------------------------------------- R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank, each using 12 OpenMP threads Activity: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % -------------------------------------------------------------------------------- Neighbor search 1 12 61 0.197 11.082 3.2 Launch PP GPU ops. 1 12 11941 0.575 32.389 9.2 Force 1 12 6001 0.220 12.371 3.5 PME GPU mesh 1 12 6001 0.225 12.686 3.6 Wait Bonded GPU 1 12 2 0.000 0.000 0.0 Wait GPU NB local 1 12 5400 0.098 5.489 1.6 Wait GPU state copy 1 12 7263 4.311 242.675 69.2 NB X/F buffer ops. 1 12 601 0.028 1.554 0.4 Write traj. 1 12 2 0.117 6.607 1.9 Rest 0.463 26.066 7.4 -------------------------------------------------------------------------------- Total 6.234 350.919 100.0 -------------------------------------------------------------------------------- Breakdown of PME mesh activities -------------------------------------------------------------------------------- Wait PME GPU gather 1 12 6001 0.098 5.522 1.6 Reduce GPU PME F 1 12 6001 0.014 0.767 0.2 Launch PME GPU ops. 1 12 54009 0.089 5.015 1.4 -------------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 74.802 6.234 1200.0 (ns/day) (hour/ns) Performance: 166.348 0.144 Finished mdrun on rank 0 Fri Mar 31 16:33:52 2023