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Gromacs 2019 adh_cubic_vsites benchmark with OpenCL on a haswell
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| :-) GROMACS - gmx mdrun, 2019 (-: | |
| GROMACS is written by: | |
| Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen | |
| Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd | |
| Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray | |
| Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang | |
| Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis | |
| Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson | |
| Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund | |
| Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall | |
| Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov | |
| Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen | |
| Christian Wennberg Maarten Wolf | |
| and the project leaders: | |
| Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel | |
| Copyright (c) 1991-2000, University of Groningen, The Netherlands. | |
| Copyright (c) 2001-2018, The GROMACS development team at | |
| Uppsala University, Stockholm University and | |
| the Royal Institute of Technology, Sweden. | |
| check out http://www.gromacs.org for more information. | |
| GROMACS is free software; you can redistribute it and/or modify it | |
| under the terms of the GNU Lesser General Public License | |
| as published by the Free Software Foundation; either version 2.1 | |
| of the License, or (at your option) any later version. | |
| GROMACS: gmx mdrun, version 2019 | |
| Executable: /home/eltonfc/.local//bin/gmx | |
| Data prefix: /home/eltonfc/.local/ | |
| Working dir: /home/eltonfc/trab/software/gromacs/bench/adh_cubic_vsites | |
| Process ID: 25079 | |
| Command line: | |
| gmx mdrun -v -maxh .5 -notunepme | |
| GROMACS version: 2019 | |
| Precision: single | |
| Memory model: 64 bit | |
| MPI library: thread_mpi | |
| OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) | |
| GPU support: OpenCL | |
| SIMD instructions: AVX2_256 | |
| FFT library: fftw-3.3.6-pl2-fma-sse2-avx-avx2-avx2_128 | |
| RDTSCP usage: enabled | |
| TNG support: enabled | |
| Hwloc support: hwloc-1.11.2 | |
| Tracing support: disabled | |
| C compiler: /usr/bin/cc GNU 7.3.0 | |
| C compiler flags: -mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast | |
| C++ compiler: /usr/bin/c++ GNU 7.3.0 | |
| C++ compiler flags: -mavx2 -mfma -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast | |
| OpenCL include dir: /usr/include | |
| OpenCL library: /usr/lib/libOpenCL.so | |
| OpenCL version: 2.0 | |
| Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU | |
| Hardware detected: | |
| CPU info: | |
| Vendor: Intel | |
| Brand: Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz | |
| Family: 6 Model: 60 Stepping: 3 | |
| Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic | |
| Hardware topology: Full, with devices | |
| Sockets, cores, and logical processors: | |
| Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] | |
| Numa nodes: | |
| Node 0 (16704245760 bytes mem): 0 1 2 3 4 5 6 7 | |
| Latency: | |
| 0 | |
| 0 1.00 | |
| Caches: | |
| L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways | |
| L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways | |
| L3: 8388608 bytes, linesize 64 bytes, assoc. 16, shared 8 ways | |
| PCI devices: | |
| 0000:00:02.0 Id: 8086:0412 Class: 0x0300 Numa: 0 | |
| 0000:00:19.0 Id: 8086:153a Class: 0x0200 Numa: 0 | |
| 0000:00:1f.2 Id: 8086:8c02 Class: 0x0106 Numa: 0 | |
| GPU info: | |
| Number of GPUs detected: 1 | |
| #0: name: Intel(R) HD Graphics Haswell GT2 Desktop, vendor: Intel, device version: OpenCL 1.2 beignet 1.3, stat: compatible | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. | |
| Lindahl | |
| GROMACS: High performance molecular simulations through multi-level | |
| parallelism from laptops to supercomputers | |
| SoftwareX 1 (2015) pp. 19-25 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl | |
| Tackling Exascale Software Challenges in Molecular Dynamics Simulations with | |
| GROMACS | |
| In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. | |
| Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl | |
| GROMACS 4.5: a high-throughput and highly parallel open source molecular | |
| simulation toolkit | |
| Bioinformatics 29 (2013) pp. 845-54 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl | |
| GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable | |
| molecular simulation | |
| J. Chem. Theory Comput. 4 (2008) pp. 435-447 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. | |
| Berendsen | |
| GROMACS: Fast, Flexible and Free | |
| J. Comp. Chem. 26 (2005) pp. 1701-1719 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| E. Lindahl and B. Hess and D. van der Spoel | |
| GROMACS 3.0: A package for molecular simulation and trajectory analysis | |
| J. Mol. Mod. 7 (2001) pp. 306-317 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| H. J. C. Berendsen, D. van der Spoel and R. van Drunen | |
| GROMACS: A message-passing parallel molecular dynamics implementation | |
| Comp. Phys. Comm. 91 (1995) pp. 43-56 | |
| -------- -------- --- Thank You --- -------- -------- | |
| ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ | |
| https://doi.org/10.5281/zenodo.2424363 | |
| -------- -------- --- Thank You --- -------- -------- | |
| Input Parameters: | |
| integrator = md | |
| tinit = 0 | |
| dt = 0.005 | |
| nsteps = 10000 | |
| init-step = 0 | |
| simulation-part = 1 | |
| comm-mode = Linear | |
| nstcomm = 100 | |
| bd-fric = 0 | |
| ld-seed = 232683026 | |
| emtol = 10 | |
| emstep = 0.01 | |
| niter = 20 | |
| fcstep = 0 | |
| nstcgsteep = 1000 | |
| nbfgscorr = 10 | |
| rtpi = 0.05 | |
| nstxout = 0 | |
| nstvout = 0 | |
| nstfout = 0 | |
| nstlog = 0 | |
| nstcalcenergy = 100 | |
| nstenergy = 500 | |
| nstxout-compressed = 0 | |
| compressed-x-precision = 1000 | |
| cutoff-scheme = Verlet | |
| nstlist = 10 | |
| ns-type = Grid | |
| pbc = xyz | |
| periodic-molecules = false | |
| verlet-buffer-tolerance = 0.005 | |
| rlist = 0.935 | |
| coulombtype = PME | |
| coulomb-modifier = Potential-shift | |
| rcoulomb-switch = 0 | |
| rcoulomb = 0.9 | |
| epsilon-r = 1 | |
| epsilon-rf = inf | |
| vdw-type = Cut-off | |
| vdw-modifier = Potential-shift | |
| rvdw-switch = 0 | |
| rvdw = 0.9 | |
| DispCorr = No | |
| table-extension = 1 | |
| fourierspacing = 0.1125 | |
| fourier-nx = 100 | |
| fourier-ny = 100 | |
| fourier-nz = 100 | |
| pme-order = 4 | |
| ewald-rtol = 1e-05 | |
| ewald-rtol-lj = 0.001 | |
| lj-pme-comb-rule = Geometric | |
| ewald-geometry = 0 | |
| epsilon-surface = 0 | |
| tcoupl = V-rescale | |
| nsttcouple = 10 | |
| nh-chain-length = 0 | |
| print-nose-hoover-chain-variables = false | |
| pcoupl = No | |
| pcoupltype = Isotropic | |
| nstpcouple = -1 | |
| tau-p = 1 | |
| compressibility (3x3): | |
| compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| ref-p (3x3): | |
| ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| refcoord-scaling = No | |
| posres-com (3): | |
| posres-com[0]= 0.00000e+00 | |
| posres-com[1]= 0.00000e+00 | |
| posres-com[2]= 0.00000e+00 | |
| posres-comB (3): | |
| posres-comB[0]= 0.00000e+00 | |
| posres-comB[1]= 0.00000e+00 | |
| posres-comB[2]= 0.00000e+00 | |
| QMMM = false | |
| QMconstraints = 0 | |
| QMMMscheme = 0 | |
| MMChargeScaleFactor = 1 | |
| qm-opts: | |
| ngQM = 0 | |
| constraint-algorithm = Lincs | |
| continuation = false | |
| Shake-SOR = false | |
| shake-tol = 0.0001 | |
| lincs-order = 6 | |
| lincs-iter = 1 | |
| lincs-warnangle = 30 | |
| nwall = 0 | |
| wall-type = 9-3 | |
| wall-r-linpot = -1 | |
| wall-atomtype[0] = -1 | |
| wall-atomtype[1] = -1 | |
| wall-density[0] = 0 | |
| wall-density[1] = 0 | |
| wall-ewald-zfac = 3 | |
| pull = false | |
| awh = false | |
| rotation = false | |
| interactiveMD = false | |
| disre = No | |
| disre-weighting = Conservative | |
| disre-mixed = false | |
| dr-fc = 1000 | |
| dr-tau = 0 | |
| nstdisreout = 100 | |
| orire-fc = 0 | |
| orire-tau = 0 | |
| nstorireout = 100 | |
| free-energy = no | |
| cos-acceleration = 0 | |
| deform (3x3): | |
| deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} | |
| simulated-tempering = false | |
| swapcoords = no | |
| userint1 = 0 | |
| userint2 = 0 | |
| userint3 = 0 | |
| userint4 = 0 | |
| userreal1 = 0 | |
| userreal2 = 0 | |
| userreal3 = 0 | |
| userreal4 = 0 | |
| applied-forces: | |
| electric-field: | |
| x: | |
| E0 = 0 | |
| omega = 0 | |
| t0 = 0 | |
| sigma = 0 | |
| y: | |
| E0 = 0 | |
| omega = 0 | |
| t0 = 0 | |
| sigma = 0 | |
| z: | |
| E0 = 0 | |
| omega = 0 | |
| t0 = 0 | |
| sigma = 0 | |
| grpopts: | |
| nrdf: 247713 | |
| ref-t: 300 | |
| tau-t: 0.1 | |
| annealing: No | |
| annealing-npoints: 0 | |
| acc: 0 0 0 | |
| nfreeze: N N N | |
| energygrp-flags[ 0]: 0 | |
| Changing rlist from 0.935 to 0.956 for non-bonded 4x2 atom kernels | |
| Changing nstlist from 10 to 40, rlist from 0.956 to 1.094 | |
| Using 1 MPI thread | |
| Using 8 OpenMP threads | |
| 1 GPU auto-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 | |
| Pinning threads with an auto-selected logical core stride of 1 | |
| 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 0.288146 nm for Ewald | |
| Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-05 | |
| Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 1018 | |
| Generated table with 1046 data points for 1-4 COUL. | |
| Tabscale = 500 points/nm | |
| Generated table with 1046 data points for 1-4 LJ6. | |
| Tabscale = 500 points/nm | |
| Generated table with 1046 data points for 1-4 LJ12. | |
| Tabscale = 500 points/nm | |
| Using GPU 4x4 nonbonded short-range kernels | |
| Using a dual 4x2 pair-list setup updated with dynamic, rolling pruning: | |
| outer list: updated every 40 steps, buffer 0.194 nm, rlist 1.094 nm | |
| inner list: updated every 4 steps, buffer 0.011 nm, rlist 0.911 nm | |
| At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: | |
| outer list: updated every 40 steps, buffer 0.304 nm, rlist 1.204 nm | |
| inner list: updated every 4 steps, buffer 0.040 nm, rlist 0.940 nm | |
| Using Lorentz-Berthelot Lennard-Jones combination rule | |
| Removing pbc first time | |
| Initializing LINear Constraint Solver | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| B. Hess | |
| P-LINCS: A Parallel Linear Constraint Solver for molecular simulation | |
| J. Chem. Theory Comput. 4 (2008) pp. 116-122 | |
| -------- -------- --- Thank You --- -------- -------- | |
| The number of constraints is 13140 | |
| 3504 constraints are involved in constraint triangles, | |
| will apply an additional matrix expansion of order 6 for couplings | |
| between constraints inside triangles | |
| ++++ 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 --- -------- -------- | |
| Center of mass motion removal mode is Linear | |
| We have the following groups for center of mass motion removal: | |
| 0: rest | |
| ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ | |
| G. Bussi, D. Donadio and M. Parrinello | |
| Canonical sampling through velocity rescaling | |
| J. Chem. Phys. 126 (2007) pp. 014101 | |
| -------- -------- --- Thank You --- -------- -------- | |
| There are: 124552 Atoms | |
| There are: 11672 VSites | |
| Constraining the starting coordinates (step 0) | |
| Constraining the coordinates at t0-dt (step 0) | |
| RMS relative constraint deviation after constraining: 3.07e-05 | |
| Initial temperature: 299.88 K | |
| Started mdrun on rank 0 Wed Jan 23 22:17:07 2019 | |
| Step Time | |
| 0 0.00000 | |
| Energies (kJ/mol) | |
| Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 | |
| 2.52212e+04 5.17017e+04 2.06788e+03 2.32931e+04 2.87705e+05 | |
| LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. | |
| 2.00473e+05 -2.26452e+06 1.95926e+04 -1.65446e+06 3.22293e+05 | |
| Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd | |
| -1.33217e+06 -1.33217e+06 3.12967e+02 4.47346e+02 6.07222e-05 | |
| Writing checkpoint, step 6000 at Wed Jan 23 22:32:12 2019 | |
| Step Time | |
| 10000 50.00000 | |
| Writing checkpoint, step 10000 at Wed Jan 23 22:42:16 2019 | |
| Energies (kJ/mol) | |
| Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 | |
| 2.39171e+04 5.14713e+04 1.90487e+03 2.33074e+04 2.88157e+05 | |
| LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. | |
| 1.97225e+05 -2.25992e+06 1.95731e+04 -1.65436e+06 3.08572e+05 | |
| Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd | |
| -1.34579e+06 -1.33699e+06 2.99642e+02 4.23996e+02 5.20327e-05 | |
| <====== ############### ==> | |
| <==== A V E R A G E S ====> | |
| <== ############### ======> | |
| Statistics over 10001 steps using 101 frames | |
| Energies (kJ/mol) | |
| Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 | |
| 2.40135e+04 5.16104e+04 1.97281e+03 2.32118e+04 2.88337e+05 | |
| LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. | |
| 1.97950e+05 -2.26159e+06 1.94700e+04 -1.65502e+06 3.09169e+05 | |
| Total Energy Conserved En. Temperature Pressure (bar) Constr. rmsd | |
| -1.34585e+06 -1.33423e+06 3.00222e+02 3.95776e+02 0.00000e+00 | |
| Total Virial (kJ/mol) | |
| 8.72490e+04 2.18022e+02 -2.04698e+01 | |
| 2.17895e+02 8.71912e+04 -3.73210e+01 | |
| -2.03466e+01 -3.83831e+01 8.75039e+04 | |
| Pressure (bar) | |
| 3.96783e+02 -5.85625e+00 8.10214e-01 | |
| -5.85304e+00 4.01535e+02 -6.28920e-01 | |
| 8.07118e-01 -6.02217e-01 3.89011e+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 4723.039760 42507.358 0.1 | |
| NxN Ewald Elec. + LJ [F] 793216.982880 52352320.870 90.7 | |
| NxN Ewald Elec. + LJ [V&F] 8092.108144 865855.571 1.5 | |
| 1,4 nonbonded interactions 562.216216 50599.459 0.1 | |
| Calc Weights 4087.128672 147136.632 0.3 | |
| Spread Q Bspline 87192.078336 174384.157 0.3 | |
| Gather F Bspline 87192.078336 523152.470 0.9 | |
| 3D-FFT 398671.243138 3189369.945 5.5 | |
| Solve PME 100.010000 6400.640 0.0 | |
| Shift-X 34.192224 205.153 0.0 | |
| Angles 325.472544 54679.387 0.1 | |
| Propers 548.454840 125596.158 0.2 | |
| Impropers 40.564056 8437.324 0.0 | |
| Virial 13.763169 247.737 0.0 | |
| Stop-CM 13.894848 138.948 0.0 | |
| Calc-Ekin 272.720448 7363.452 0.0 | |
| Lincs 131.439420 7886.365 0.0 | |
| Lincs-Mat 3692.627456 14770.510 0.0 | |
| Constraint-V 1391.078160 11128.625 0.0 | |
| Constraint-Vir 12.719940 305.279 0.0 | |
| Settle 376.112800 121484.434 0.2 | |
| Virtual Site 3 21.012160 777.450 0.0 | |
| Virtual Site 3fd 19.880736 1888.670 0.0 | |
| Virtual Site 3fad 3.313456 583.168 0.0 | |
| Virtual Site 3out 57.217728 4977.942 0.0 | |
| Virtual Site 4fdn 16.486464 4187.562 0.0 | |
| ----------------------------------------------------------------------------- | |
| Total 57716385.269 100.0 | |
| ----------------------------------------------------------------------------- | |
| 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 8 OpenMP threads | |
| Computing: Num Num Call Wall time Giga-Cycles | |
| Ranks Threads Count (s) total sum % | |
| ----------------------------------------------------------------------------- | |
| Vsite constr. 1 8 10001 1.000 28.733 0.1 | |
| Neighbor search 1 8 251 5.410 155.445 0.4 | |
| Launch GPU ops. 1 8 10001 1353.401 38888.866 89.6 | |
| Force 1 8 10001 6.941 199.443 0.5 | |
| PME mesh 1 8 10001 121.314 3485.853 8.0 | |
| Wait GPU NB local 1 8 10001 0.425 12.220 0.0 | |
| NB X/F buffer ops. 1 8 19751 6.577 188.988 0.4 | |
| Vsite spread 1 8 10102 1.572 45.169 0.1 | |
| Write traj. 1 8 2 0.505 14.506 0.0 | |
| Update 1 8 10001 5.537 159.111 0.4 | |
| Constraints 1 8 10003 6.719 193.054 0.4 | |
| Rest 0.691 19.863 0.0 | |
| ----------------------------------------------------------------------------- | |
| Total 1510.092 43391.251 100.0 | |
| ----------------------------------------------------------------------------- | |
| Breakdown of PME mesh computation | |
| ----------------------------------------------------------------------------- | |
| PME spread 1 8 10001 40.884 1174.769 2.7 | |
| PME gather 1 8 10001 29.190 838.744 1.9 | |
| PME 3D-FFT 1 8 20002 48.085 1381.693 3.2 | |
| PME solve Elec 1 8 10001 3.060 87.920 0.2 | |
| ----------------------------------------------------------------------------- | |
| GPU timings | |
| ----------------------------------------------------------------------------- | |
| Computing: Count Wall t (s) ms/step % | |
| ----------------------------------------------------------------------------- | |
| Pair list H2D 251 0.377 1.500 0.0 | |
| X / q H2D 10001 18.341 1.834 0.0 | |
| Nonbonded F kernel 990055340232448.731 5589922469 50.0 | |
| Nonbonded F+ene k. 101 62.366 617.484 0.0 | |
| Pruning kernel 251 6.736 26.836 0.0 | |
| F D2H 1000155340232519.377 5533469904 50.0 | |
| ----------------------------------------------------------------------------- | |
| Total 110680465055.927 1106693981 100.0 | |
| ----------------------------------------------------------------------------- | |
| *Dynamic pruning 4750 25.872 5.447 0.0 | |
| ----------------------------------------------------------------------------- | |
| Average per-step force GPU/CPU evaluation time ratio: 11066939811.612 ms/12.824 ms = 862973673.837 | |
| For optimal resource utilization this ratio should be close to 1 | |
| NOTE: The GPU has >25% more load than the CPU. This imbalance wastes | |
| CPU resources. | |
| Core t (s) Wall t (s) (%) | |
| Time: 12080.732 1510.092 800.0 | |
| (ns/day) (hour/ns) | |
| Performance: 2.861 8.389 | |
| Finished mdrun on rank 0 Wed Jan 23 22:42:17 2019 | |
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