:-) GROMACS - gmx mdrun, 2019.1 (-: 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 2019.1 Executable: /share/pkg.7/gromacs/2019.1_openmpi_3.1.4/install/bin/gmx_mpi Data prefix: /share/pkg.7/gromacs/2019.1_openmpi_3.1.4/install Working dir: /project/scv/examples/chemistry/basic Process ID: 166193 Command line: gmx_mpi mdrun -v -deffnm sample -c sample.gro GROMACS version: 2019.1 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: SSE4.1 FFT library: Intel MKL RDTSCP usage: disabled TNG support: enabled Hwloc support: hwloc-1.11.8 Tracing support: disabled C compiler: /usr/bin/gcc GNU 4.8.5 C compiler flags: -msse4.1 -pthread -O2 -funroll-loops -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/g++ GNU 4.8.5 C++ compiler flags: -msse4.1 -pthread -O2 -funroll-loops -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /share/pkg.7/cuda/9.2/install/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Tue_Jun_12_23:07:04_CDT_2018;Cuda compilation tools, release 9.2, V9.2.148 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;;; ;-msse4.1;-pthread;-O2;-funroll-loops;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver: 0.0 CUDA runtime: N/A NOTE: Detection of GPUs failed. The API reported: No valid CUDA driver found GROMACS cannot run tasks on a GPU. Running on 1 node with total 28 cores, 28 logical cores, 0 compatible GPUs Hardware detected on host scc2 (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Family: 6 Model: 79 Stepping: 1 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] [ 2] [ 4] [ 6] [ 8] [ 10] [ 12] [ 14] [ 16] [ 18] [ 20] [ 22] [ 24] [ 26] Socket 1: [ 1] [ 3] [ 5] [ 7] [ 9] [ 11] [ 13] [ 15] [ 17] [ 19] [ 21] [ 23] [ 25] [ 27] Numa nodes: Node 0 (137340850176 bytes mem): 0 2 4 6 8 10 12 14 16 18 20 22 24 26 Node 1 (137438953472 bytes mem): 1 3 5 7 9 11 13 15 17 19 21 23 25 27 Latency: 0 1 0 1.00 2.10 1 2.10 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways PCI devices: 0000:08:00.0 Id: 102b:0534 Class: 0x0300 Numa: 0 0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0 0000:81:00.0 Id: 8086:10fb Class: 0x0200 Numa: 1 0000:81:00.1 Id: 8086:10fb Class: 0x0200 Numa: 1 Highest SIMD level requested by all nodes in run: AVX2_256 SIMD instructions selected at compile time: SSE4.1 This program was compiled for different hardware than you are running on, which could influence performance. The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. ++++ 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.2564764 -------- -------- --- Thank You --- -------- -------- The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Input Parameters: integrator = md tinit = 0 dt = 0.001 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 10 bd-fric = 0 ld-seed = 1993 emtol = 1 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstcalcenergy = 10 nstenergy = 10 nstxout-compressed = 10 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 2 coulombtype = Cut-off coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 2 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = Berendsen 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 = 4 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: 9 ref-t: 300 tau-t: 0.25 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 10 to 100, rlist from 2 to 2 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. System total charge: 0.000 Potential shift: LJ r^-12: -2.441e-04 r^-6: -1.562e-02, Coulomb -5e-01 Generated table with 1500 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1500 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1500 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x4 nonbonded short-range kernels Using a 4x4 pair-list setup: updated every 100 steps, buffer 0.000 nm, rlist 2.000 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: updated every 100 steps, buffer 0.000 nm, rlist 2.000 nm Using geometric Lennard-Jones combination rule Removing pbc first time 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 ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- There are: 4 Atoms Initial temperature: 129.339 K Started mdrun on rank 0 Wed Aug 28 10:48:08 2019 Step Time 0 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.95324e-03 5.21107e-01 0.00000e+00 -2.23963e-01 3.57551e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 3.34853e-01 4.75024e+00 5.08509e+00 Conserved En. Temperature Pressure (bar) 5.08509e+00 1.26961e+02 6.49595e-02 Step Time 10 0.01000 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 6.40838e-01 9.81149e-01 1.62400e-03 -2.25835e-01 3.59702e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 1.43375e+00 3.93405e+00 5.36780e+00 Conserved En. Temperature Pressure (bar) 5.10527e+00 1.05146e+02 9.21058e-01 Step Time 20 0.02000 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 2.48764e+00 1.23756e+00 1.01913e-02 -2.25424e-01 3.59189e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 3.54588e+00 2.15422e+00 5.70011e+00 Conserved En. Temperature Pressure (bar) 5.15731e+00 5.75764e+01 -1.78771e+00 Step Time 30 0.03000 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.54768e+00 1.04707e+00 2.91944e-02 -2.28740e-01 3.65662e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 2.43177e+00 3.60285e+00 6.03462e+00 Conserved En. Temperature Pressure (bar) 5.12915e+00 9.62942e+01 1.24769e+00 Step Time 40 0.04000 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.17220e+00 8.69765e-01 5.00236e-02 -2.28755e-01 3.65750e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 1.89981e+00 4.42345e+00 6.32325e+00 Conserved En. Temperature Pressure (bar) 5.10381e+00 1.18226e+02 8.46999e-01 Step Time 50 0.05000 Writing checkpoint, step 50 at Wed Aug 28 10:48:08 2019 Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.75418e+00 1.44590e+00 5.82927e-02 -2.28239e-01 3.63834e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 3.06652e+00 3.56485e+00 6.63136e+00 Conserved En. Temperature Pressure (bar) 5.14518e+00 9.52783e+01 -1.25195e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 51 steps using 6 frames Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.26741e+00 1.01709e+00 2.48877e-02 -2.26826e-01 3.61948e-02 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.00000e+00 0.00000e+00 2.11876e+00 3.73828e+00 5.85704e+00 Conserved En. Temperature Pressure (bar) 5.12097e+00 9.99136e+01 6.84061e-03 Total Virial (kJ/mol) -2.56414e+00 -1.63403e+00 1.51537e-01 -1.63401e+00 4.99587e+00 -2.28750e+00 1.51469e-01 -2.28760e+00 6.88622e-01 Pressure (bar) 1.14669e-01 5.82083e-02 2.15153e-04 5.82077e-02 -1.10534e-01 7.75511e-02 2.17429e-04 7.75546e-02 1.63870e-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 0.000018 0.000 0.2 NxN RF Elec. + LJ [F] 0.000720 0.027 33.4 NxN RF Elec. + LJ [V&F] 0.000096 0.005 6.3 1,4 nonbonded interactions 0.000051 0.005 5.6 Shift-X 0.000004 0.000 0.0 Bonds 0.000153 0.009 11.0 Angles 0.000102 0.017 20.9 Propers 0.000051 0.012 14.2 Virial 0.000294 0.005 6.5 Stop-CM 0.000028 0.000 0.3 Calc-Ekin 0.000048 0.001 1.6 ----------------------------------------------------------------------------- Total 0.082 100.0 ----------------------------------------------------------------------------- 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 Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 1 1 0.000 0.000 1.1 Force 1 1 51 0.000 0.001 4.9 NB X/F buffer ops. 1 1 101 0.000 0.000 0.8 Write traj. 1 1 6 0.005 0.013 80.5 Update 1 1 51 0.000 0.000 1.1 Rest 0.001 0.002 11.5 ----------------------------------------------------------------------------- Total 0.007 0.016 100.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 0.006 0.007 94.5 (ns/day) (hour/ns) Performance: 670.699 0.036 Finished mdrun on rank 0 Wed Aug 28 10:48:08 2019