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:-) GROMACS - gmx mdrun, 2019.3-dev-20190610-7e3521c2d (-:
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GROMACS is written by:
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Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
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Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
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Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
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Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
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Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
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Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
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Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
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Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
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Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
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Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
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Christian Wennberg Maarten Wolf
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and the project leaders:
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Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2018, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS: gmx mdrun, version 2019.3-dev-20190610-7e3521c2d
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Executable: /home/pszilard/projects/gromacs/gromacs-19/build_clang7_ocl/bin/gmx
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Data prefix: /home/pszilard/projects/gromacs/gromacs-19 (source tree)
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Working dir: /home/pszilard/projects/gromacs/regressiontests-19/complex/position-restraints
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Process ID: 10249
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Command line:
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gmx mdrun -ntmpi 1 -notunepme
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GROMACS version: 2019.3-dev-20190610-7e3521c2d
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GIT SHA1 hash: 7e3521c2dd4d57f1cd730f45afac12decb2abd8e
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Precision: single
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Memory model: 64 bit
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MPI library: thread_mpi
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support: OpenCL
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SIMD instructions: AVX2_256
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FFT library: fftw-3.3.7-sse2-avx
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RDTSCP usage: enabled
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TNG support: enabled
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Hwloc support: disabled
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Tracing support: disabled
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C compiler: /home/pszilard/programs/clang/7.0.0/bin/clang Clang 7.0.0
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C compiler flags: -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG
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C++ compiler: /home/pszilard/programs/clang/7.0.0/bin/clang++ Clang 7.0.0
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C++ compiler flags: -mavx2 -mfma -std=c++11 -Wdeprecated -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-prototypes -Wall -O3 -DNDEBUG
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OpenCL include dir: /usr/include
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OpenCL library: /usr/lib/x86_64-linux-gnu/libOpenCL.so
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OpenCL version: 2.2
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Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
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Hardware detected:
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CPU info:
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Vendor: Intel
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Brand: Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
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Family: 6 Model: 142 Stepping: 10
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Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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Hardware topology: Basic
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Sockets, cores, and logical processors:
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Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
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GPU info:
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Number of GPUs detected: 1
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#0: name: Intel(R) Gen9 HD Graphics NEO, vendor: Intel(R) Corporation, device version: OpenCL 2.1 NEO , stat: compatible
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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integrator = md
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tinit = 0
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dt = 0.002
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nsteps = 10
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init-step = 0
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simulation-part = 1
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comm-mode = None
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nstcomm = 0
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bd-fric = 0
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ld-seed = 1993
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emtol = 20
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emstep = 0.01
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niter = 20
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fcstep = 0
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nstcgsteep = 200
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nbfgscorr = 10
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rtpi = 0.05
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nstxout = 10
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nstvout = 10
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nstfout = 10
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nstlog = 0
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nstcalcenergy = 10
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nstenergy = 10
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nstxout-compressed = 0
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compressed-x-precision = 1000
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cutoff-scheme = Verlet
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nstlist = 10
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ns-type = Grid
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pbc = xyz
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periodic-molecules = false
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verlet-buffer-tolerance = 0.005
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rlist = 1.046
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coulombtype = Cut-off
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coulomb-modifier = Potential-shift
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rcoulomb-switch = 0
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rcoulomb = 1
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epsilon-r = 1
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epsilon-rf = 1
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vdw-type = Cut-off
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vdw-modifier = Potential-shift
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rvdw-switch = 0
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rvdw = 1
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DispCorr = No
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table-extension = 1
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fourierspacing = 0.12
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fourier-nx = 0
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fourier-ny = 0
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fourier-nz = 0
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pme-order = 4
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ewald-rtol = 1e-05
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ewald-rtol-lj = 0.001
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lj-pme-comb-rule = Geometric
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ewald-geometry = 0
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epsilon-surface = 0
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tcoupl = V-rescale
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nsttcouple = 10
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nh-chain-length = 0
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print-nose-hoover-chain-variables = false
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pcoupl = No
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pcoupltype = Isotropic
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nstpcouple = -1
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tau-p = 1
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compressibility (3x3):
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compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p (3x3):
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ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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refcoord-scaling = No
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posres-com (3):
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posres-com[0]= 0.00000e+00
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posres-com[1]= 0.00000e+00
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posres-com[2]= 0.00000e+00
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posres-comB (3):
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posres-comB[0]= 0.00000e+00
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posres-comB[1]= 0.00000e+00
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posres-comB[2]= 0.00000e+00
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QMMM = false
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QMconstraints = 0
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QMMMscheme = 0
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MMChargeScaleFactor = 1
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qm-opts:
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ngQM = 0
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constraint-algorithm = Lincs
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continuation = false
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Shake-SOR = false
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shake-tol = 0.0001
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lincs-order = 3
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lincs-iter = 2
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lincs-warnangle = 30
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nwall = 0
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wall-type = 9-3
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wall-r-linpot = -1
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wall-atomtype[0] = -1
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wall-atomtype[1] = -1
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wall-density[0] = 0
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wall-density[1] = 0
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wall-ewald-zfac = 3
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pull = false
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awh = false
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rotation = false
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interactiveMD = false
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disre = No
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disre-weighting = Equal
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disre-mixed = false
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dr-fc = 200
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dr-tau = 0
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nstdisreout = 20
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orire-fc = 0
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orire-tau = 0
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nstorireout = 20
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free-energy = no
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cos-acceleration = 0
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deform (3x3):
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deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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simulated-tempering = false
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swapcoords = no
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userint1 = 0
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userint2 = 0
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userint3 = 0
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userint4 = 0
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userreal1 = 0
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userreal2 = 0
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userreal3 = 0
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userreal4 = 0
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applied-forces:
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electric-field:
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x:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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y:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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z:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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grpopts:
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nrdf: 2537
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ref-t: 300
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tau-t: 0.1
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annealing: No
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annealing-npoints: 0
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acc: 0 0 0
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nfreeze: N N N
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energygrp-flags[ 0]: 0
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Changing rlist from 1.046 to 1.051 for non-bonded 4x2 atom kernels
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Changing nstlist from 10 to 50, rlist from 1.051 to 1.286
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Using 1 MPI thread
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Using 8 OpenMP threads
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1 GPU selected for this run.
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Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
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PP:0
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PP tasks will do (non-perturbed) short-ranged interactions on the GPU
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Pinning threads with an auto-selected logical core stride of 1
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System total charge: 0.000
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Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Coulomb -1e+00
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Generated table with 1143 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1143 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1143 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using GPU 4x4 nonbonded short-range kernels
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Using a dual 4x2 pair-list setup updated with dynamic, rolling pruning:
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outer list: updated every 50 steps, buffer 0.286 nm, rlist 1.286 nm
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inner list: updated every 4 steps, buffer 0.019 nm, rlist 1.019 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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outer list: updated every 50 steps, buffer 0.346 nm, rlist 1.346 nm
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inner list: updated every 4 steps, buffer 0.025 nm, rlist 1.025 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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Removing pbc first time
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Initializing LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
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LINCS: A Linear Constraint Solver for molecular simulations
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326
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J. Comp. Chem. 18 (1997) pp. 1463-1472
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 484
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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G. Bussi, D. Donadio and M. Parrinello
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333
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Canonical sampling through velocity rescaling
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J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 1007 Atoms
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 7.29e-07
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343
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Initial temperature: 305.424 K
|
|
344
|
|
|
345
|
Started mdrun on rank 0 Mon Jun 10 23:46:41 2019
|
|
346
|
|
|
347
|
Step Time
|
|
348
|
0 0.00000
|
|
349
|
|
|
350
|
Energies (kJ/mol)
|
|
351
|
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
|
|
352
|
8.49567e+02 2.38781e+03 1.86323e+03 1.57600e+02 -3.65167e+02
|
|
353
|
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Position Rest.
|
|
354
|
9.32330e+02 1.40818e+04 -1.09261e+03 -2.00354e+04 5.96811e-05
|
|
355
|
Potential Kinetic En. Total Energy Conserved En. Temperature
|
|
356
|
-1.22083e+03 3.19570e+03 1.97487e+03 1.97487e+03 3.02999e+02
|
|
357
|
Pressure (bar) Constr. rmsd
|
|
358
|
-6.87667e+01 1.02829e-06
|
|
359
|
|
|
360
|
Step Time
|
|
361
|
10 0.02000
|
|
362
|
|
|
363
|
Writing checkpoint, step 10 at Mon Jun 10 23:46:41 2019
|
|
364
|
|
|
365
|
|
|
366
|
Energies (kJ/mol)
|
|
367
|
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
|
|
368
|
9.58721e+02 2.29668e+03 1.85409e+03 1.53329e+02 -3.93716e+02
|
|
369
|
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Position Rest.
|
|
370
|
8.96268e+02 1.41027e+04 -1.13006e+03 -1.99805e+04 9.25166e+00
|
|
371
|
Potential Kinetic En. Total Energy Conserved En. Temperature
|
|
372
|
-1.23317e+03 3.20385e+03 1.97068e+03 1.96817e+03 3.03772e+02
|
|
373
|
Pressure (bar) Constr. rmsd
|
|
374
|
-7.89550e+00 1.08599e-06
|
|
375
|
|
|
376
|
<====== ############### ==>
|
|
377
|
<==== A V E R A G E S ====>
|
|
378
|
<== ############### ======>
|
|
379
|
|
|
380
|
Statistics over 11 steps using 2 frames
|
|
381
|
|
|
382
|
Energies (kJ/mol)
|
|
383
|
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
|
|
384
|
9.04144e+02 2.34225e+03 1.85866e+03 1.55465e+02 -3.79441e+02
|
|
385
|
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Position Rest.
|
|
386
|
9.14299e+02 1.40923e+04 -1.11133e+03 -2.00080e+04 4.62586e+00
|
|
387
|
Potential Kinetic En. Total Energy Conserved En. Temperature
|
|
388
|
-1.22700e+03 3.19977e+03 1.97277e+03 1.97152e+03 3.03385e+02
|
|
389
|
Pressure (bar) Constr. rmsd
|
|
390
|
-3.83311e+01 0.00000e+00
|
|
391
|
|
|
392
|
Total Virial (kJ/mol)
|
|
393
|
7.97700e+02 -1.67735e+01 -5.88908e+01
|
|
394
|
-1.67593e+01 1.45876e+03 4.68493e+01
|
|
395
|
-5.13903e+01 -4.49568e+01 2.11402e+03
|
|
396
|
|
|
397
|
Pressure (bar)
|
|
398
|
2.50920e+01 3.65013e+00 5.49980e+00
|
|
399
|
3.64874e+00 -3.97868e+01 -6.87132e+00
|
|
400
|
4.76306e+00 2.14635e+00 -1.00299e+02
|
|
401
|
|
|
402
|
|
|
403
|
M E G A - F L O P S A C C O U N T I N G
|
|
404
|
|
|
405
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
|
406
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
|
407
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
|
408
|
V&F=Potential and force V=Potential only F=Force only
|
|
409
|
|
|
410
|
Computing: M-Number M-Flops % Flops
|
|
411
|
-----------------------------------------------------------------------------
|
|
412
|
Pair Search distance check 0.050000 0.450 0.3
|
|
413
|
NxN RF Elec. + LJ [F] 2.507760 95.295 67.6
|
|
414
|
NxN RF Elec. + LJ [V&F] 0.557280 30.093 21.4
|
|
415
|
1,4 nonbonded interactions 0.029183 2.626 1.9
|
|
416
|
Shift-X 0.001007 0.006 0.0
|
|
417
|
Bonds 0.006017 0.355 0.3
|
|
418
|
Propers 0.025916 5.935 4.2
|
|
419
|
Impropers 0.001870 0.389 0.3
|
|
420
|
Pos. Restr. 0.002112 0.106 0.1
|
|
421
|
Virial 0.002104 0.038 0.0
|
|
422
|
Calc-Ekin 0.004028 0.109 0.1
|
|
423
|
Lincs 0.006292 0.378 0.3
|
|
424
|
Lincs-Mat 0.024050 0.096 0.1
|
|
425
|
Constraint-V 0.011616 0.093 0.1
|
|
426
|
Constraint-Vir 0.000968 0.023 0.0
|
|
427
|
CMAP 0.000682 1.159 0.8
|
|
428
|
Urey-Bradley 0.020405 3.734 2.7
|
|
429
|
-----------------------------------------------------------------------------
|
|
430
|
Total 140.885 100.0
|
|
431
|
-----------------------------------------------------------------------------
|
|
432
|
|
|
433
|
|
|
434
|
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
|
|
435
|
|
|
436
|
On 1 MPI rank, each using 8 OpenMP threads
|
|
437
|
|
|
438
|
Computing: Num Num Call Wall time Giga-Cycles
|
|
439
|
Ranks Threads Count (s) total sum %
|
|
440
|
-----------------------------------------------------------------------------
|
|
441
|
Neighbor search 1 8 1 0.001 0.012 3.3
|
|
442
|
Launch GPU ops. 1 8 11 0.004 0.071 20.1
|
|
443
|
Force 1 8 11 0.002 0.034 9.5
|
|
444
|
Wait GPU NB local 1 8 11 0.001 0.021 5.9
|
|
445
|
NB X/F buffer ops. 1 8 21 0.001 0.019 5.3
|
|
446
|
Write traj. 1 8 2 0.011 0.168 47.2
|
|
447
|
Update 1 8 11 0.000 0.005 1.4
|
|
448
|
Constraints 1 8 13 0.001 0.020 5.6
|
|
449
|
Rest 0.000 0.006 1.8
|
|
450
|
-----------------------------------------------------------------------------
|
|
451
|
Total 0.022 0.356 100.0
|
|
452
|
-----------------------------------------------------------------------------
|
|
453
|
|
|
454
|
GPU timings
|
|
455
|
-----------------------------------------------------------------------------
|
|
456
|
Computing: Count Wall t (s) ms/step %
|
|
457
|
-----------------------------------------------------------------------------
|
|
458
|
Pair list H2D 1 0.000 0.016 0.5
|
|
459
|
X / q H2D 11 0.000 0.004 1.2
|
|
460
|
Nonbonded F kernel 9 0.002 0.205 54.5
|
|
461
|
Nonbonded F+ene k. 2 0.001 0.681 40.2
|
|
462
|
Pruning kernel 1 0.000 0.068 2.0
|
|
463
|
F D2H 11 0.000 0.005 1.6
|
|
464
|
-----------------------------------------------------------------------------
|
|
465
|
Total 0.003 0.308 100.0
|
|
466
|
-----------------------------------------------------------------------------
|
|
467
|
*Dynamic pruning 4 0.000 0.022 2.6
|
|
468
|
-----------------------------------------------------------------------------
|
|
469
|
|
|
470
|
Average per-step force GPU/CPU evaluation time ratio: 0.308 ms/0.194 ms = 1.586
|
|
471
|
|
|
472
|
Core t (s) Wall t (s) (%)
|
|
473
|
Time: 0.178 0.022 796.1
|
|
474
|
(ns/day) (hour/ns)
|
|
475
|
Performance: 85.019 0.282
|
|
476
|
Finished mdrun on rank 0 Mon Jun 10 23:46:41 2019
|
|
477
|
|