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Log file opened on Fri Mar 22 09:18:11 2019
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Host: r2c01cn3.leibniz pid: 11618 rank ID: 0 number of ranks: 112
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:-) GROMACS - gmx mdrun, 2018.3 (-:
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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 Aldert van Buuren Rudi van Drunen Anton Feenstra
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Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
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Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
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Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
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Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola
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Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov
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Michael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2017, 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 2018.3
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Executable: /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe/bin/gmx_mpi
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Data prefix: /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe
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Working dir: /scratch/gromacs-2019/test2018
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Command line:
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gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/test2018/0519.trr -x /scratch/gromacs-2019/test2018/0519.xtc -cpo /scratch/gromacs-2019/test2018/0519.cpt -c /scratch/gromacs-2019/test2018/0519.gro -e /scratch/gromacs-2019/test2018/0519.edr -dhdl /scratch/gromacs-2019/test2018/0519.xvg -g /scratch/gromacs-2019/test2018/0519.log -px /scratch/gromacs-2019/test2018/0519.x.xvg -pf /scratch/gromacs-2019/test2018/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1
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GROMACS version: 2018.3
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Precision: single
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Memory model: 64 bit
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MPI library: MPI
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support: disabled
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SIMD instructions: AVX2_256
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FFT library: Intel MKL
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RDTSCP usage: enabled
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TNG support: enabled
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Hwloc support: hwloc-1.11.2
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Tracing support: disabled
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Built on: 2018-09-03 09:39:43
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Built by: ...@r2c10cn3.leibniz [CMAKE]
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Build OS/arch: Linux 3.10.0-693.17.1.el7.x86_64 x86_64
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Build CPU vendor: Intel
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Build CPU brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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Build CPU family: 6 Model: 79 Stepping: 1
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Build CPU 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
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C compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410
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C compiler flags: -march=core-avx2 -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
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C++ compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410
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C++ compiler flags: -march=core-avx2 -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
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Running on 4 nodes with total 112 cores, 112 logical cores
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Cores per node: 28
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Logical cores per node: 28
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Hardware detected on host r2c01cn3.leibniz (the node of MPI rank 0):
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CPU info:
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Vendor: Intel
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Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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Family: 6 Model: 79 Stepping: 1
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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
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Hardware topology: Full, with devices
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Sockets, cores, and logical processors:
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Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13]
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Socket 1: [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27]
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Numa nodes:
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Node 0 (68600541184 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11 12 13
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Node 1 (68719476736 bytes mem): 14 15 16 17 18 19 20 21 22 23 24 25 26 27
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Latency:
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0 1
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0 1.00 2.10
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1 2.10 1.00
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Caches:
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L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways
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PCI devices:
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0000:01:00.0 Id: 8086:1521 Class: 0x0200 Numa: 0
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0000:01:00.1 Id: 8086:1521 Class: 0x0200 Numa: 0
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0000:02:00.0 Id: 15b3:1013 Class: 0x0207 Numa: 0
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0000:00:11.4 Id: 8086:8d62 Class: 0x0106 Numa: 0
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0000:07:00.0 Id: 1a03:2000 Class: 0x0300 Numa: 0
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0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0
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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 = 500000
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init-step = 0
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simulation-part = 1
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comm-mode = Linear
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nstcomm = 100
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bd-fric = 0
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ld-seed = -350048814
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emtol = 10
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emstep = 0.01
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niter = 20
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fcstep = 0
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nstcgsteep = 1000
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nbfgscorr = 10
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rtpi = 0.05
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nstxout = 0
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nstvout = 0
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nstfout = 0
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nstlog = 50000
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nstcalcenergy = 100
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nstenergy = 50000
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nstxout-compressed = 50000
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compressed-x-precision = 1000
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cutoff-scheme = Verlet
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nstlist = 20
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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 = 1.223
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coulombtype = PME
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coulomb-modifier = Potential-shift
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rcoulomb-switch = 0
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rcoulomb = 1.2
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epsilon-r = 1
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epsilon-rf = inf
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vdw-type = Cut-off
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vdw-modifier = Potential-shift
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rvdw-switch = 1
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rvdw = 1.2
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DispCorr = EnerPres
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table-extension = 1
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fourierspacing = 0.16
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fourier-nx = 96
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fourier-ny = 84
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fourier-nz = 80
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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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implicit-solvent = No
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gb-algorithm = Still
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nstgbradii = 1
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rgbradii = 1
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gb-epsilon-solvent = 80
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gb-saltconc = 0
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gb-obc-alpha = 1
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gb-obc-beta = 0.8
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gb-obc-gamma = 4.85
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gb-dielectric-offset = 0.009
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sa-algorithm = Ace-approximation
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sa-surface-tension = 2.05016
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tcoupl = V-rescale
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nsttcouple = 20
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nh-chain-length = 0
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print-nose-hoover-chain-variables = false
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pcoupl = Berendsen
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pcoupltype = Isotropic
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nstpcouple = 20
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tau-p = 2
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compressibility (3x3):
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compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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ref-p (3x3):
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ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
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refcoord-scaling = COM
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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 = true
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Shake-SOR = false
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shake-tol = 0.0001
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lincs-order = 4
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lincs-iter = 1
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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 = true
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pull-cylinder-r = 1.5
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pull-constr-tol = 1e-06
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pull-print-COM = true
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pull-print-ref-value = true
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pull-print-components = true
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pull-nstxout = 50000
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pull-nstfout = 50000
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pull-ngroups = 3
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pull-group 0:
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atom: not available
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weight: not available
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pbcatom = -1
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pull-group 1:
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atom (1):
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atom[0]=1442
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weight: not available
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pbcatom = -1
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pull-group 2:
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atom (2):
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atom[0]=4641
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atom[1]=4643
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weight: not available
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pbcatom = 4641
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pull-ncoords = 1
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pull-coord 0:
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type = umbrella
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geometry = distance
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group[0] = 1
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group[1] = 2
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dim (3):
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dim[0]=1
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dim[1]=1
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dim[2]=1
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origin (3):
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origin[0]= 0.00000e+00
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origin[1]= 0.00000e+00
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origin[2]= 0.00000e+00
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vec (3):
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vec[0]= 0.00000e+00
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vec[1]= 0.00000e+00
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vec[2]= 0.00000e+00
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start = true
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init = 0.518654
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rate = 0
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k = 1000
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kB = 1000
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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 = Conservative
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disre-mixed = false
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dr-fc = 1000
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dr-tau = 0
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nstdisreout = 100
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orire-fc = 0
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orire-tau = 0
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nstorireout = 100
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|
321
|
free-energy = no
|
|
322
|
cos-acceleration = 0
|
|
323
|
deform (3x3):
|
|
324
|
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
|
|
325
|
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
|
|
326
|
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
|
|
327
|
simulated-tempering = false
|
|
328
|
swapcoords = no
|
|
329
|
userint1 = 0
|
|
330
|
userint2 = 0
|
|
331
|
userint3 = 0
|
|
332
|
userint4 = 0
|
|
333
|
userreal1 = 0
|
|
334
|
userreal2 = 0
|
|
335
|
userreal3 = 0
|
|
336
|
userreal4 = 0
|
|
337
|
applied-forces:
|
|
338
|
electric-field:
|
|
339
|
x:
|
|
340
|
E0 = 0
|
|
341
|
omega = 0
|
|
342
|
t0 = 0
|
|
343
|
sigma = 0
|
|
344
|
y:
|
|
345
|
E0 = 0
|
|
346
|
omega = 0
|
|
347
|
t0 = 0
|
|
348
|
sigma = 0
|
|
349
|
z:
|
|
350
|
E0 = 0
|
|
351
|
omega = 0
|
|
352
|
t0 = 0
|
|
353
|
sigma = 0
|
|
354
|
grpopts:
|
|
355
|
nrdf: 12909.9 439152
|
|
356
|
ref-t: 300 300
|
|
357
|
tau-t: 0.1 0.1
|
|
358
|
annealing: No No
|
|
359
|
annealing-npoints: 0 0
|
|
360
|
acc: 0 0 0
|
|
361
|
nfreeze: N N N
|
|
362
|
energygrp-flags[ 0]: 0
|
|
363
|
|
|
364
|
Changing nstlist from 20 to 80, rlist from 1.223 to 1.326
|
|
365
|
|
|
366
|
|
|
367
|
Initializing Domain Decomposition on 112 ranks
|
|
368
|
Dynamic load balancing: locked
|
|
369
|
Minimum cell size due to atom displacement: 0.625 nm
|
|
370
|
Initial maximum inter charge-group distances:
|
|
371
|
two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780
|
|
372
|
multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780
|
|
373
|
Minimum cell size due to bonded interactions: 0.487 nm
|
|
374
|
User supplied maximum distance required for P-LINCS: 0.700 nm
|
|
375
|
Guess for relative PME load: 0.13
|
|
376
|
Will use 96 particle-particle and 16 PME only ranks
|
|
377
|
This is a guess, check the performance at the end of the log file
|
|
378
|
Using 16 separate PME ranks, as guessed by mdrun
|
|
379
|
Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111
|
|
380
|
Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm
|
|
381
|
The maximum allowed number of cells is: X 18 Y 17 Z 15
|
|
382
|
Domain decomposition grid 4 x 4 x 6, separate PME ranks 16
|
|
383
|
PME domain decomposition: 4 x 4 x 1
|
|
384
|
Interleaving PP and PME ranks
|
|
385
|
This rank does only particle-particle work.
|
|
386
|
|
|
387
|
Domain decomposition rank 0, coordinates 0 0 0
|
|
388
|
|
|
389
|
The initial number of communication pulses is: X 1 Y 1 Z 1
|
|
390
|
The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm
|
|
391
|
|
|
392
|
The maximum allowed distance for charge groups involved in interactions is:
|
|
393
|
non-bonded interactions 1.326 nm
|
|
394
|
(the following are initial values, they could change due to box deformation)
|
|
395
|
two-body bonded interactions (-rdd) 1.326 nm
|
|
396
|
multi-body bonded interactions (-rdd) 1.326 nm
|
|
397
|
atoms separated by up to 5 constraints (-rcon) 2.003 nm
|
|
398
|
|
|
399
|
When dynamic load balancing gets turned on, these settings will change to:
|
|
400
|
The maximum number of communication pulses is: X 1 Y 1 Z 1
|
|
401
|
The minimum size for domain decomposition cells is 1.326 nm
|
|
402
|
The requested allowed shrink of DD cells (option -dds) is: 0.90
|
|
403
|
The allowed shrink of domain decomposition cells is: X 0.37 Y 0.40 Z 0.66
|
|
404
|
The maximum allowed distance for charge groups involved in interactions is:
|
|
405
|
non-bonded interactions 1.326 nm
|
|
406
|
two-body bonded interactions (-rdd) 1.326 nm
|
|
407
|
multi-body bonded interactions (-rdd) 1.326 nm
|
|
408
|
atoms separated by up to 5 constraints (-rcon) 1.326 nm
|
|
409
|
|
|
410
|
Using two step summing over 4 groups of on average 24.0 ranks
|
|
411
|
|
|
412
|
Using 112 MPI processes
|
|
413
|
Using 1 OpenMP thread per MPI process
|
|
414
|
|
|
415
|
|
|
416
|
Overriding thread affinity set outside gmx mdrun
|
|
417
|
|
|
418
|
Pinning threads with an auto-selected logical core stride of 1
|
|
419
|
System total charge: -0.000
|
|
420
|
Will do PME sum in reciprocal space for electrostatic interactions.
|
|
421
|
|
|
422
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
423
|
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
|
|
424
|
A smooth particle mesh Ewald method
|
|
425
|
J. Chem. Phys. 103 (1995) pp. 8577-8592
|
|
426
|
-------- -------- --- Thank You --- -------- --------
|
|
427
|
|
|
428
|
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
|
|
429
|
Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
|
|
430
|
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
|
|
431
|
|
|
432
|
Long Range LJ corr.: <C6> 3.1361e-04
|
|
433
|
Generated table with 1163 data points for Ewald.
|
|
434
|
Tabscale = 500 points/nm
|
|
435
|
Generated table with 1163 data points for LJ6.
|
|
436
|
Tabscale = 500 points/nm
|
|
437
|
Generated table with 1163 data points for LJ12.
|
|
438
|
Tabscale = 500 points/nm
|
|
439
|
Generated table with 1163 data points for 1-4 COUL.
|
|
440
|
Tabscale = 500 points/nm
|
|
441
|
Generated table with 1163 data points for 1-4 LJ6.
|
|
442
|
Tabscale = 500 points/nm
|
|
443
|
Generated table with 1163 data points for 1-4 LJ12.
|
|
444
|
Tabscale = 500 points/nm
|
|
445
|
|
|
446
|
Using SIMD 4x8 nonbonded short-range kernels
|
|
447
|
|
|
448
|
Using a dual 4x8 pair-list setup updated with dynamic pruning:
|
|
449
|
outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm
|
|
450
|
inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm
|
|
451
|
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
|
|
452
|
outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm
|
|
453
|
inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm
|
|
454
|
|
|
455
|
Using full Lennard-Jones parameter combination matrix
|
|
456
|
|
|
457
|
|
|
458
|
Will apply potential COM pulling
|
|
459
|
with 1 pull coordinate and 2 groups
|
|
460
|
Pull group 1: 1 atoms, mass 13.019
|
|
461
|
Pull group 2: 2 atoms, mass 26.018
|
|
462
|
Will use a sub-communicator for pull communication
|
|
463
|
|
|
464
|
Initializing Parallel LINear Constraint Solver
|
|
465
|
|
|
466
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
467
|
B. Hess
|
|
468
|
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
|
|
469
|
J. Chem. Theory Comput. 4 (2008) pp. 116-122
|
|
470
|
-------- -------- --- Thank You --- -------- --------
|
|
471
|
|
|
472
|
The number of constraints is 1073
|
|
473
|
There are inter charge-group constraints,
|
|
474
|
will communicate selected coordinates each lincs iteration
|
|
475
|
|
|
476
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
477
|
S. Miyamoto and P. A. Kollman
|
|
478
|
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
|
|
479
|
Water Models
|
|
480
|
J. Comp. Chem. 13 (1992) pp. 952-962
|
|
481
|
-------- -------- --- Thank You --- -------- --------
|
|
482
|
|
|
483
|
|
|
484
|
Linking all bonded interactions to atoms
|
|
485
|
|
|
486
|
|
|
487
|
The -noconfout functionality is deprecated, and may be removed in a future version.
|
|
488
|
|
|
489
|
Intra-simulation communication will occur every 20 steps.
|
|
490
|
Center of mass motion removal mode is Linear
|
|
491
|
We have the following groups for center of mass motion removal:
|
|
492
|
0: rest
|
|
493
|
|
|
494
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
495
|
G. Bussi, D. Donadio and M. Parrinello
|
|
496
|
Canonical sampling through velocity rescaling
|
|
497
|
J. Chem. Phys. 126 (2007) pp. 014101
|
|
498
|
-------- -------- --- Thank You --- -------- --------
|
|
499
|
|
|
500
|
There are: 224238 Atoms
|
|
501
|
Atom distribution over 96 domains: av 2335 stddev 86 min 2090 max 2430
|
|
502
|
|
|
503
|
Started mdrun on rank 0 Fri Mar 22 09:18:14 2019
|
|
504
|
Step Time
|
|
505
|
0 0.00000
|
|
506
|
|
|
507
|
Energies (kJ/mol)
|
|
508
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
509
|
5.09960e+03 7.77425e+03 4.85656e+03 2.47900e+03 -1.61705e+02
|
|
510
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
511
|
6.64263e+04 5.11422e+05 -1.65591e+04 -3.68724e+06 1.05264e+04
|
|
512
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
513
|
6.82855e-14 -3.09538e+06 9.65238e+03 -3.08573e+06 -3.08550e+06
|
|
514
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
515
|
5.13609e+00 -1.19286e+02 -1.38954e+03 2.44671e-06
|
|
516
|
|
|
517
|
DD step 79 load imb.: force 4.9% pme mesh/force 0.852
|
|
518
|
|
|
519
|
|
|
520
|
step 240 Turning on dynamic load balancing, because the performance loss due to load imbalance is 3.8 %.
|
|
521
|
|
|
522
|
|
|
523
|
step 8000 Turning off dynamic load balancing, because it is degrading performance.
|
|
524
|
|
|
525
|
Atom distribution over 96 domains: av 2335 stddev 86 min 2110 max 2401
|
|
526
|
|
|
527
|
step 24000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.7 %.
|
|
528
|
|
|
529
|
|
|
530
|
step 25600 Turning off dynamic load balancing, because it is degrading performance.
|
|
531
|
|
|
532
|
Atom distribution over 96 domains: av 2335 stddev 89 min 2078 max 2408
|
|
533
|
|
|
534
|
step 32000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.0 %.
|
|
535
|
|
|
536
|
|
|
537
|
step 35200 Turning off dynamic load balancing, because it is degrading performance.
|
|
538
|
|
|
539
|
Atom distribution over 96 domains: av 2335 stddev 87 min 2092 max 2408
|
|
540
|
|
|
541
|
step 40000 Will no longer try dynamic load balancing, as it degraded performance.
|
|
542
|
|
|
543
|
DD step 49999 load imb.: force 5.3% pme mesh/force 0.644
|
|
544
|
|
|
545
|
Step Time
|
|
546
|
50000 100.00000
|
|
547
|
|
|
548
|
Energies (kJ/mol)
|
|
549
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
550
|
4.83032e+03 7.91144e+03 4.75862e+03 2.58501e+03 -1.28384e+02
|
|
551
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
552
|
6.65623e+04 5.12972e+05 -1.65428e+04 -3.69199e+06 1.06877e+04
|
|
553
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
554
|
3.75102e+00 -3.09835e+06 5.63326e+05 -2.53502e+06 -3.10342e+06
|
|
555
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
556
|
2.99749e+02 -1.19052e+02 -1.98544e+00 2.95643e-06
|
|
557
|
|
|
558
|
DD step 99999 load imb.: force 5.7% pme mesh/force 0.647
|
|
559
|
|
|
560
|
Step Time
|
|
561
|
100000 200.00000
|
|
562
|
|
|
563
|
Energies (kJ/mol)
|
|
564
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
565
|
4.75345e+03 7.58282e+03 4.85553e+03 2.57402e+03 -1.79248e+02
|
|
566
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
567
|
6.64540e+04 5.11097e+05 -1.65655e+04 -3.68951e+06 1.06834e+04
|
|
568
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
569
|
3.31456e+00 -3.09825e+06 5.64329e+05 -2.53392e+06 -3.10198e+06
|
|
570
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
571
|
3.00283e+02 -1.19378e+02 -2.32919e+01 2.76256e-06
|
|
572
|
|
|
573
|
DD step 149999 load imb.: force 5.5% pme mesh/force 0.641
|
|
574
|
|
|
575
|
Step Time
|
|
576
|
150000 300.00000
|
|
577
|
|
|
578
|
Energies (kJ/mol)
|
|
579
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
580
|
5.04330e+03 7.84732e+03 4.76267e+03 2.59187e+03 -1.62709e+02
|
|
581
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
582
|
6.63614e+04 5.11111e+05 -1.65646e+04 -3.68670e+06 1.05392e+04
|
|
583
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
584
|
6.31904e+00 -3.09516e+06 5.63786e+05 -2.53138e+06 -3.10055e+06
|
|
585
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
586
|
2.99994e+02 -1.19365e+02 1.36845e+01 2.96967e-06
|
|
587
|
|
|
588
|
Writing checkpoint, step 188880 at Fri Mar 22 09:33:14 2019
|
|
589
|
|
|
590
|
|
|
591
|
DD step 199999 load imb.: force 3.8% pme mesh/force 0.657
|
|
592
|
|
|
593
|
Step Time
|
|
594
|
200000 400.00000
|
|
595
|
|
|
596
|
Energies (kJ/mol)
|
|
597
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
598
|
4.94785e+03 7.55779e+03 4.90840e+03 2.40698e+03 -7.60589e+01
|
|
599
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
600
|
6.66943e+04 5.10013e+05 -1.65563e+04 -3.68945e+06 1.06891e+04
|
|
601
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
602
|
1.73298e+01 -3.09885e+06 5.65413e+05 -2.53344e+06 -3.09905e+06
|
|
603
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
604
|
3.00859e+02 -1.19246e+02 -6.90249e+01 2.82245e-06
|
|
605
|
|
|
606
|
DD step 249999 load imb.: force 5.9% pme mesh/force 0.640
|
|
607
|
|
|
608
|
Step Time
|
|
609
|
250000 500.00000
|
|
610
|
|
|
611
|
Energies (kJ/mol)
|
|
612
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
613
|
5.04615e+03 7.56546e+03 4.92053e+03 2.49466e+03 -1.13046e+02
|
|
614
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
615
|
6.66422e+04 5.12506e+05 -1.65587e+04 -3.69014e+06 1.06123e+04
|
|
616
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
617
|
1.24707e+01 -3.09701e+06 5.64644e+05 -2.53237e+06 -3.09746e+06
|
|
618
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
619
|
3.00450e+02 -1.19281e+02 1.69750e+01 3.14922e-06
|
|
620
|
|
|
621
|
DD step 299999 load imb.: force 5.1% pme mesh/force 0.645
|
|
622
|
|
|
623
|
Step Time
|
|
624
|
300000 600.00000
|
|
625
|
|
|
626
|
Energies (kJ/mol)
|
|
627
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
628
|
4.87397e+03 7.61933e+03 4.95450e+03 2.49306e+03 -1.36325e+02
|
|
629
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
630
|
6.64239e+04 5.13536e+05 -1.65692e+04 -3.69342e+06 1.05761e+04
|
|
631
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
632
|
1.48148e+01 -3.09963e+06 5.64550e+05 -2.53508e+06 -3.09601e+06
|
|
633
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
634
|
3.00400e+02 -1.19431e+02 3.83472e+01 3.14445e-06
|
|
635
|
|
|
636
|
DD step 349999 load imb.: force 6.2% pme mesh/force 0.638
|
|
637
|
|
|
638
|
Step Time
|
|
639
|
350000 700.00000
|
|
640
|
|
|
641
|
Energies (kJ/mol)
|
|
642
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
643
|
5.08991e+03 7.69764e+03 4.89299e+03 2.53503e+03 -1.66483e+02
|
|
644
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
645
|
6.63619e+04 5.11430e+05 -1.65514e+04 -3.68938e+06 1.05755e+04
|
|
646
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
647
|
9.36988e+00 -3.09751e+06 5.63559e+05 -2.53395e+06 -3.09443e+06
|
|
648
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
649
|
2.99873e+02 -1.19176e+02 -4.38299e+01 2.81165e-06
|
|
650
|
|
|
651
|
Writing checkpoint, step 377760 at Fri Mar 22 09:48:14 2019
|
|
652
|
|
|
653
|
|
|
654
|
DD step 399999 load imb.: force 5.4% pme mesh/force 0.640
|
|
655
|
|
|
656
|
Step Time
|
|
657
|
400000 800.00000
|
|
658
|
|
|
659
|
Energies (kJ/mol)
|
|
660
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
661
|
4.83583e+03 7.86137e+03 4.79819e+03 2.54585e+03 -1.37643e+02
|
|
662
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
663
|
6.65807e+04 5.13211e+05 -1.65584e+04 -3.69136e+06 1.06535e+04
|
|
664
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
665
|
1.91043e+01 -3.09755e+06 5.63681e+05 -2.53387e+06 -3.09296e+06
|
|
666
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
667
|
2.99938e+02 -1.19276e+02 7.98090e+00 3.10775e-06
|
|
668
|
|
|
669
|
DD step 449999 load imb.: force 3.9% pme mesh/force 0.623
|
|
670
|
|
|
671
|
Step Time
|
|
672
|
450000 900.00000
|
|
673
|
|
|
674
|
Energies (kJ/mol)
|
|
675
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
676
|
5.03504e+03 7.58068e+03 4.95366e+03 2.55010e+03 -7.27573e+01
|
|
677
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
678
|
6.67311e+04 5.10533e+05 -1.65552e+04 -3.68593e+06 1.06144e+04
|
|
679
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
680
|
9.14612e+00 -3.09455e+06 5.63459e+05 -2.53109e+06 -3.09145e+06
|
|
681
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
682
|
2.99820e+02 -1.19230e+02 2.88342e+00 2.83940e-06
|
|
683
|
|
|
684
|
DD step 499999 load imb.: force 5.3% pme mesh/force 0.629
|
|
685
|
|
|
686
|
Step Time
|
|
687
|
500000 1000.00000
|
|
688
|
|
|
689
|
Energies (kJ/mol)
|
|
690
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
691
|
4.86851e+03 7.78448e+03 5.02171e+03 2.57295e+03 -1.99886e+02
|
|
692
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
693
|
6.65664e+04 5.11263e+05 -1.65511e+04 -3.69094e+06 1.05802e+04
|
|
694
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
695
|
5.72201e+00 -3.09903e+06 5.61760e+05 -2.53727e+06 -3.08991e+06
|
|
696
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
697
|
2.98916e+02 -1.19172e+02 -8.74913e+01 2.84239e-06
|
|
698
|
|
|
699
|
<====== ############### ==>
|
|
700
|
<==== A V E R A G E S ====>
|
|
701
|
<== ############### ======>
|
|
702
|
|
|
703
|
Statistics over 500001 steps using 5001 frames
|
|
704
|
|
|
705
|
Energies (kJ/mol)
|
|
706
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
707
|
4.91060e+03 7.67629e+03 4.91081e+03 2.55615e+03 -1.84510e+02
|
|
708
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
709
|
6.65040e+04 5.12981e+05 -1.65579e+04 -3.69164e+06 1.05927e+04
|
|
710
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
711
|
8.79495e+00 -3.09824e+06 5.63645e+05 -2.53459e+06 -3.09749e+06
|
|
712
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
713
|
2.99919e+02 -1.19269e+02 1.04596e+00 0.00000e+00
|
|
714
|
|
|
715
|
Box-X Box-Y Box-Z
|
|
716
|
1.45132e+01 1.32261e+01 1.20182e+01
|
|
717
|
|
|
718
|
Total Virial (kJ/mol)
|
|
719
|
1.87733e+05 1.80507e+01 -5.28405e+01
|
|
720
|
1.99566e+01 1.87843e+05 1.49384e+01
|
|
721
|
-5.10672e+01 1.46297e+01 1.87851e+05
|
|
722
|
|
|
723
|
Pressure (bar)
|
|
724
|
2.00325e+00 -4.36769e-01 8.11049e-01
|
|
725
|
-4.64232e-01 5.17693e-01 -1.78615e-01
|
|
726
|
7.85505e-01 -1.74166e-01 6.16928e-01
|
|
727
|
|
|
728
|
T-protein_and_gpfT-water_and_ions
|
|
729
|
2.99993e+02 2.99916e+02
|
|
730
|
|
|
731
|
|
|
732
|
M E G A - F L O P S A C C O U N T I N G
|
|
733
|
|
|
734
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
|
735
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
|
736
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
|
737
|
V&F=Potential and force V=Potential only F=Force only
|
|
738
|
|
|
739
|
Computing: M-Number M-Flops % Flops
|
|
740
|
-----------------------------------------------------------------------------
|
|
741
|
Pair Search distance check 845339.861640 7608058.755 0.1
|
|
742
|
NxN Ewald Elec. + LJ [F] 53531920.679536 3533106764.849 51.0
|
|
743
|
NxN Ewald Elec. + LJ [V&F] 540836.388816 57869493.603 0.8
|
|
744
|
NxN LJ [F] 77728.720608 2565047.780 0.0
|
|
745
|
NxN LJ [V&F] 785.026592 33756.143 0.0
|
|
746
|
NxN Ewald Elec. [F] 50759238.604624 3096313554.882 44.7
|
|
747
|
NxN Ewald Elec. [V&F] 512821.787472 43077030.148 0.6
|
|
748
|
1,4 nonbonded interactions 3669.507339 330255.661 0.0
|
|
749
|
Calc Weights 336357.672714 12108876.218 0.2
|
|
750
|
Spread Q Bspline 7175630.351232 14351260.702 0.2
|
|
751
|
Gather F Bspline 7175630.351232 43053782.107 0.6
|
|
752
|
3D-FFT 12450329.900610 99602639.205 1.4
|
|
753
|
Solve PME 16128.032256 1032194.064 0.0
|
|
754
|
Reset In Box 1400.814786 4202.444 0.0
|
|
755
|
CG-CoM 1401.711738 4205.135 0.0
|
|
756
|
Bonds 1849.003698 109091.218 0.0
|
|
757
|
Angles 3514.507029 590437.181 0.0
|
|
758
|
Propers 1640.503281 375675.251 0.0
|
|
759
|
Impropers 1287.002574 267696.535 0.0
|
|
760
|
Virial 5714.178558 102855.214 0.0
|
|
761
|
Stop-CM 1121.414238 11214.142 0.0
|
|
762
|
P-Coupling 5606.174238 33637.045 0.0
|
|
763
|
Calc-Ekin 11212.348476 302733.409 0.0
|
|
764
|
Lincs 566.014829 33960.890 0.0
|
|
765
|
Lincs-Mat 954.342888 3817.372 0.0
|
|
766
|
Constraint-V 121602.252436 972818.019 0.0
|
|
767
|
Constraint-Vir 6052.042015 145249.008 0.0
|
|
768
|
Settle 40156.740926 12970627.319 0.2
|
|
769
|
-----------------------------------------------------------------------------
|
|
770
|
Total 6926980934.302 100.0
|
|
771
|
-----------------------------------------------------------------------------
|
|
772
|
|
|
773
|
|
|
774
|
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
|
|
775
|
|
|
776
|
av. #atoms communicated per step for force: 2 x 447044.7
|
|
777
|
av. #atoms communicated per step for LINCS: 2 x 21812.1
|
|
778
|
|
|
779
|
|
|
780
|
Dynamic load balancing report:
|
|
781
|
DLB got disabled because it was unsuitable to use.
|
|
782
|
Average load imbalance: 7.8%.
|
|
783
|
The balanceable part of the MD step is 87%, load imbalance is computed from this.
|
|
784
|
Part of the total run time spent waiting due to load imbalance: 6.7%.
|
|
785
|
Average PME mesh/force load: 0.628
|
|
786
|
Part of the total run time spent waiting due to PP/PME imbalance: 5.0 %
|
|
787
|
|
|
788
|
NOTE: 6.7 % of the available CPU time was lost due to load imbalance
|
|
789
|
in the domain decomposition.
|
|
790
|
You might want to use dynamic load balancing (option -dlb.)
|
|
791
|
|
|
792
|
|
|
793
|
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
|
|
794
|
|
|
795
|
On 96 MPI ranks doing PP, and
|
|
796
|
on 16 MPI ranks doing PME
|
|
797
|
|
|
798
|
Computing: Num Num Call Wall time Giga-Cycles
|
|
799
|
Ranks Threads Count (s) total sum %
|
|
800
|
-----------------------------------------------------------------------------
|
|
801
|
Domain decomp. 96 1 6250 17.190 3960.630 0.6
|
|
802
|
DD comm. load 96 1 173 0.004 0.867 0.0
|
|
803
|
DD comm. bounds 96 1 157 0.007 1.726 0.0
|
|
804
|
Send X to PME 96 1 500001 1.973 454.537 0.1
|
|
805
|
Neighbor search 96 1 6251 33.463 7709.991 1.2
|
|
806
|
Comm. coord. 96 1 493750 38.782 8935.419 1.4
|
|
807
|
Force 96 1 500001 2026.176 466836.010 73.0
|
|
808
|
Wait + Comm. F 96 1 500001 103.307 23802.143 3.7
|
|
809
|
PME mesh * 16 1 500001 1402.994 53875.529 8.4
|
|
810
|
PME wait for PP * 976.796 37509.361 5.9
|
|
811
|
Wait + Recv. PME F 96 1 500001 5.720 1317.844 0.2
|
|
812
|
NB X/F buffer ops. 96 1 1487501 21.655 4989.357 0.8
|
|
813
|
COM pull force 96 1 500001 6.986 1609.659 0.3
|
|
814
|
Write traj. 96 1 13 0.036 8.262 0.0
|
|
815
|
Update 96 1 500001 5.806 1337.611 0.2
|
|
816
|
Constraints 96 1 500001 112.219 25855.418 4.0
|
|
817
|
Comm. energies 96 1 25001 3.201 737.606 0.1
|
|
818
|
Rest 3.280 755.727 0.1
|
|
819
|
-----------------------------------------------------------------------------
|
|
820
|
Total 2379.805 639698.273 100.0
|
|
821
|
-----------------------------------------------------------------------------
|
|
822
|
(*) Note that with separate PME ranks, the walltime column actually sums to
|
|
823
|
twice the total reported, but the cycle count total and % are correct.
|
|
824
|
-----------------------------------------------------------------------------
|
|
825
|
Breakdown of PME mesh computation
|
|
826
|
-----------------------------------------------------------------------------
|
|
827
|
PME redist. X/F 16 1 1000002 198.588 7625.860 1.2
|
|
828
|
PME spread 16 1 500001 460.457 17681.751 2.8
|
|
829
|
PME gather 16 1 500001 289.656 11122.896 1.7
|
|
830
|
PME 3D-FFT 16 1 1000002 317.011 12173.346 1.9
|
|
831
|
PME 3D-FFT Comm. 16 1 2000004 107.426 4125.187 0.6
|
|
832
|
PME solve Elec 16 1 500001 28.890 1109.375 0.2
|
|
833
|
-----------------------------------------------------------------------------
|
|
834
|
|
|
835
|
Core t (s) Wall t (s) (%)
|
|
836
|
Time: 266538.111 2379.805 11200.0
|
|
837
|
39:39
|
|
838
|
(ns/day) (hour/ns)
|
|
839
|
Performance: 36.306 0.661
|
|
840
|
Finished mdrun on rank 0 Fri Mar 22 09:57:54 2019
|