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mahmoodn

gmx-tunepme

Feb 7th, 2021
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  1. $ ../single86/bin/gmx mdrun -nb gpu -v -deffnm nvt_20k
  2. :-) GROMACS - gmx mdrun, 2021 (-:
  3.  
  4. GROMACS is written by:
  5. Andrey Alekseenko Emile Apol Rossen Apostolov
  6. Paul Bauer Herman J.C. Berendsen Par Bjelkmar
  7. Christian Blau Viacheslav Bolnykh Kevin Boyd
  8. Aldert van Buuren Rudi van Drunen Anton Feenstra
  9. Gilles Gouaillardet Alan Gray Gerrit Groenhof
  10. Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
  11. Aleksei Iupinov Christoph Junghans Joe Jordan
  12. Dimitrios Karkoulis Peter Kasson Jiri Kraus
  13. Carsten Kutzner Per Larsson Justin A. Lemkul
  14. Viveca Lindahl Magnus Lundborg Erik Marklund
  15. Pascal Merz Pieter Meulenhoff Teemu Murtola
  16. Szilard Pall Sander Pronk Roland Schulz
  17. Michael Shirts Alexey Shvetsov Alfons Sijbers
  18. Peter Tieleman Jon Vincent Teemu Virolainen
  19. Christian Wennberg Maarten Wolf Artem Zhmurov
  20. and the project leaders:
  21. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  22.  
  23. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  24. Copyright (c) 2001-2019, The GROMACS development team at
  25. Uppsala University, Stockholm University and
  26. the Royal Institute of Technology, Sweden.
  27. check out http://www.gromacs.org for more information.
  28.  
  29. GROMACS is free software; you can redistribute it and/or modify it
  30. under the terms of the GNU Lesser General Public License
  31. as published by the Free Software Foundation; either version 2.1
  32. of the License, or (at your option) any later version.
  33.  
  34. GROMACS: gmx mdrun, version 2021
  35. Executable: /home/mnaderan/gromacs-2021/nvt/../single86/bin/gmx
  36. Data prefix: /home/mnaderan/gromacs-2021/nvt/../single86
  37. Working dir: /home/mnaderan/gromacs-2021/nvt
  38. Command line:
  39. gmx mdrun -nb gpu -v -deffnm nvt_20k
  40.  
  41.  
  42. Back Off! I just backed up nvt_20k.log to ./#nvt_20k.log.5#
  43. Reading file nvt_20k.tpr, VERSION 2019.3 (single precision)
  44. Note: file tpx version 116, software tpx version 122
  45. Changing nstlist from 20 to 100, rlist from 1.023 to 1.147
  46.  
  47. 1 GPU selected for this run.
  48. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  49. PP:0,PME:0
  50. PP tasks will do (non-perturbed) short-ranged interactions on the GPU
  51. PP task will update and constrain coordinates on the CPU
  52. PME tasks will do all aspects on the GPU
  53. Using 1 MPI thread
  54. Using 16 OpenMP threads
  55.  
  56.  
  57. Back Off! I just backed up nvt_20k.trr to ./#nvt_20k.trr.5#
  58.  
  59. Back Off! I just backed up nvt_20k.edr to ./#nvt_20k.edr.5#
  60. starting mdrun 'Protein'
  61. 20000 steps, 40.0 ps.
  62. step 4600: timed with pme grid 64 80 60, coulomb cutoff 1.000: 394.6 M-cycles
  63. step 4800: timed with pme grid 60 72 56, coulomb cutoff 1.075: 417.7 M-cycles
  64. step 5000: timed with pme grid 52 64 52, coulomb cutoff 1.210: 509.6 M-cycles
  65. step 5200: timed with pme grid 52 72 52, coulomb cutoff 1.196: 508.4 M-cycles
  66. step 5400: timed with pme grid 56 72 52, coulomb cutoff 1.144: 489.8 M-cycles
  67. step 5600: timed with pme grid 56 72 56, coulomb cutoff 1.111: 426.2 M-cycles
  68. step 5800: timed with pme grid 60 72 56, coulomb cutoff 1.075: 415.7 M-cycles
  69. step 6000: timed with pme grid 60 80 56, coulomb cutoff 1.062: 413.0 M-cycles
  70. step 6200: timed with pme grid 60 80 60, coulomb cutoff 1.037: 406.6 M-cycles
  71. step 6400: timed with pme grid 64 80 60, coulomb cutoff 1.000: 396.5 M-cycles
  72. optimal pme grid 64 80 60, coulomb cutoff 1.000
  73. step 19900, remaining wall clock time: 0 s
  74. Writing final coordinates.
  75.  
  76. Back Off! I just backed up nvt_20k.gro to ./#nvt_20k.gro.4#
  77. step 20000, remaining wall clock time: 0 s
  78. Core t (s) Wall t (s) (%)
  79. Time: 430.120 26.883 1600.0
  80. (ns/day) (hour/ns)
  81. Performance: 128.565 0.187
  82.  
  83. GROMACS reminds you: "There's only music to make new ringtones" (Arctic Monkeys)
  84.  
  85.  
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