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MarcHoemberger Mar 1st, 2018 18 Never
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  1.     |   |   |   |   | :-) GROMACS - gmx mdrun, 2016.4 (-:
  2.  
  3.     |   |   |   |   |   |   GROMACS is written by:
  4.     |Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
  5.  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
  6.  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
  7.     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
  8.   Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund
  9.    Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz
  10.   Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman
  11.   Teemu Virolainen  Christian Wennberg    Maarten Wolf
  12.     |   |   |   |   |   |  and the project leaders:
  13.     |   Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  14.  
  15. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  16. Copyright (c) 2001-2017, The GROMACS development team at
  17. Uppsala University, Stockholm University and
  18. the Royal Institute of Technology, Sweden.
  19. check out http://www.gromacs.org for more information.
  20.  
  21. GROMACS is free software; you can redistribute it and/or modify it
  22. under the terms of the GNU Lesser General Public License
  23. as published by the Free Software Foundation; either version 2.1
  24. of the License, or (at your option) any later version.
  25.  
  26. GROMACS:      gmx mdrun, version 2016.4
  27. Executable:   /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2/bin/gmx_mpi
  28. Data prefix:  /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2
  29. Working dir:  /home/hoemberg/ADK/PRESSURE/EADK/CLOSED/TMD_KAPPA_TEST/GPU/TMD_1000_GPU
  30. Command line:
  31.   gmx_mpi mdrun -pin on -pinoffset 0 -gpu_id 0 -ntomp 8 -v -cpi -s TMD_1000.tpr -o TMD_1000.trr -x TMD_1000.xtc -g TMD_1000.log -c eADK_TMD_1000.gro
  32.  
  33. Warning: No checkpoint file found with -cpi option. Assuming this is a new run.
  34.  
  35.  
  36. Running on 1 node with total 16 cores, 16 logical cores, 4 compatible GPUs
  37. Hardware detected on host gpu-compute-5-8.local (the node of MPI rank 0):
  38.   CPU info:
  39.     Vendor: Intel
  40.     Brand:  Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
  41.     SIMD instructions most likely to fit this hardware: AVX_256
  42.     SIMD instructions selected at GROMACS compile time: SSE4.1
  43.  
  44.   Hardware topology: Basic
  45.   GPU info:
  46.     Number of GPUs detected: 4
  47.     #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
  48.     #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
  49.     #2: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
  50.     #3: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat: compatible
  51.  
  52. Compiled SIMD instructions: SSE4.1, GROMACS could use AVX_256 on this machine, which is better.
  53. Reading file TMD_1000.tpr, VERSION 2016.4 (single precision)
  54. Changing nstlist from 10 to 40, rlist from 1.2 to 1.28
  55.  
  56. Using 1 MPI process
  57. Using 8 OpenMP threads
  58.  
  59. 1 GPU user-selected for this run.
  60. Mapping of GPU ID to the 1 PP rank in this node: 0
  61.  
  62.  
  63. Overriding thread affinity set outside gmx mdrun
  64.  
  65. starting mdrun 'eADK in Water'
  66. 26000000 steps,  52000.0 ps.
  67. ^Mstep   80: timed with pme grid 72 72 72, coulomb cutoff 1.200: 563.4 M-cycles
  68. ^Mstep  160: timed with pme grid 60 60 60, coulomb cutoff 1.280: 508.9 M-cycles
  69.  
  70. Step 222, time 0.444 (ps)  LINCS WARNING
  71. relative constraint deviation after LINCS:
  72. rms 0.000020, max 0.000432 (between atoms 2101 and 2102)
  73. bonds that rotated more than 30 degrees:
  74.  atom 1 atom 2  angle  previous, current, constraint length
  75.    2101   2103   34.0    0.1178   0.1111      0.1111
  76.  
  77. Step 223, time 0.446 (ps)  LINCS WARNING
  78. relative constraint deviation after LINCS:
  79. rms 0.000082, max 0.002613 (between atoms 2101 and 2103)
  80. bonds that rotated more than 30 degrees:
  81.  atom 1 atom 2  angle  previous, current, constraint length
  82.    2101   2103   35.2    0.1105   0.1114      0.1111
  83.  
  84. Step 228, time 0.456 (ps)  LINCS WARNING
  85. relative constraint deviation after LINCS:
  86. rms 0.005702, max 0.257592 (between atoms 2101 and 2102)
  87. bonds that rotated more than 30 degrees:
  88.  atom 1 atom 2  angle  previous, current, constraint length
  89.    2101   2102   90.0    0.1111   0.1397      0.1111
  90.    2104   2106   90.0    0.1111   0.1348      0.1111
  91.  
  92. Step 229, time 0.458 (ps)  LINCS WARNING
  93. relative constraint deviation after LINCS:
  94. rms 0.001372, max 0.080100 (between atoms 2101 and 2102)
  95. bonds that rotated more than 30 degrees:
  96.  atom 1 atom 2  angle  previous, current, constraint length
  97.    2101   2102   90.0    0.1397   0.1200      0.1111
  98.    2104   2106   75.4    0.1348   0.1109      0.1111
  99.  
  100. Step 230, time 0.46 (ps)  LINCS WARNING
  101. relative constraint deviation after LINCS:
  102. rms 0.003682, max 0.173647 (between atoms 2101 and 2102)
  103. bonds that rotated more than 30 degrees:
  104.  atom 1 atom 2  angle  previous, current, constraint length
  105.    2101   2102   90.0    0.1200   0.1304      0.1111
  106.    2104   2106   90.0    0.1109   0.1254      0.1111
  107.  
  108. Step 231, time 0.462 (ps)  LINCS WARNING
  109. relative constraint deviation after LINCS:
  110. rms 172.973862, max 7198.149414 (between atoms 2104 and 2105)
  111. bonds that rotated more than 30 degrees:
  112.  atom 1 atom 2  angle  previous, current, constraint length
  113.    2098   2101   55.5    0.1528   0.0888      0.1530
  114.    2101   2102  132.5    0.1304 796.0084      0.1111
  115.    2101   2103   90.0    0.1121   3.2097      0.1111
  116.    2101   2104   90.4    0.1531   0.3915      0.1530
  117.    2104   2106   89.9    0.1254   0.6856      0.1111
  118.    2104   2107   90.4    0.1474   0.2691      0.1480
  119.    2107   2108   90.5    0.1040   0.0861      0.1040
  120.    2107   2109   90.3    0.1039   0.0785      0.1040
  121.    2107   2110   90.4    0.1041   0.0993      0.1040
  122. Wrote pdb files with previous and current coordinates
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