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mahmoodn

gromacs-nb-cpu-pme-gpu

Mar 2nd, 2018
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  1. Log file opened on Fri Mar 2 16:12:01 2018
  2. Host: orca pid: 14856 rank ID: 0 number of ranks: 1
  3. :-) GROMACS - gmx mdrun, 2018 (-:
  4.  
  5. GROMACS is written by:
  6. Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
  7. Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
  8. Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
  9. Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
  10. Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff
  11. Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
  12. Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
  13. Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
  14. and the project leaders:
  15. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  16.  
  17. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  18. Copyright (c) 2001-2017, The GROMACS development team at
  19. Uppsala University, Stockholm University and
  20. the Royal Institute of Technology, Sweden.
  21. check out http://www.gromacs.org for more information.
  22.  
  23. GROMACS is free software; you can redistribute it and/or modify it
  24. under the terms of the GNU Lesser General Public License
  25. as published by the Free Software Foundation; either version 2.1
  26. of the License, or (at your option) any later version.
  27.  
  28. GROMACS: gmx mdrun, version 2018
  29. Executable: /usr/local/gromacs/bin/gmx
  30. Data prefix: /usr/local/gromacs
  31. Working dir: /home/mahmood/gromacs-2018/bench/lysozyme
  32. Command line:
  33. gmx mdrun -nobackup -nb cpu -pme gpu -deffnm md_0_1
  34.  
  35. GROMACS version: 2018
  36. Precision: single
  37. Memory model: 64 bit
  38. MPI library: thread_mpi
  39. OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
  40. GPU support: CUDA
  41. SIMD instructions: AVX2_128
  42. FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
  43. RDTSCP usage: enabled
  44. TNG support: enabled
  45. Hwloc support: disabled
  46. Tracing support: disabled
  47. Built on: 2018-02-23 17:10:06
  48. Built by: mahmood@orca [CMAKE]
  49. Build OS/arch: Linux 4.10.0-28-generic x86_64
  50. Build CPU vendor: AMD
  51. Build CPU brand: AMD Ryzen 7 1800X Eight-Core Processor
  52. Build CPU family: 23 Model: 1 Stepping: 1
  53. Build CPU features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  54. C compiler: /usr/bin/cc GNU 5.4.0
  55. C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  56. C++ compiler: /usr/bin/c++ GNU 5.4.0
  57. C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
  58. CUDA compiler: /usr/local/cuda-9.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, V9.0.176
  59. CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
  60. CUDA driver: 9.0
  61. CUDA runtime: 9.0
  62.  
  63.  
  64. Running on 1 node with total 16 cores, 16 logical cores, 1 compatible GPU
  65. Hardware detected:
  66. CPU info:
  67. Vendor: AMD
  68. Brand: AMD Ryzen 7 1800X Eight-Core Processor
  69. Family: 23 Model: 1 Stepping: 1
  70. Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  71. Hardware topology: Basic
  72. Sockets, cores, and logical processors:
  73. Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15]
  74. GPU info:
  75. Number of GPUs detected: 1
  76. #0: NVIDIA Quadro M2000, compute cap.: 5.2, ECC: no, stat: compatible
  77.  
  78.  
  79. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  80. M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
  81. Lindahl
  82. GROMACS: High performance molecular simulations through multi-level
  83. parallelism from laptops to supercomputers
  84. SoftwareX 1 (2015) pp. 19-25
  85. -------- -------- --- Thank You --- -------- --------
  86.  
  87.  
  88. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  89. S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
  90. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
  91. GROMACS
  92. In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
  93. -------- -------- --- Thank You --- -------- --------
  94.  
  95.  
  96. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  97. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
  98. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
  99. GROMACS 4.5: a high-throughput and highly parallel open source molecular
  100. simulation toolkit
  101. Bioinformatics 29 (2013) pp. 845-54
  102. -------- -------- --- Thank You --- -------- --------
  103.  
  104.  
  105. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  106. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  107. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  108. molecular simulation
  109. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  110. -------- -------- --- Thank You --- -------- --------
  111.  
  112.  
  113. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  114. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  115. Berendsen
  116. GROMACS: Fast, Flexible and Free
  117. J. Comp. Chem. 26 (2005) pp. 1701-1719
  118. -------- -------- --- Thank You --- -------- --------
  119.  
  120.  
  121. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  122. E. Lindahl and B. Hess and D. van der Spoel
  123. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  124. J. Mol. Mod. 7 (2001) pp. 306-317
  125. -------- -------- --- Thank You --- -------- --------
  126.  
  127.  
  128. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  129. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  130. GROMACS: A message-passing parallel molecular dynamics implementation
  131. Comp. Phys. Comm. 91 (1995) pp. 43-56
  132. -------- -------- --- Thank You --- -------- --------
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