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- Log file opened on Fri Mar 2 16:12:01 2018
- Host: orca pid: 14856 rank ID: 0 number of ranks: 1
- :-) GROMACS - gmx mdrun, 2018 (-:
- GROMACS is written by:
- Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
- Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
- Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
- Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
- Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff
- Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
- Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
- Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
- and the project leaders:
- Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
- Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- Copyright (c) 2001-2017, The GROMACS development team at
- Uppsala University, Stockholm University and
- the Royal Institute of Technology, Sweden.
- check out http://www.gromacs.org for more information.
- GROMACS is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License
- as published by the Free Software Foundation; either version 2.1
- of the License, or (at your option) any later version.
- GROMACS: gmx mdrun, version 2018
- Executable: /usr/local/gromacs/bin/gmx
- Data prefix: /usr/local/gromacs
- Working dir: /home/mahmood/gromacs-2018/bench/lysozyme
- Command line:
- gmx mdrun -nobackup -nb cpu -pme gpu -deffnm md_0_1
- GROMACS version: 2018
- Precision: single
- Memory model: 64 bit
- MPI library: thread_mpi
- OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
- GPU support: CUDA
- SIMD instructions: AVX2_128
- FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
- RDTSCP usage: enabled
- TNG support: enabled
- Hwloc support: disabled
- Tracing support: disabled
- Built on: 2018-02-23 17:10:06
- Built by: mahmood@orca [CMAKE]
- Build OS/arch: Linux 4.10.0-28-generic x86_64
- Build CPU vendor: AMD
- Build CPU brand: AMD Ryzen 7 1800X Eight-Core Processor
- Build CPU family: 23 Model: 1 Stepping: 1
- 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
- C compiler: /usr/bin/cc GNU 5.4.0
- C compiler flags: -march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
- C++ compiler: /usr/bin/c++ GNU 5.4.0
- C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
- 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
- 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;
- CUDA driver: 9.0
- CUDA runtime: 9.0
- Running on 1 node with total 16 cores, 16 logical cores, 1 compatible GPU
- Hardware detected:
- CPU info:
- Vendor: AMD
- Brand: AMD Ryzen 7 1800X Eight-Core Processor
- Family: 23 Model: 1 Stepping: 1
- 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
- Hardware topology: Basic
- Sockets, cores, and logical processors:
- Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15]
- GPU info:
- Number of GPUs detected: 1
- #0: NVIDIA Quadro M2000, compute cap.: 5.2, ECC: no, stat: compatible
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
- Lindahl
- GROMACS: High performance molecular simulations through multi-level
- parallelism from laptops to supercomputers
- SoftwareX 1 (2015) pp. 19-25
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
- Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
- GROMACS
- In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
- Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
- GROMACS 4.5: a high-throughput and highly parallel open source molecular
- simulation toolkit
- Bioinformatics 29 (2013) pp. 845-54
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
- GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
- molecular simulation
- J. Chem. Theory Comput. 4 (2008) pp. 435-447
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
- Berendsen
- GROMACS: Fast, Flexible and Free
- J. Comp. Chem. 26 (2005) pp. 1701-1719
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- E. Lindahl and B. Hess and D. van der Spoel
- GROMACS 3.0: A package for molecular simulation and trajectory analysis
- J. Mol. Mod. 7 (2001) pp. 306-317
- -------- -------- --- Thank You --- -------- --------
- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
- H. J. C. Berendsen, D. van der Spoel and R. van Drunen
- GROMACS: A message-passing parallel molecular dynamics implementation
- Comp. Phys. Comm. 91 (1995) pp. 43-56
- -------- -------- --- Thank You --- -------- --------
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