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#em.log.1#
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:-) GROMACS - gmx mdrun, 2020.1-Ubuntu-2020.1-1 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
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) 2001-2019, 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 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/dhnchandan/Notebooks/Bioinformatics/Gromacs/gromacs-experimet
Process ID: 38771
Command line:
gmx mdrun -ntmpi 2 -ntomp 1 -deffnm em -v -pin on -nb gpu
GROMACS version: 2020.1-Ubuntu-2020.1-1
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: SSE2
FFT library: fftw-3.3.8-sse2-avx
RDTSCP usage: disabled
TNG support: enabled
Hwloc support: hwloc-2.1.0
Tracing support: disabled
C compiler: /usr/bin/cc GNU 9.3.0
C compiler flags: -msse2 -fexcess-precision=fast -funroll-all-loops
C++ compiler: /usr/bin/c++ GNU 9.3.0
C++ compiler flags: -msse2 -fexcess-precision=fast -funroll-all-loops -fopenmp
Running on 1 node with total 6 cores, 12 logical cores
Hardware detected:
CPU info:
Vendor: AMD
Brand: AMD Ryzen 5 2600X Six-Core Processor
Family: 23 Model: 8 Stepping: 2
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: Full, with devices
Sockets, cores, and logical processors:
Socket 0: [ 0 1] [ 2 3] [ 4 5] [ 6 7] [ 8 9] [ 10 11]
Numa nodes:
Node 0 (16785735680 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11
Latency:
0
0 1.00
Caches:
L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L2: 524288 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
L3: 8388608 bytes, linesize 64 bytes, assoc. 16, shared 6 ways
PCI devices:
0000:01:00.0 Id: 1987:5013 Class: 0x0108 Numa: 0
0000:03:00.1 Id: 1022:43c8 Class: 0x0106 Numa: 0
0000:25:00.0 Id: 10ec:8168 Class: 0x0200 Numa: 0
0000:26:00.0 Id: 10de:1d01 Class: 0x0300 Numa: 0
0000:28:00.2 Id: 1022:7901 Class: 0x0106 Numa: 0
Highest SIMD level requested by all nodes in run: AVX2_128
SIMD instructions selected at compile time: SSE2
This program was compiled for different hardware than you are running on,
which could influence performance.
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
++++ 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 --- -------- --------