[gmx-users] How to properly use tune_pme?
Marcin Mielniczuk
marcin at golem.network
Thu Nov 21 17:15:49 CET 2019
Hi,
I'm trying to make use of tune_pme to find out the optimal number of PME
ranks. My command line is:
UCX_LOG_LEVEL=info MPIRUN="mpirun" ./gmx_mpi tune_pme -v -s
../tip4p_min2 -mdrun "./gmx_mpi mdrun" -np 4
When started in such a way, Gromacs exits with a fatal error, as shown
in the attached log file, `tune_pme.txt`. OTOH, benchtest.log is empty.
While these logs were created using Gromacs 2019.3, the same issue
persists with 2019.4.
Manually executing the command `mpirun -np 4 ./gmx_mpi mdrun -version
-maxh 0.001` succeeds, as in the attached log file `mpirun.txt`.
What's the correct way to use tune_pme then?
It looks to me that what I'm doing is exactly what the documentation
says to.
Thanks,
Marcin
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[1572284841.118415] [azathoth:18290:0] ucp_worker.c:1516 UCX INFO ep_cfg[1]: tag(self/memory cma/memory);
:-) GROMACS - gmx tune_pme, 2019.3 (-:
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
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) 2001-2018, 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 tune_pme, version 2019.3
Executable: /home/marcin/gromacs/gromacs-2019.3/build/bin/./gmx_mpi
Data prefix: /home/marcin/gromacs/gromacs-2019.3 (source tree)
Working dir: /home/marcin/gromacs/gromacs-2019.3/build/bin
Command line:
gmx_mpi tune_pme -v -s ../tip4p_min2 -mdrun './gmx_mpi mdrun' -np 4
Reading file ../tip4p_min2.tpr, VERSION 2019.3 (single precision)
Back Off! I just backed up perf.out to ./#perf.out.4#
Will test 1 tpr file.
Back Off! I just backed up benchtest.log to ./#benchtest.log.3#
-------------------------------------------------------
Program: gmx tune_pme, version 2019.3
Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 739)
Fatal error:
Cannot execute mdrun. Please check benchtest.log for problems!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Making sure that mdrun can be executed. Trying 'mpirun -np 4 ./gmx_mpi mdrun -version -maxh 0.001 1> benchtest.log 2>&1' ... --------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
-------------- next part --------------
:-) GROMACS - gmx mdrun, 2019.3 (-:
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
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) 2001-2018, 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 2019.3
Executable: /home/marcin/gromacs/gromacs-2019.3/build/bin/./gmx_mpi
Data prefix: /home/marcin/gromacs/gromacs-2019.3 (source tree)
Working dir: /home/marcin/gromacs/gromacs-2019.3/build/bin
Command line:
gmx_mpi mdrun -version -maxh 0.001
GROMACS version: 2019.3
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: disabled
SIMD instructions: AVX2_256
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.6
Tracing support: disabled
C compiler: /usr/local/bin/mpicc GNU 7.4.0
C compiler flags: -mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/local/bin/mpicxx GNU 7.4.0
C++ compiler flags: -mavx2 -mfma -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
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