[gmx-users] configure gmx with external mpi library - an error
Gil Vernik
GILV at il.ibm.com
Sun Dec 8 16:53:31 CET 2019
Thank you very much. Using gmx_mpi resolved the issue for me.
Perhaps i missed that part in the documentation that i need to use
gmx_mpi.
Thanks again
Gil
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: 08/12/2019 15:47
Subject: [EXTERNAL] Re: [gmx-users] configure gmx with external mpi
library - an error
Sent by: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
Hi,
A build with cmake -DGMX_MPI=on will suffix the installed binaries and
libraries with "_mpi" by default. Gil just needs to use gmx_mpi, not gmx
Mark
On Sun, 8 Dec 2019 at 14:29, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 12/8/19 8:22 AM, Gil Vernik wrote:
> > I installed open-mpi (mpirun (Open MPI) 4.0.2) on my laptop
> > I then follow instructions
> >
https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_2019.4_install-2Dguide_index.html-23id1&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=daJQTfoUDLYkGPJOgf9t9EVUOBDYB0aep-61rOQWycQ&e=
to install
> > gromacs on my mac.
> > I used
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on
> >
> > I then tried to follow the following tutorial
> >
>
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Tutorials_GROMACS-5FUSA-5FWorkshop-5Fand-5FConference-5F2013_An-5Fintroduction-5Fto-5Freplica-5Fexchange-5Fsimulations-253A-5FMark-5FAbraham-252C-5FSession-5F1B&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=mFwI4IOAR3jAz1hKA1CiTfU-dBJLqlLtaNjwQI-iKTQ&e=
> >
> > However running mpirun -np 4 gmx mdrun -multidir equil[0123]
> > Results in the following error. Please assist.
> >
> > Thanks a lot
> > Gil
> >
> >
> > mpirun -np 4 gmx mdrun -multidir equil[0123]
> > :-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> > 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 :-) GROMACS - gmx mdrun,
2019.4
> > (-:
> >
> > 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:
> > :-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> > 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.
> > :-) GROMACS - gmx mdrun, 2019.4 (-:
> >
> > 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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=EA4TKuNHIwkswGxuNkf9QcTxjHOQ0-IgghI6S_PaIaA&e=
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.
> >
> > 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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=EA4TKuNHIwkswGxuNkf9QcTxjHOQ0-IgghI6S_PaIaA&e=
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 2019.4 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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=EA4TKuNHIwkswGxuNkf9QcTxjHOQ0-IgghI6S_PaIaA&e=
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 2019.4
> > Copyright (c) 2001-2018, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=EA4TKuNHIwkswGxuNkf9QcTxjHOQ0-IgghI6S_PaIaA&e=
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 2019.4
> > GROMACS: gmx mdrun, version 2019.4
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/gilv/Dev/hpc/gromacs/tutorial-archive/stage1
> > Command line:
> > gmx mdrun -multidir equil0 equil1 equil2 equil3
> >
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2019.4
> > Source file: src/gromacs/mdrun/multisim.cpp (line 70)
> >
> > Fatal error:
> > mdrun -multidir is only supported when GROMACS has been configured
with a
> > proper external MPI library.
> >
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Errors&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=Rlp7v4nbOkYLHmXaGagO4XSlC-9QcmOOFRsF8IFZmEg&e=
> > -------------------------------------------------------
> >
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/gilv/Dev/hpc/gromacs/tutorial-archive/stage1
> > Command line:
> > gmx mdrun -multidir equil0 equil1 equil2 equil3
> >
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2019.4
> > Source file: src/gromacs/mdrun/multisim.cpp (line 70)
> >
> > Fatal error:
> > mdrun -multidir is only supported when GROMACS has been configured
with a
> > proper external MPI library.
> >
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Errors&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=Rlp7v4nbOkYLHmXaGagO4XSlC-9QcmOOFRsF8IFZmEg&e=
> > -------------------------------------------------------
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/gilv/Dev/hpc/gromacs/tutorial-archive/stage1
> > Command line:
> > gmx mdrun -multidir equil0 equil1 equil2 equil3
> >
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2019.4
> > Source file: src/gromacs/mdrun/multisim.cpp (line 70)
> >
> > Fatal error:
> > mdrun -multidir is only supported when GROMACS has been configured
with a
> > proper external MPI library.
> >
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Errors&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=Rlp7v4nbOkYLHmXaGagO4XSlC-9QcmOOFRsF8IFZmEg&e=
> > -------------------------------------------------------
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/gilv/Dev/hpc/gromacs/tutorial-archive/stage1
> > Command line:
> > gmx mdrun -multidir equil0 equil1 equil2 equil3
> >
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2019.4
> > Source file: src/gromacs/mdrun/multisim.cpp (line 70)
> >
> > Fatal error:
> > mdrun -multidir is only supported when GROMACS has been configured
with a
> > proper external MPI library.
> >
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Documentation_Errors&d=DwICAg&c=jf_iaSHvJObTbx-siA1ZOg&r=-YRCpkqZQamrCezWyJCIug&m=QMcYSW_KdJfRaj2thk3M6s_b2JFc-d4TJgMPEDaowNg&s=Rlp7v4nbOkYLHmXaGagO4XSlC-9QcmOOFRsF8IFZmEg&e=
> > -------------------------------------------------------
> >
>
--------------------------------------------------------------------------
> > Primary job terminated normally, but 1 process returned
> > a non-zero exit code. Per user-direction, the job has been aborted.
> >
>
--------------------------------------------------------------------------
> >
>
--------------------------------------------------------------------------
> > mpirun detected that one or more processes exited with non-zero
status,
> > thus causing
> > the job to be terminated. The first process to do so was:
> >
> > Process name: [[53918,1],3]
> > Exit code: 1
> >
>
--------------------------------------------------------------------------
> >
> > Here is the print of gmx-version
> >
> > GROMACS version: 2019.4
> > Precision: single
> > Memory model: 64 bit
> > MPI library: thread_mpi
>
> The above line indicates your gmx binary was not compiled against
> OpenMPI. Be careful if you're installing different binaries - maybe you
> later installed again with the built-in thread-MPI library and simply
> overwrote your gmx binary? Normally it's a good idea to suffix the MPI
> version of gmx as gmx_mpi.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
>
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>
> ==================================================
>
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