[gmx-users] configure gmx with external mpi library - an error
Mark Abraham
mark.j.abraham at gmail.com
Sun Dec 8 14:46:20 CET 2019
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
> > http://manual.gromacs.org/2019.4/install-guide/index.html#id1 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
> >
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
> >
> > 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 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.
> >
> > 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 2019.4 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 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 2019.4
> > 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 2019.4
> > 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 http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > 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 http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > 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 http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > 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 http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > 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
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list