[gmx-users] configure gmx with external mpi library - an error
Justin Lemkul
jalemkul at vt.edu
Sun Dec 8 14:28:47 CET 2019
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
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