[gmx-users] problems in MPI run for REMD in GROMACS

[Pabitra Mohan]

Dear Gromacs Users,
Can any body suggest the solutions to my problem appearing during REMD run
in GROMACS

While executing the following command these error messages are coming

pabitra at pabitra-Dell-System-XPS-L502X:~/Desktop/ctld_remd/stage2$ mpirun
-np 4 mdrun_mpi -v -multidir sim0 sim1 sim2 sim3 sim4 -replex 500
GROMACS:    mdrun_mpi, VERSION 5.0.6

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     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) 2001-2014, 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:      mdrun_mpi, VERSION 5.0.6
Executable:   /usr/bin/mdrun_mpi.openmpi
Library dir:  /usr/share/gromacs/top
Command line:
  mdrun_mpi -v -multidir sim0 sim1 sim2 sim3 sim4 -replex 500


-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/main.cpp, line: 383

Fatal error:
The number of ranks (4) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 2, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 2 out of 4

-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/main.cpp, line: 383

Fatal error:
The number of ranks (4) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 0, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 0 out of 4

-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/main.cpp, line: 383

Fatal error:
The number of ranks (4) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 1, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 1 out of 4

-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/main.cpp, line: 383

Fatal error:
The number of ranks (4) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 3, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 3 out of 4

gcq#11: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 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.
--------------------------------------------------------------------------

gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !"
(Monty Python)


gcq#268: "It's Not Dark Yet, But It's Getting There" (Bob Dylan)


gcq#49: "I'll Master Your Language, and In the Meantime I'll Create My Own"
(Tricky)

--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 3232 on
node pabitra-Dell-System-XPS-L502X exiting improperly. There are two
reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[pabitra-Dell-System-XPS-L502X:03229] 3 more processes have sent help
message help-mpi-api.txt / mpi-abort
[pabitra-Dell-System-XPS-L502X:03229] Set MCA parameter
"orte_base_help_aggregate" to 0 to see all help / error messages


Thank you very much for helping

-- 
Dr. Pabitra Mohan Behera
National Post-Doctoral Fellow (DST-SERB)
Computational Biology and Bioinformatics Lab
Institute of Life Sciences, Bhubaneswar
An Autonomous Organization of
Department of Biotechnology, Government of India
Nalco Square, Bhubaneswar
Odisha, Pin-751023 (India)
Mobile No: +91-9776503664, +91-9439770247
E-mail: pabitra at ils.res.in, uniquepabs at gmail.com