On Tue, May 3, 2016 at 2:50 PM, Pabitra Mohan <uniquep...@gmail.com> wrote:
> 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@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 > > Hi, The real problem is here. Your command line arguments will not work. This is by design, not a bug. Do what the error suggests. Cheers Terry > 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: pabi...@ils.res.in, uniquep...@gmail.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? 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