Hi, I just tried that and I got the following error message (bench.log). Any idea what could be wrong?
Thank you very much, Max Initializing Domain Decomposition on 48 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452 multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452 Minimum cell size due to bonded interactions: 0.464 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm Estimated maximum distance required for P-LINCS: 0.218 nm ------------------------------------------------------- Program mdrun_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_setup.c, line: 728 Fatal error: The number of ranks you selected (37) contains a large prime factor 37. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Donnerstag, 25. September 2014 19:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi Hi, don't invoke g_tune_pme with 'mpirun', because it is a serial executable that itself invokes parallel MD runs for testing. use export MDRUN=mdrun_mpi g_tune_pme -np 24 -s 1ZG4_nvt.tpr -launch see also g_tune_pme -h You may need to recompile g_tune_pme without MPI enabled (depends on your queueing system) Best, Carsten On 25 Sep 2014, at 15:10, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > Dear list, > > I tried using g_tune_pme_mpi with the command: > > mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch > > on GROMACS 5.0.1 but I get the following error message: > ---------------------------------------------------------------------- > ---- mpirun was unable to launch the specified application as it could > not find an executable: > > Executable: mdrun > Node: xxxx > > while attempting to start process rank 0. > ---------------------------------------------------------------------- > ---- > 24 total processes failed to start > > > Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead? > > Thank you very much, > > Max > -- > 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-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.