Hi, is this the only output?
Don’t you get a perf.out file that lists which settings are optimal? What exactly was the command line you used? Carsten On 29 Sep 2014, at 15:01, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > 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. -- 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.