export MPIRUN=$(which srun) should be all you need to help g_tune_pme to understand how to start an MPI calc. g_tune_pme runs in serial, but it needs to *call* srun.
Mark On Thu, Aug 15, 2013 at 11:46 AM, Jernej Zidar <jernej.zi...@gmail.com> wrote: > Hi, > I would like to determine the optimum number of PP/PME nodes to be > used for my simulation. I found the tool g_tune_pme can be used. > The cluster is a BlueGene/Q machine using SLUR as the scheduler. I > tried using the following scirpt: > !/bin/bash > #SBATCH --time=1:00:00 > #SBATCH --nodes=16 > #SBATCH --ntasks-per-node=16 > #SBATCH -J "tune" > #SBATCH -o "tuning.out" > #SBATCH -p "normal" > file=my_tpr_file > source /home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/GMXRC > export MDRUN="/home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/mdrun" > srun g_tune_pme -np 256 -s "$file" -steps 1000 -ntpr 1 > > - - - - > But it didn't work: > Program g_tune_pme, VERSION 4.6.3 > Source code file: > /home/ihpczidj/scratch/gromacs-4.6.3/src/tools/gmx_tune_pme.c, line: > 665 > > Fatal error: > Output from test run could not be found. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Any suggestions? I'm trying to find the location of the 'srun' > wrapper but I'm unable to find it. > > Thanks, > Jernej > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists