[gmx-users] Running g_tune_pme on a BlueGene/Q cluster
mark.j.abraham at gmail.com
Thu Aug 15 12:18:50 CEST 2013
export MPIRUN=$(which srun) should be all you need to help g_tune_pme
to understand how to start an MPI calc. g_tune_pme runs in serial, but
it needs to *call* srun.
On Thu, Aug 15, 2013 at 11:46 AM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> I would like to determine the optimum number of PP/PME nodes to be
> used for my simulation. I found the tool g_tune_pme can be used.
> The cluster is a BlueGene/Q machine using SLUR as the scheduler. I
> tried using the following scirpt:
> #SBATCH --time=1:00:00
> #SBATCH --nodes=16
> #SBATCH --ntasks-per-node=16
> #SBATCH -J "tune"
> #SBATCH -o "tuning.out"
> #SBATCH -p "normal"
> source /home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/GMXRC
> export MDRUN="/home/ihpczidj/scratch/gromacs-4.6.3-bgq/bin/mdrun"
> srun g_tune_pme -np 256 -s "$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:
> 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.
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