[gmx-users] Running g_tune_pme on a BlueGene/Q cluster

Jernej Zidar jernej.zidar at gmail.com
Thu Aug 15 11:46:10 CEST 2013

  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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