[gmx-users] How to initiate parallel run on GPU cluster

Venkat Reddy venkat4bt at gmail.com
Thu Apr 7 12:59:41 CEST 2016

Dear all,
I am trying to execute mdrun our GPU
#! /bin/bash
#PBS -l cput=5000:00:00
#PBS -l select=2:ncpus=16:ngpus=2
#PBS -e errorfile.err
#PBS -o logfile.log
tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
mkdir -p $tempdir
cd $tempdir
cp -R $PBS_O_WORKDIR/* .
mpiexec.hydra -np 2 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
mdrun -v -dlb yes  -ntomp 16 -gpu_id 0101 -s equilibration3.tpr

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node. gmx_mpi was started with 1 PP MPI process per node, but you
provided 4 GPUs.

With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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