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

Venkat Reddy venkat4bt at gmail.com
Thu Apr 7 13:13:47 CEST 2016

Dear all,

Please neglect my previous mail which was incomplete.

I am trying to execute mdrun our GPU cluster with 7 nodes where each node
is populated by 16 processors and two K40 GPU cards. I have no problem with
mdrun on single node. However, when I try to execute parallel run on two
nodes with gmx_mpi executable (gromacs-5.1.2),  the performance is very
slow. When I logged into individual nodes, I found that mdrun is not
utilizing both GPUs. The generated log file shows the following message.

Using 1 MPI process
Using 16 OpenMP threads

2 compatible GPUs are present, with IDs 0,1
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0

NOTE: potentially sub-optimal launch configuration, gmx_mpi started with
      PP MPI process per node than GPUs available.
      Each PP MPI process can use only one GPU, 1 GPU per node will be used.

I read the manual and instructions in
execute the parallel run. But I couldn't find the right flags to initiate
it. Please help me in this aspect. The script I used to execute the
parallel run is given below.

#! /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 1 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
mdrun -v -dlb yes  -ntomp 16 -s equilibration3.tpr

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

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