[gmx-users] GPU performance

[Justin Lemkul]

On 8/5/18 11:06 AM, RAHUL SURESH wrote:
> Hi users
>
> I generated my 200ns production Tpr file in 2016 version and running it on
> version 2018, in the cluster supported by gpu.
> 32 core and 1 P100 GPU card.
>
> In the output file, I get a message stating " Multiple energy groups is not
> implemented for GPUs, falling back to the CPU." What is this about and how
> to overcome it.?

You can't use multiple energygrps in any .tpr file that will be run on a 
GPU. Previous versions ran but the energy group output was garbage. 
Separate groups should only be specified as analysis and done with mdrun 
-rerun on CPU.

-Justin

> Also, the output files are not being generated simultaneously in the
> working directory.
>
> *script as follows*
>
> *#!/bin/bash*
> *#PBS -S /bin/bash*
> *#PBS -N gromax-alz*
> *#PBS -l select=1:ncpus=32:mpiprocs=1:ompthreads=32:ngpus=1*
> *#PBS -l walltime=360:00:00*
> *#PBS -q gpu*
> *#PBS -joe*
> *#PBS -V*
>
> *#export I_MPI_FABRICS=shm:tmi*
> *#export I_MPI_PROVIDER=psm2*
> *#export I_MPI_FALLBACK=0*
>
> *cd $PBS_O_WORKDIR*
> *cat $PBS_NODEFILE > pbs_nodes*
> *echo Working directory is $PBS_O_WORKDIR*
> *NPROCS=`wc -l < $PBS_NODEFILE`*
> *NNODES=`uniq $PBS_NODEFILE | wc -l`*
>
>
> *if [ "$NNODES" == "1" ]*
> *then*
> *jid=`echo $PBS_JOBID | awk -F'.' '{print $1}'`*
> *mkdir /scratch/$jid/*
> *export TMPDIR=/scratch/$jid/*
> *else*
> *jid=`echo $PBS_JOBID | awk -F'.' '{print $1}'`*
> *usern=`echo $USER`*
> *mkdir -p /home/$usern/scratch/$jid*
> *export TMPDIR=/home/$usern/scratch/$jid*
> *fi*
>
> *cd $TMPDIR*
>
> *export IntelPath=/apps/intel2017u7*
> *source $IntelPath/bin/compilervars.sh intel64*
> *source $IntelPath/mkl/bin/mklvars.sh intel64*
> *source $IntelPath/impi/*/bin64/mpivars.sh intel64*
> *source /apps/batch-scripts/cuda92.sh*
>
> *source /apps/gromacs/gpu/2018.2/intel/2017u7/cuda/9.2/bin/GMXRC*
>
> *cp $PBS_O_WORKDIR/alz.tpr $TMPDIR/*
>
>
> *gmx_mpi mdrun -v -deffnm alz 2>&1 | tee $PBS_O_WORKDIR/OUTPUT.txt*
>
>
> *mkdir $PBS_O_WORKDIR/out*
>
> *cp --force $TMPDIR/* $PBS_O_WORKDIR/out/*
>
> *rm -rf $TMPDIR*
> *date*
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================