[AMBER] Export command not found (export CUDA_VISIBLE_DEVICES)

From: Amen Shamim <amenshamim.gmail.com>
Date: Tue, 9 Jul 2019 03:05:54 +0900

Hi,

I am using script for pmemd.cuda.MPI. It was working fine last time but
this time it gave me error export command not found. My script and ~/bashrc
file is below

#!/bin/csh
export CUDA_VISIBLE_DEVICES=0,1
set AMBERHOME="/home/hpclab/Amen/amber16"
set MDSTARTJOB=1
set MDENDJOB=1000
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=0
echo -n "Starting Script at: "
date
echo ""

while ( $MDCURRENTJOB <= $MDENDJOB )
   echo -n "Job $MDCURRENTJOB started at: "
   date
   . MDINPUT = $MDCURRENTJOB - 1
   mpirun -np 2 pmemd.cuda.MPI -O -i prod.in \
                                  -o prod$MDCURRENTJOB.out \
                                  -p polyAT_wat1.prmtop \
                                  -c prod$MDINPUT.rst \
                                  -r prod$MDCURRENTJOB.rst \
                                  -x prod$MDCURRENTJOB.mdcrd \
                                  -e prod$MDCURRENTJOB.mden

          -inf prod$MDCURRENTJOB.info

   echo -n "Job $MDCURRENTJOB finished at: "
   date
   . MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"

//bashrc
export CUDA_HOME=/usr/local/cuda-8.0
export PATH=$CUDA_HOME/bin:$PATH
export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH
export MPI_HOME=/opt/mpi/gcc-4.8.5/openmpi-1.10.7
export PATH=$MPI_HOME/bin:$PATH
export MANPATH=$MPI_HOME/man:$MANPATH
export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH

Can you figure out my problem? With above script, I am getting output but
its very slow.
Thank you

Best
Amen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 08 2019 - 11:30:02 PDT
Custom Search