It says #!/bin/csh, instead of #!/bin/bash in your script. If you change it to bash instead of csh, I think the issue would be resolved.
Supriyo
On Monday, July 8, 2019, 11:09:25 AM PDT, Amen Shamim <amenshamim.gmail.com> wrote:
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
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Received on Mon Jul 08 2019 - 12:00:03 PDT
