I.e. you'd have to rewrite the csh parts to bash.
> ~/bashrc
It's ~/.bashrc (notice dot) in case that's not a typo.
Bill
On 7/8/19 11:44 AM, Supriyo Bhattacharya wrote:
> 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 - 14:00:02 PDT
