Hi Amen,
Change the first line from
#!/bin/csh
with
#!/bin/bash
and change 'set' to 'export'
On another note I don't recommend using multi GPUs for regular MD runs these days (save it for TI, REMD etc). You will be better off doing export CUDA_VISIBLE_DEVICES=0 and just running pmemd.cuda without the mpirun. Then you can run a completely independent run at the same time on the other GPU by setting CUDA_VISIBLE_DEVICES=1.
All the best
Ross
> On Jul 8, 2019, at 14:05, 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 - 19:30:01 PDT
