Hello from Argentina,
The following script show how to run N cycles of MD under LSF.
It is a sh enviroment. I hope to hepl you.
Greeting,
Hector.
#
#!/bin/sh
# BSUB -q normal
i="10"
#---- STEPS --------------------
while [ $i -le 11 ]
do
mv md.rst md.crd
mpirun -np 8 ~/bin/sander7_mpi.x -O \
-i md_N.in -o md.out \
-p md.top -c md.crd \
-x md.trj -e md.ene \
-inf infomd -r md.rst
mv md.out md_$i.out
mv md.trj md_$i.trj
mv md.ene md_$i.ene
cp md.rst md_$i.rst
mv logfile logfile_$i
gzip -f md_$i.out
gzip -f md_$i.trj
gzip -f md_$i.ene
gzip -f md_$i.rst
i=`expr $i + 1`
done
#-------------------------------FIN---
> Dear All,
>
> I'm a rookie in amber, I just compiled amber8 successfully on a linux
> cluster, the serial version was tesed completely correct, while I
> don't know how to use the parallel version (compiled with mpich) in
> our cluster. Our cluster use the Platform LSF product as job
> management, computations were performed on computating nodes (dual
> Xeon) after submitting a job script on management nodes. The head of
> script is as follows, now my question is how to perform parallel MD in
> my job script? and anything else need to be done? such as set
> environment variable...
>
> Thanks for your help and kindness!
>
>
> #-----script head-------
> #!/bin/bash
> #BSUB -q normal
> #BSUB -J jobname
> #BSUB -o %J.output
> #BSUB -n 8
> #BSUB -R span[ptile=2]
>
> (how to write here to perform parallel MD?)
>
> #------------------------
>
>
> yours sincerely, Zhihong
>
>
>
> -----------------------------------------------------------------------
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>
---------------------------------
Dr. Hector A. Baldoni
Departamento de Quimica - UNSL
Chacabuco 917
(D5700BWS) San Luis - Argentina
hbaldoni.unsl.edu.ar
Tel.:+54-(0)2652-423789 ext. 157
----------------------------------
The chemists are a strange class of mortals impelled by an almost insane
impulse to seek their pleasure among smoke and vapor, soot and flame,
poisons and poverty; yet among all these evils I seem to live so sweetly,
that I may die if I would change places with the Persian king.
-- Johann Joachim Becher, 1635-1682.
Acta Laboratorii Chymica Monacensis, 1669.
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Received on Sun Apr 30 2006 - 06:07:18 PDT
