AMBER Archive (2006)

Subject: Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product

From: Hector A. Baldoni (
Date: Sat Apr 29 2006 - 19:08:30 CDT

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.


# BSUB -q normal


#---- STEPS --------------------

while [ $i -le 11 ]

mv md.rst md.crd

 mpirun -np 8 ~/bin/sander7_mpi.x -O \
         -i -o md.out \
         -p -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`


> 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
 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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