LaoTsao's Weblog (老曹的網路記)

integration of schrodinger with SGE

We present a POC of integration of schrodinger with SGE

I have good advice from the help@schrodinger.com.

Schrodinger can use the MPI environmnet to run on multiple CPUs on multiple system.

As a shared grid environmnet one would like to submit jobs through a queue system.

Schrodinger support queue system: NQS , PBS and LSF, we need to create a similary environment so user can use the SGE env.

under the schrodinger root directory there is queues directory and it contains NQS, PBS and LSF.

we use cp -a NQS SGE to copy the NQS evvironment

there are five files

cancel, config, status.pl, submit and templates.sh

first one need to update the variables

QPATH=/opt/gridengine/bin/lx24-amd64 <--change

QDEL=qdel <--same as NQS

QSUB=qsub <-- same as NQS

QSTAT=qstat <-- same as NQS

templates.sh got the most update

#!/bin/sh

#$ -N %NAME%

#$ -o %LOGDIR%/%JOBID%.qlog

#$ -j y

#$ -pe mpich %NPROC%

QPATH=/opt/gridengine/bin/lx24-amd64

curdir=`echo $0 |sed -e 's#/[^/]*$##'`

if [ -f "$curdir/config" ]; then

. $curdir/config

fi

PATH=$QPATH:$PATH

export SCHRODINGER_BATCHID

SCHRODINGER_BATCHID=$JOB_ID <-- from SGE

SCHORDINGER_NODEFILE=$TMPDIR/machines <-- frm SGE

export SCHRODINGER_NODEFILE

%ENVIRONMENTS%

%COMMAND%

the schrodinger_hosts file need an update entry

name: localhost

schrodinger: /opt/schrodinger35

env: SCHRODINGER_RSH=ssh

env: SCHRODINGER_RCP=scp

name: testcluster

host: testcluster.local

hostname: testcluster.local

processors: 16

tmpdir; /state/partition1

name: sge

host: testcluster.local

hotname: testcluster.local

Queue: SGE

Qargs: ""

processors: 16

tmpdir: /state/partition1

Posted at 09:35AM Apr 09, 2005 by hstsao in N1 Grid  |  Comments[5]