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

About laotsao 老曹

HopBit GridComputing LLC Rockscluster Gridengine Solaris Zone, Solaris Cluster, OVM SPARC/Ldom Exadata, SPARC SuperCluster
This entry was posted in N1 Grid. Bookmark the permalink.

5 Responses to integration of schrodinger with SGE

  1. Rayson says:

    Nice info, but the formating got messed up😦

  2. I also found it useful to know it works, but can’t figure out much of what they did due to formatting…

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