I don't know about the Rocks component, but we're running Gaussian 09 +
Linda 8.2 in our SGE 6.2u5 cluster. We had to settle on a Gaussian
specific parallel environment which always uses modulo 4 processors.
$ qconf -sp gaussian
pe_name gaussian
slots 9999
user_lists NONE
xuser_lists NONE
start_proc_args /cluster/app/sge/6.2/g09/startg09.sh $pe_hostfile
stop_proc_args /cluster/app/sge/6.2/g09/stopg09.sh
allocation_rule 4
control_slaves FALSE
job_is_first_task TRUE
urgency_slots min
accounting_summary FALSE
***** startg09.sh script (variant of startmpi.sh) *****
#!/bin/sh
#
# preparation of the Default.Route file
#
# usage: startg09.sh <pe_hostfile>
#
#
PeHostfile2DefaultRouteFile()
{
workers=""
while read line; do
# echo $line
host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
nslots=`echo $line|cut -f2 -d" "`
numworkers=`expr $nslots / 4`
if [ "${workers}" != "" ]; then
workers="${host}:${numworkers},${workers}"
else
workers="${host}:${numworkers}"
fi
done < $1
echo "-W- ${workers}"
}
#
# startup of MPI conforming with the Grid Engine
# Parallel Environment interface
#
# on success the job will find a Default.Route file in
$SGE_O_WORKDIR/Default.Route
#
me=`basename $0`
# test number of args
if [ $# -ne 1 ]; then
echo "$me: got wrong number of arguments" >&2
exit 1
fi
# Make sure we got a multiple of 4 slots
slotschk=`expr $NSLOTS % 4`
echo "requested $NSLOTS slots"
if [ $slotschk -ne 0 ]; then
echo "Number of slots not a multiple of 4!"
exit 4
fi
# get arguments
pe_hostfile=$1
# ensure pe_hostfile is readable
if [ ! -r $pe_hostfile ]; then
echo "$me: can't read $pe_hostfile" >&2
exit 1
fi
# create Default.Route file
#
defroutefile="$SGE_O_WORKDIR/Default.Route"
echo "Creating $defroutefile..."
echo "-P- 4" > $defroutefile
PeHostfile2DefaultRouteFile $pe_hostfile >> $defroutefile
# trace defroutefile file
cat $defroutefile
# signal success to caller
exit 0
***** stopg09.sh *****
#!/bin/sh
#
# shutdown of Gaussian conforming with the Grid Engine
# Parallel Environment interface
#
# Just remove Default.Route-file that was written by startg09.sh
#
rm $SGE_O_WORKDIR/Default.Route
exit 0
--Gary Smith, HPC Lead Engineer
Vertex Pharmaceuticals
From: Gowtham <[email protected]>
To: NPACI Rocks Discussion List <[email protected]>, SGE
Discussion List <[email protected]>
Date: 08/03/2011 11:50 AM
Subject: [gridengine users] Rocks 5.4: Gaussian 09 B.01 + Linda 8.2
+ SGE 6.5
Sent by: [email protected]
Dear fellow users,
If any of you have successfully managed to run Gaussian 09 with Linda 8.2
and
integrate it with SGE on Rocks 5.4, I'd appreciate some tips. I have read
through the mailing list and tried a few things on my own, but in vain so
far.
Thanks in advance for your time and help.
Best,
g
--
Gowtham
Advanced IT Research Support
Michigan Technological University
(906) 487/3593
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