[gridengine users] Rocks 5.4: Gaussian 09 B.01 + Linda 8.2 + SGE 6.5

[Gary_Smith at vrtx.com]

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 <sgowtham at mtu.edu>
To:     NPACI Rocks Discussion List <npaci-rocks-discussion at sdsc.edu>, SGE 
Discussion List <users at gridengine.org>
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:        users-bounces at gridengine.org




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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