In our setup, we did not want to risk (or rely on) modifying the user's
Gaussian script. Gaussian will use the Default.Route file in its current
working directory to override any other default parameters. The only
issue is that you can't run multiple Gaussian jobs out of the same working
directory for collision reasons. It is on the user to make sure they have
a separate cwd for each of their Gaussian jobs.
--Gary Smith, HPC Lead Engineer
Vertex Pharmaceuticals
From: Reuti <[email protected]>
To: [email protected]
Cc: SGE Discussion List <[email protected]>
Date: 08/03/2011 12:11 PM
Subject: Re: [gridengine users] Rocks 5.4: Gaussian 09 B.01 + Linda
8.2 + SGE 6.5
Am 03.08.2011 um 17:59 schrieb [email protected]:
> 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
Hi, where is the connection from the created Default.Route to the job or
inputfile? I always thought that you can have a route file per
application, but not per job.
THereforte my approach is to copy the input file to the scratch directory
of the node, remove any user supplied %nproc lines and add a new one with
lindaworkers conforming to the granted hostlist by a short awk script.
-- Reuti
>
> # 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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