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 > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users > > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
