Am 03.08.2011 um 18:17 schrieb [email protected]: > In our setup, we did not want to risk (or rely on) modifying the user's > Gaussian script.
Yeah, therefore I only touch a copy. As I found users supplying %nproc commands while submitting a serial job - hence I like to change it anyway ;-) Or some forgot to repeat it after each -link1- command. > Gaussian will use the Default.Route file in its current working directory to > override any other default parameters. Maybe this way the reason that I dropped the idea when I started to look into. Nevertheless: if the current working directory is in the scratch directory of the node it would work again. -- Reuti > 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 > > > > _______________________________________________ > > 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
