Please ignore last mail, I found attachment few minutes later, sorry.
----- Original Message -----
From: Reuti <[email protected]>
Date: Friday, January 20, 2012 13:42
Subject: Re: [gridengine users] How I can integrate GAMESS under SGE?
To: Semion Chernin <[email protected]>
Cc: Mazouzi <[email protected]>, "[email protected]" <[email protected]>
> So, the idea is to prepare a list of hosts in the
> start_proc_args, which can directly be used by ddikick.x.
>
> Please find attached the both start/stop_proc_args. They are
> meant to be put in /usr/sge/cluster - otherwise please check all
> the directories inside and adjust them. All the stuff which I
> don't want to be destroyed by an update of SGE I put in
> /usr/sge/cluster (like some prolog and epilog scripts).
> Important is, that you compiled GAMESS to use just `rsh`for
> remote calls (i.e. left it untouched), so that SGE's wrapper can
> catch it and route it to any startup method you like. But it's
> also possible to define in the job script "export DDI_RSH=rsh"
> in case you have something else compiled in.
>
> ====
> $ qconf -sp gamess
> pe_name gamess
> slots 128
> user_lists NONE
> xuser_lists NONE
> start_proc_args
> /usr/sge/cluster/gamess/startgamess.sh -catch_rsh \
> $pe_hostfile
> stop_proc_args
> /usr/sge/cluster/gamess/stopgamess.shallocation_rule $round_robin
> control_slaves TRUE
> job_is_first_task TRUE
> urgency_slots min
> accounting_summary FALSE
> ====
>
> Then you have a jobscript:
>
> ====
> #!/bin/sh
> #$ -N foobar
> #$ -o /home/reuti/err/foobar.stdout_$JOB_ID -e
> /home/reuti/err/foobar.stderr_$JOB_ID#$ -m ea
> #$ -A gamess_serial
> export
> LD_LIBRARY_PATH=/opt/chemsoft/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}cd
> $TMPDIR
> cp /home/reuti/foobar.in foobar.F05
> ln -s /home/reuti/foobar.orb
> JOB=foobar
> CUSTOM_TMPDIR=/home/reuti/scr
> BINARY_LOCATION=/opt/chemsoft/$ARC/GAMESS_OCT012010R3
> EXTERNAL_BASISSET=/dev/null
> . /home/soft/scripts/subgms_export
> unset JOB
> unset CUSTOM_TMPDIR
> unset BINARY_LOCATION
> unset EXTERNAL_BASISSET
> rm -f $IRCDATA
> rm -f $PUNCH
> rm -f $SIMEN
> rm -f $SIMCOR
> HOSTFILE=`hostname`
> /opt/chemsoft/$ARC/GAMESS_OCT012010R3/ddikick.x
> /opt/chemsoft/$ARC/GAMESS_OCT012010R3/gamess.00.x foobar -ddi 1
> 1 $HOSTFILE -scr $TMPDIR < /dev/null > /home/reuti/foobar.out
> ====
>
> And for parallel:
>
> ====
> #!/bin/sh
> #$ -N foobar
> #$ -o /home/reuti/err/foobar.stdout_$JOB_ID -e
> /home/reuti/err/foobar.stderr_$JOB_ID#$ -m ea
> #$ -A gamess_parallel
> #$ -R y
> #$ -pe gamess 4
> export
> LD_LIBRARY_PATH=/opt/chemsoft/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}JOB=foobar
> CUSTOM_TMPDIR=/home/reuti/scr
> BINARY_LOCATION=/opt/chemsoft/$ARC/GAMESS_OCT012010R3
> cd $TMPDIR
> cp /home/reuti/foobar.in foobar.F05
> . /home/soft/scripts/subgms_export
> unset JOB
> unset CUSTOM_TMPDIR
> unset BINARY_LOCATION
> rm -f $IRCDATA
> rm -f $PUNCH
> rm -f $SIMEN
> rm -f $SIMCOR
> HOSTFILE=`cat $TMPDIR/machines`
> /opt/chemsoft/$ARC/GAMESS_OCT012010R3/ddikick.x
> /opt/chemsoft/$ARC/GAMESS_OCT012010R3/gamess.00.x foobar -ddi
> $NHOSTS 4 $HOSTFILE -scr $TMPDIR < /dev/null >
> /home/reuti/foobar.out====
>
> The installation of GAMESS then need only:
>
> reuti@foobar:/opt/chemsoft/lx24-amd64> ls GAMESS_OCT012010R3
> auxdata ddikick.x gamess.00.x
> reuti@foobar:/opt/chemsoft/lx24-amd64> ls GAMESS_OCT012010R3/auxdata/
> BASES MCP QUANPOL ericfmt.dat
>
>
> I'll prepare the "subgms_export" now, it will just set all
> variables which are normally set in rungms and post it ASAP.
>
> -- Reuti
>
> PS: Both job scripts are in fact created by a wrapper for the
> users, but I think for a first test it's better to start with a
> plain job script to avoid an additonal layer of trouble. The
> wrapper I could send you later, when it's working in principle.
>
>
> Am 19.01.2012 um 20:33 schrieb Semion Chernin:
>
> > Please send me qconf -sp gamess and start & stop scripts.
> >
> > ----- Original Message -----
> > From: Mazouzi <[email protected]>
> > Date: Thursday, January 19, 2012 17:32
> > Subject: Re: [gridengine users] How I can integrate GAMESS
> under SGE?
> > To: Reuti <[email protected]>
> > Cc: Semi <[email protected]>, "[email protected]"
> <[email protected]>>
> > > Hi,
> > >
> > > In our cluster, we use GAMESS with a special PE (gamess) using
> > > allocation_rule 2.
> > >
> > > The user MUST request an even number of slots ex ( 2*n).
> > >
> > > the command line is :
> > >
> > > gamess -n $NSLOTS my-job.inp >& my-job.out
> > >
> > >
> > > Hope this will help.
> > >
> > > On Thu, Jan 19, 2012 at 4:01 PM, Reuti <[email protected]
> > > marburg.de> wrote:
> > >
> > > > Hi,
> > > >
> > > > Am 19.01.2012 um 14:22 schrieb Semi:
> > > >
> > > > > How I can integrate GAMESS under SGE?
> > > > >
> > > > > I found some info about this in file called gms, but
> without pe,
> > > > start&stop scripts, example how to use this wrapper.
> > > > >
> > > > > # SGE job submission:
> > > > > # A 'parallel environment' named 'ddi'
> was
> > > set up on ISU's cluster,
> > > > > # this SGE prolog file creates the SGE
> > > directory $TMPDIR on every
> > > > node,
> > > > > # and this epilog script erases
> $TMPDIR,
> > > to be sure the scratch disk
> > > > is
> > > > > # always cleaned up, and to remove
> dead
> > > semaphores.> > #
> > > > > # SGE command 'qconf -sp ddi' shows
> the
> > > details of this environment,
> > > > > # including pathnames to prolog/epilog
> > > scripts. Also, 'qconf -spl'.
> > > > > # Other useful SGE commands: 'qconf -
> sc'
> > > shows config for resources.
> > > > > #
> > > > > # Mirabile dictu! SGE allows you
> to
> > > pass args to a job script by
> > > > > # just placing them behind the script
> > > name. In all my living days,
> > > > > # I've never seen a batch program that
> > > permitted this. Glory be!
> > > > > #
> > > > > if ($SCHED == SGE) then
> > > > > qsub -cwd -o $LOGFILE -j yes -pe ddi $NNODES
> -N
> > > $JOBNAME> $SGE_RESOURCES \
> > > >
> > >
> > ~/scr/$JOB.script $JOB $VERNO $NCPUS $PPN
> > > > > endif
> > > >
> > > > I think this is something set up by your site already.
> I've
> > > never seen it
> > > > before.
> > > >
> > > > The rungms they provide with GAMESS seems targeting in the
> > > first place the
> > > > clusters of the author, what is understandable. But I
> would
> > > have really
> > > > liked that they provide a file which you have to source to
> set
> > > all their
> > > > environment variables and then just just issue ddikik.x
> with
> > > the correct
> > > > parameters and you are done.
> > > >
> > > > I could only send you my scripts to set it up from
> scratch.
> > > The export
> > > > list of variables I would have to refresh, as I have it
> for
> > > the October 01,
> > > > 2010 R3 version only right now.
> > > >
> > > > -- Reuti
> > > > _______________________________________________
> > > > users mailing list
> > > > [email protected]
> > > > https://gridengine.org/mailman/listinfo/users
> > > >
> > >
> >
>
>
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