[GE users] Gaussian09 with Linda 8.2

flengyel flengyel at gc.cuny.edu
Fri Dec 4 18:26:38 GMT 2009


We've done it, but in SGE 6.0.

It's not optimal: we use the mpi start and stop scripts that come
with SGE:

qconf -sp gauss4
pe_name           gauss4
slots             10000
user_lists        Research deadlineusers
xuser_lists       NONE
start_proc_args   /usr/local/sge/mpi/startmpi.sh -catch_rsh $pe_hostfile
stop_proc_args    /usr/local/sge/mpi/stopmpi.sh
allocation_rule   $fill_up
control_slaves    FALSE
job_is_first_task TRUE
urgency_slots     min


A gaussian 09 test script:

#!/bin/csh
#$ -S /bin/csh
#$ -N t_cp.com
#$ -cwd
#$ -pe gauss4 16
#$ -q octo.q
#$ -R y

setenv g09root /home/nept/apps64/gaussian-linda
source ${g09root}/g09/bsd/g09.login
setenv SGE_ROOT /usr/local/sge
source  /usr/local/sge/default/common/settings.csh
setenv GAUSS_SCRDIR     /tmp
setenv PGI /home/nept/apps64/pgi
set PATH = ( $PGI/linux86-64/9.0-4/bin  $PATH)
setenv LM_LICENSE_FILE $PGI/license.dat

setenv GAUSS_LFLAGS '-vv'

g09 g09_kayers.gjf


Now I see that we didn't resolve how g09 is picking up
which host to go to. This is hardcoded into the scrript,
which defeats the purpose

%mem=2000mb
%nprocshared=8
%lindaworkers=m63,m64
...

One could  omit the %procshared and
%lindaworkers statements from the gaussian input file,
and append these based on the SGE environment.
This is reminding me that we need to do this. Another group
at CUNY is running 6.2. A group of us worked it out for them
at one point--I'll check my email archives.

We have dual-processor E5420 quads of which two were
used in this test; we request 16 slots and set
%nprocshared=8 (each host has 8 cores and we define
the number of slots/host to be the number of cores).

By the way, this works with loose integration. We've have
not had any luck with tight integration.

Florian Lengyel, Ph.D.
Assistant Director for Research Computing, IT
& Adjunct Professor in Computer Science
CUNY Graduate Center
365 Fifth Avenue, Room 4435
New York, NY 10016
Web: http://research.gc.cuny.edu
Phone: 212 817-7374
________________________________________
From: buudo [uschmidt at mpi-halle.de]
Sent: Friday, December 04, 2009 10:51 AM
To: users at gridengine.sunsource.net
Subject: [GE users] Gaussian09 with Linda 8.2

Dear all,
I have to configure the parallel environment to run the gaussian09 package with Linda 8.2. There are some unusual variables to create from $pe_hostfile to make a special machines file. As well it seems to me I need a special wrapper script for the ssh communication.  The gaussian09 in  serial works fine. I want have the full control by the sge. has anyone created already a special gauss_linda_start.sh and gauss_linda_stop.sh script ? I am using sge 6.2u4.
Regards
Udo

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