LaoTsao's Weblog (老曹的網路記)

Integration of gaussian 03 with SGE

Recently in a POC at customer site, we use the ROCKS cluster SW.

One of the requirement for POC is the running gaussian 03 under SGE.

In linux environment g03 can use linda parallel environmnet to use multiple processors on multiple nodes.

For simplicity we just use the SGE's PE mpi.

The hardest part for this exercise is understanding how to run g03 and how g03 work with queue system

After working with customer to create a input file and learn how to run the g03l and read through some documentation and example on the web on PBS and g03 and g03 and SGE and getting some example g03 script without SGE from barbara perz

I created two scripts

one is for customer to change the inputfile and number of nodes for the g03's jobs

one is the driver for g03 input file.

our s.csh is very simple

it will take two agrument

$1=number of %Nprocl +1

$2=input file

qsub -pe mpi sge-g01l.csh

Under g03l one can specifi Number of Process used in Linda,

one can add the %Nprocl in the input file and since linda will also use one

processor, so we allocate %Nprocl +1 from SGE's PE mpi environment.

We will use the user's input to change the inputfile then submit the job to g03l

#!/bin/csh -f

setenv g03root

source $g03root/g03/bsd/g03.login

set scratch=$TMPDIR <-- SGE's tmpdir

setenv GAUSS_SCRDIR $scratch

#$ -cwd

#$ -j y

set nodefile=$TMPDIR/machines <-- SGE's nodefile assign by -pe mpi

set ncpus=`expr $NSLOTS -1 ` <-- NSLOTS from -pe mpi

set input=$1 <-- inputfile

set tempinp=tmp$$ <-- new input file

echo "%nprocl=$nprocs " > $tmpinp

cat $input >> $tmpinp

cp $tmpinp $tmpinp.com <--rename

setenv GAUS_LFLAGS "-vv -mp 2 -nodefile $nodefile" <-- assign 2 processor per node

g03l $tmpinp.com $input.$ncpus.log

Posted at 07:08PM Apr 07, 2005 by hstsao in N1 Grid  |  Comments[3]