AW: [GE users] Help from Gaussian users

owissdorf oliver.wissdorf at boehringer-ingelheim.com
Wed Jul 14 12:40:47 BST 2010


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Hi,

we modify the user?s gaussian input file to make sure the users are using our parallel file system (lustre). Therefore we use a gaussian start script. In this script we prepare the environment for the gaussian job (e.g. number of cpus, use linda or not, chose the cluster,?) and inside the start script we write a job script, that will be send to the cluster. In this script we modify the Gaussian input file depending on the needs.

E.g:

#!/bin/env perl
?
# read command line options
 read_commandline();
?
# write command line scripts
  write_cluster_script ();
?
$submit = "$sge_dir/bin/lx24-amd64/qsub  $root_dir/$hidden_jobdir/$g09_job.sh";
system $submit;
?
sub write_cluster_script {

 # Write cluster job script file to Project Dir
   open (BASH,">$hidden_jobdir/$g09_job.sh") || die "Cannot create $hidden_jobdir/$g09_job.sh !";
print BASH <<EOF
#!/bin/bash
#\$ -S /bin/bash
#\$ -N $g09_job
#\$ -cwd
#\$ $pe_gauss $num_proc
#\$ $queue
?

#g09 environment
export g09root="/apps/prod/gauss"
source \${g09root}/g09/bsd/g09.profile
export GAUSS_SCRDIR="/scratch/$USER/BG09_\$QUEUE"_"\$JOB_ID/"
export GAUSS_LFLAGS='-opt "Tsnet.Node.lindarsharg: ssh"'

#sge environment
export SGE_ROOT="/opt/sge/sge"
source  \$SGE_ROOT/default/common/settings.sh

sed -i -r -e \"s|%[Cc][Hh][Kk]=.*|%chk=/scratch/$USER/BG09_\$QUEUE"_"\$JOB_ID/$g09_job.chk|\" $g09_job.job
?
g09 $root_dir/$hidden_jobdir/$g09_job.job
?
#do something after calculation
EOF
;
close BASH;
chmod 0755, "$root_dir/$jobdir/$g09_job.sh";
}

So you can have control where the files are and after the calculation you can copy, move or delete them how  you want to.

Oli

Von: fjmodrego [mailto:modrego at unizar.es]
Gesendet: Mittwoch, 14. Juli 2010 12:35
An: users at gridengine.sunsource.net
Betreff: Re: [GE users] Help from Gaussian users


El 14/07/2010, a las 12:14, reuti escribió:

for Linda I posted this some time ago. To avoid the scratch files to mess up your home directory, you might need a `cd $TMPDIR`.

Thanks,  I have read your hints (I think) but this is not the case... scratch files are note in the user's home directory but in a common temporary partition where ALL the users leave their temporary Gau-nnnn files.  I have looking in google about sge g03 scratch and so on and I have only found places where the system manager ask the users to clean themselves the leftovers... not quite I need...

Thanks
            F.J. Modrego


-- Reuti

PS: Please don't hijack a thread.


Ps.:
Uh??? What have I done???? please send me a private message...





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