AW: [GE users] Help from Gaussian users

reuti reuti at staff.uni-marburg.de
Wed Jul 14 14:00:32 BST 2010


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Hi,

Am 14.07.2010 um 13:40 schrieb owissdorf:

> 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.

yep, this is the way to go. I would like, when you could specify all the options on the command line instead of adding it to the input file.


>  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/"

Why is $TMPDIR not set to /scratch. So SGE would create the temporary directories and also remove them automatically after the job without user interaction.


> export GAUSS_LFLAGS='-opt "Tsnet.Node.lindarsharg: ssh"'

Do you still have a tight integration of Linda into SGE? It would need a modified start_proc_args script to generate a link called "ssh" there in. I changed the hard coded /usr/bin/rsh in linda_rsh and SGE is doing the rest by catching it and routing to whatever startup mechanism is defined in SGE's setup.

-- Reuti


>  #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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