[GE users] PVM and SGE

John Saalwaechter johnsaalwaechter at yahoo.com
Fri Jun 23 21:37:44 BST 2006


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I was looking at this issue today.  I think I have a solution
that allows one to embed the path information in the job script,
and avoids changes to pvmstart.sh and ~/.ep files.
 
Here's what I did:
 
Originally I tried setting PVM_PATH=/path/to/progs and
PVM_EXPORT=PVM_PATH in the job script.  This did not work
because these variables really affect pvmd (I think).
When the job script runs, the pvmds are already running,
so their environment cannot be modified.
 
So next it occurred to me that setting PVM_PATH and
PVM_EXPORT in the qsub call would get this information
to the pvm PE scripts. That works.  So I just embedded
that into the job script with #$ options.
 
Here is an example job script for the FRED docking program:

 #!/bin/sh
 #
 #$ -j y
 #$ -cwd
 #$ -N FRED
 #$ -pe pvm-reuti 6
 #$ -v PVM_PATH=/path/to/progs/bin,PVM_EXPORT=PVM_PATH
 #$ -r n

 date
 hostname

 PVM_TMP=$TMPDIR
 export PVM_TMP

 awk 'NR != 1 {print "host",$1,$2}' $PE_HOSTFILE > FREDWORKERS.txt

 time /path/to/progs/bin/fred2 \
     -pro foo.pdb \
     -box bar.mol2 \
     -addbox 4.0 \
     -dbase ligs.oeb.gz \
     -chemgauss \
     -plp \
     -pvmconf FREDWORKERS.txt \
     -oformat mol2

 date

Another thing I came across while solving this is
the $HOME/.pvmprofile file.  If you ran pvm jobs
across multiple PVM_ARCHs, you could use this file
instead of the method above to set a custom
PVM_PATH on each type of machine.

John

--- Reuti <reuti at staff.uni-marburg.de> wrote:

> Am 06.06.2006 um 03:34 schrieb Bernard Li:
> 
> > Hi Reuti:
> >
> > Thanks for the response.
> >
> > I am aware of the -ep <dirname> argument, however that's set by the
>  
> > system and does not provide a per-user setting (eg. maybe the user 
> 
> > wants to setup their own paths).  Is there another option?
> 
> The easiest would be to extend the startpvm.sh script with something 
> 
> like this I think:
> 
> # enhance the search path if requested
> if [ "x$path_enhancement" != "x" ]; then
>     echo "* ep=$path_enhancement" >> $pvm_hostfile
> elif [ -f ~/.ep -a -r ~/.ep ]; then
>     cat ~/.ep >> $pvm_hostfile
> fi
> 
> and have a .ep prepared for the individual user.
> 
> HTH - Reuti
> 
> >
> > Thanks,
> >
> > Bernard
> >
> > From: Reuti [mailto:reuti at staff.uni-marburg.de]
> > Sent: Mon 05/06/2006 12:29
> > To: users at gridengine.sunsource.net
> > Subject: Re: [GE users] PVM and SGE
> >
> > Hi Bernard,
> >
> > Am 05.06.2006 um 21:24 schrieb Bernard Li:
> >
> > > I have a quick question regarding PVM and SGE.  How does the user
> > > specify where PVM is to locate the binaries the user wants to  
> > run?  If
> > > you are to manually bootup pvmd you can specify "ep" in the hosts
> > > file,
> > > but booting up pvmd is handled by SGE, is there an environment
> > > variable
> > > that sets this path up?
> >
> > you can specify -ep <dirname> for start_proc_args. Please have a
> look
> > into the startpvm.sh script for details.
> >
> > Cheers - Reuti
> >
> >
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> 


--
johnsaalwaechter at yahoo.com

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