[GE users] running magma / talus in SGE with qrsh

adary adary at marvell.com
Wed Jun 3 11:38:24 BST 2009

Issue resolved.

If appears that Magma themselves know to detect if working on SGE, and they wrote a piece of code that will emulate pty for magma when running through qrs. This is great for versions prior to 6.2 but 6.2 with built in interactive breaks magma. The solution was to edit magma wrapper script and remove the code. Once that was done everything works perfectly.

-----Original Message-----
From: adary [mailto:adary at marvell.com]
Sent: Wednesday, June 03, 2009 9:58 AM
To: users at gridengine.sunsource.net
Subject: RE: [GE users] running magma / talus in SGE with qrsh

There wasn't real tweaking except our setup for ssh in interactive jobs in SGE 6.1u3. But I already have a decent lead toward the solution for this since our magma tools are wrapped in at least 3 scripts before they get to the binary itself. The first is a perl wrapper, and the second and third are tcl wrappers. I have a feeling that the signals get lost somewhere between those shells. In any case if I manage to solve this I will write about the solution.

-----Original Message-----
From: Harald.Pollinger at Sun.COM [mailto:Harald.Pollinger at Sun.COM]
Sent: Tuesday, June 02, 2009 11:36 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] running magma / talus in SGE with qrsh

adary wrote:
>> Hmm.. how exactly do you start the mamga tools? Do you "qrsh" to a
>> host and then start the magma tools there, or do you "qrsh
>> $MAGMA_TOOLS"? In the second case, adding the "-pty yes" switch
>> could help, i.e. # qrsh -pty yes $MAGMA_TOOLS
>> Regards, Harald
> Hi Harald,
> We use a wrapper for all qsub and qrsh tools.
> In the end the actual submit command looks like this: (a lot of -v
> options removed to make it more readable)
> qrsh  -pty yes -P kirkwood_FullChip -N blast -q heavy -M
> adary at marvell.com -cwd  -p 0 -m a -e
> "$SGE_FILESDIR"/sungrid.\$JOB_ID.error -b y -o
> "$SGE_FILESDIR"/sungrid.\$JOB_ID.log -noshell  -v
> SGE_BACKSLASH_ARGV=0 -hard -l a_tmp_prj=100M -l a_tmp=100M -l
> site=yokneam -l a_dumps=100M -l mem_free=2.6G -l heavy_0=1
> /nfs/local/eda/areas/DAtools/galenv/tools/SGE/SGE_6.2u2%001/bin/mqjob
> mantle
> the mqjob script takes care of preparing the environment for magma.
> Any other shell tool manages to capture ^C without problems, with the
> exception of talus and mantle (both magma tools)

This is really interesting. It seems the pty is set differently than the
tty, and the magma tools are the only who care about this difference.

You wrote that you needed some tweaking to make mantle work with ssh -
what was this tweaking?
Perhaps it's possible to do the same tweaking in the starter script of
the magma tools.


Sun Microsystems GmbH         Harald Pollinger
Dr.-Leo-Ritter-Str. 7         Sun Grid Engine Engineering
D-93049 Regensburg            Phone: +49 (0)941 3075-209  (x60209)
Germany                       Fax: +49 (0)941 3075-222  (x60222)
mailto:harald.pollinger at sun.com
Sitz der Gesellschaft:
Sun Microsystems GmbH, Sonnenallee 1, D-85551 Kirchheim-Heimstetten
Amtsgericht Muenchen: HRB 161028
Geschaeftsfuehrer: Thomas Schroeder, Wolfgang Engels, Wolf Frenkel
Vorsitzender des Aufsichtsrates: Martin Haering


To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].


To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].


To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].

More information about the gridengine-users mailing list