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

adary adary at marvell.com
Wed Jun 3 13:20:09 BST 2009


I just implemented the fix in our environment, and instead of editing the actual tool in 14 different versions we have installed I just added "unsetenv QRSH_COMMAND" to our wrapper script. All magma tools look for $QRSH_COMMAND and if they find it they assume they started with SGE, and their wrapper starts the actual magma binary with their own pty implementation.

Works like a charm if you cant touch vendor tools.


-----Original Message-----
From: Harald.Pollinger at Sun.COM [mailto:Harald.Pollinger at Sun.COM]
Sent: Wednesday, June 03, 2009 3:14 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] running magma / talus in SGE with qrsh

I'm glad to hear this!
I didn't know they had a special code. Thanks for investigating this!

Regards,
Harald

adary wrote:
> 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.
>
> Regards, Harald
>
> -- 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) http://www.sun.com/gridware
> 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
>
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--
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)
http://www.sun.com/gridware
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

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