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

pollinger harald.pollinger at sun.com
Tue Jun 2 21:35:30 BST 2009

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
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