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

adary adary at marvell.com
Sun May 31 11:28:27 BST 2009


>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)

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