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Old 04-17-2014, 07:51 AM   #28
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Location: East Coast USA

Join Date: Feb 2008
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Originally Posted by Brian Bushnell View Post
Our clusters use UGE (formerly known as SGE) and set 'ulimit' according to the qsub memory request. I don't know if that is universal or just a local policy, but at least here, users should be able to use the shellscripts without specifying -Xmx, and they should work. I'd be happy if someone elsewhere tried it without setting -Xmx and reported what happens.
With LSF, not setting the -Xmx flag is leading to default allocation of 4G (at least on our cluster, things may be set up differently at other locations) which results in Java running out of heap space. I am also not using exclusive nodes option so far and it seems to be working fine.

BTW: The latest code for BBMap (32.06) seems to have shell script files in DOS format (wasn't the case before on previous versions).
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