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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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LSF cluster #178

Open khayer opened 11 years ago

khayer commented 11 years ago

Not all LSF clusters have plus queue.

delagoya commented 11 years ago

Same could be said for the SGE command line. Specifically not all SGE clusters have a make queue, and, more importantly, if that queue may not have the $pe_slots allocation rule. In the case of $fill_up would make a best effort to schedule the parallel jobs onto the same node, but they may end up on different nodes, which would do two things:

1) it would run the job twice 2) It has the possibility of overloading the execution node's resources, since one of the threads would not be accounted for.

khayer commented 11 years ago

Good point. For now --platform-flags can be over-written, but this is certainly not the ideal solution.