Software: Data Processing: High Performance Computing (HPC) Queue

Software: Data Processing: High Performance Computing (HPC) Queue

High Performance Computing (HPC) Queue


To use compute/cpu resources at the BIC requires the user to employ a job queuing system called Sun Grid Engine, or SGE. It is used to submit jobs to the distributed compute nodes on all the Linux boxes at the BIC.

SGE uses the commands qsub (along with qrsh and qlogin), qdel, qstat and qhost to submit, delete and query jobs and queues states. For inexperienced users, a simple script/wrapper around SGE is available: qbatch. It can be used instead of the more complicated qsub command. A few examples are given below.

Extensive documentation for SGE is available on all BIC hosts. Just type apropos -s 1 SGE (or man -s 1 -k sge). Don’t be overwhelmed at the length and complexity of the man pages! The learning curve for SGE is very steep as for any queueing system that can scale from tens up to thousands of nodes. Notwithstanding this, what is written below should be sufficient to get you going as a sophomore SGE user just learning the ropes.

More how-to guides on the BIC forum here.





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