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Cluster Computing Applications for Bioinformatics

Cluster Computing Applications for Bioinformatics. Thurs., Sept. 20, 2007 process management shell scripting Sun Grid Engine running parallel programs. Accessing the Cluster. ssh username@server -X to enable X forwarding ssh compute-#-# to access specific node

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Cluster Computing Applications for Bioinformatics

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  1. Cluster Computing Applications for Bioinformatics • Thurs., Sept. 20, 2007 • process management • shell scripting • Sun Grid Engine • running parallel programs

  2. Accessing the Cluster • ssh username@server • -X to enable X forwarding • ssh compute-#-# to access specific node • qrsh to access the least busy node • cluster-fork command to run on every node

  3. Managing Processes • ps – list your running processes • -f : show file information • -e : list everyone's processes • top – current top processes by CPU and memory use • kill – terminate a process by number • killall to kill by program name • command & - run in background • bg - show background tasks • nice / renice – set priority

  4. cd ~ ls -a vi .bash_profile echo $PATH The Shell • Unix command interpreter • bash – Bourne Again Shell • .bashrc and .bash_profile • settings for your shell environment

  5. mkdir ~/bin cd /share/bio/examples/ cp makeseqdir ~/bin cd TFL makeseqdir Shell Scripting • Automate common tasks • create directory structure required for sequence assembly

  6. cd /share/bio/examples/ cp assemble ~/bin assemble Distributed Shell Scripts • Preface CPU intensive commands with qrsh -cwd • qtcsh • shell that does this automatically based on ~/.qtask file • Does not work

  7. Sun Grid Engine - SGE • Job queue and load balancing • commands: • qrsh / qtcsh • qstat -f : show status of jobs / queues • qdel : delete a job from the queue • qmon : graphical interface • qsub : submit job

  8. cd /share/bio/examples cp .ncbirc ~ cp mpiblast.sh ~ cd ~ qsub -pe mpich 8 mpiblast.sh Running Parallel Programs • MPI – Message Passing Interface • must be launched with mpirun or as a script with qsub • mpiblast - parallel version of BLAST • modify ~/.ncbirc • first run mpiformatdb –nfrags=n

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