1 / 8

Cluster Computing Applications for Bioinformatics

This guide offers insights into cluster computing applications for bioinformatics, focusing on efficient process management and shell scripting. Learn how to access the cluster using SSH, manage processes with commands like `ps`, `top`, and `kill`, and automate tasks through scripting. Discover how to utilize Sun Grid Engine (SGE) for job scheduling and load balancing, and run parallel programs using MPI. Gain proficiency in setting up your shell environment and executing commands that enhance performance and streamline workflow in bioinformatics projects.

gillian-castillo
Télécharger la présentation

Cluster Computing Applications for Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related