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Cluster Installation: Difference between revisions
→XDS Cluster setup
(remove out-of-date grid engine installation stuff; update to show forkxds and DLS UGE usage (thanks to Graeme W!)) |
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XDS can be run in cluster mode using any command line job scheduling software such as Grid Engine, Condor, Torque/PBS, LSF, SLURM etc. We implemented Grid Engine. It is a distributed resource management system which monitors the CPU and memory usage of the available computing resources and schedules the job to the least used computer. Grid Engine was chosen due to its high scalability, cost effectiveness, ease of maintenance and high throughput. Grid Engine was developed by Sun Microsystems (Sun Grid Engine, SGE) and later acquired by Oracle and subsequently acquired by UNIVA. The latest versions became closed source, but the older ones are open source supplied with many Linux distributions including Redhat/CentOS 6.x. There is also open source Open Grid Scheduler [[http://gridscheduler.sourceforge.net/]], Son of Gridengine [[https://arc.liv.ac.uk/trac/SGE ]] | XDS can be run in cluster mode using any command line job scheduling software such as Grid Engine, Condor, Torque/PBS, LSF, SLURM etc. We implemented Grid Engine. It is a distributed resource management system which monitors the CPU and memory usage of the available computing resources and schedules the job to the least used computer. Grid Engine was chosen due to its high scalability, cost effectiveness, ease of maintenance and high throughput. Grid Engine was developed by Sun Microsystems (Sun Grid Engine, SGE) and later acquired by Oracle and subsequently acquired by UNIVA. The latest versions became closed source, but the older ones are open source supplied with many Linux distributions including Redhat/CentOS 6.x. There is also open source Open Grid Scheduler [[http://gridscheduler.sourceforge.net/]], Son of Gridengine [[https://arc.liv.ac.uk/trac/SGE ]] | ||
== | The following does ''not'' refer to the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#CLUSTER_NODES= CLUSTER_NODES=] setup. The latter does not require a queueing system. | ||
In order to setup XDS | == setup of XDS for a batch queue system == | ||
In order to setup XDS for a queuing system, the ''forkxds'' script need to be changed to access the environment and send jobs to different machines. Example scripts used for Univa Grid Engine (UGA) at Diamond (from https://github.com/DiamondLightSource/fast_dp/tree/master/etc/uge_array - thanks to Graeme Winter!) are below; they may need to be changed according to the environment. Observe this uses the ''qsub'' command which submits forkxds_job to grid engine. | |||
<pre> | <pre> | ||
#forkxds | # forkxds | ||
#!/bin/bash | #!/bin/bash | ||
# forkxds Version DLS-2017/08 | # forkxds Version DLS-2017/08 | ||
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fi | fi | ||
qsub $qsub_opt -sync y -V -cwd -pe smp $maxcpu -t 1-$ntask | qsub $qsub_opt -sync y -V -cwd -pe smp $maxcpu -t 1-$ntask `which forkxds_job` | ||
`which forkxds_job` | |||
</pre> | </pre> | ||