Cluster Installation: Difference between revisions

Cluster Installation (view source)

Revision as of 11:06, 10 August 2017

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 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!
-XDS can be run in a cluster using any command line job scheduling software such as Grid Engine, Condor, Torque/PBS, LSF, SLURM etc. These are distributed resource management system which monitor the CPU and memory usage of the available computing resources and schedule jobs to the least used computers.
+XDS can be run in a cluster using any batch job scheduling software such as Grid Engine, Condor, Torque/PBS, LSF, SLURM etc. These are distributed resource management system which monitor the CPU and memory usage of the available computing resources and schedule jobs to the least used computers.
 == setup of XDS for a batch queue system ==
-In order to setup XDS for a queuing system, the ''forkxds'' script needs to be changed to access the environment and send jobs to different machines, and to switch off the ssh-based mechanism which the CLUSTER_NODES keyword employs. 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.
+In order to setup XDS for a queuing system, the ''forkxds'' script needs to be changed to use qsub instead of ssh. 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 for the specific environment and queueing system.
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 echo $SGE_TASK_ID | $JOB
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+== Performance ==
+For the qsub command at the end of the script, it is not necessary to stick to the value of maxcpu as provided by $2 of forkxds (which is supplied by xds_par). If the cluster has nodes with more cores than the node where xds_par was started, it may be more efficient to override maxcpu, by grep-ing MAXIMUM_NUMBER_OF_PROCESSORS from XDS.INP, or by supplying it to the script from an environment variable, or to hard-code the value. If the cluster is homogeneous then this is of course no concern.