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Cluster Installation: Difference between revisions
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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! | 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 | 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 == | == 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 | 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. | ||
<pre> | <pre> | ||
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</pre> | </pre> | ||
<pre> | <pre> | ||
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echo $SGE_TASK_ID | $JOB | echo $SGE_TASK_ID | $JOB | ||
</pre> | </pre> | ||
== 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. | |||