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Cluster Installation: Difference between revisions
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Grid Engine consists of a master node daemon named sgemaster which schedules jobs to execution nodes. On each execution node a daemon named sge_execd runs a job and sends a completion signal back to sgemaster. Jobs are submitted to sgemaster using command such as qsub or using DRMAA C, JAVA or IDL bindings from any applications want to run XDS. | Grid Engine consists of a master node daemon named sgemaster which schedules jobs to execution nodes. On each execution node a daemon named sge_execd runs a job and sends a completion signal back to sgemaster. Jobs are submitted to sgemaster using command such as qsub or using DRMAA C, JAVA or IDL bindings from any applications want to run XDS. | ||
'''XDS Cluster setup''' | |||
XDS Cluster setup | |||
In order to setup XDS in cluster mode, forkcolspot and forkintegrate scripts need to be changed to access the gridengine environment and send jobs to different machines. Example scripts are below, need to be changed according to the environment. | In order to setup XDS in cluster mode, forkcolspot and forkintegrate scripts need to be changed to access the gridengine environment and send jobs to different machines. Example scripts are below, need to be changed according to the environment. | ||
<code> | <code> | ||
#forkcolspot | <nowiki>#forkcolspot | ||
ntask=$1 #total number of jobs | ntask=$1 #total number of jobs | ||
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wait #wait for all background processes issued by this shell | wait #wait for all background processes issued by this shell | ||
rm -f mcolspot.tmp #this temporary file was generated by xds | rm -f mcolspot.tmp #this temporary file was generated by xds | ||
rm -rf fork*job* | rm -rf fork*job*</nowiki> | ||
</code> | </code> | ||
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<code> | <code> | ||
#forkcolspot_job | <nowiki>#forkcolspot_job | ||
#!/bin/csh | #!/bin/csh | ||
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set itask=$1 | set itask=$1 | ||
echo $itask | mcolspot_par | echo $itask | mcolspot_par</nowiki> | ||
</code> | </code> | ||
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<code> | <code> | ||
#forkintegate | <nowiki>#forkintegate | ||
fframe=$1 #id number of the first image | fframe=$1 #id number of the first image | ||
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wait #wait for all background processes issued by this shell | wait #wait for all background processes issued by this shell | ||
rm -f mintegrate.tmp #this temporary file was generated by mintegrate | rm -f mintegrate.tmp #this temporary file was generated by mintegrate | ||
rm -rf fork*job* | rm -rf fork*job*</nowiki> | ||
</code> | </code> | ||
<code> | <code> | ||
#forkintegrate_job | <nowiki>#forkintegrate_job | ||
#!/bin/bash | #!/bin/bash | ||
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set host=`uname -a | awk '{print $2}'` | set host=`uname -a | awk '{print $2}'` | ||
echo $image1 $nitask $itask $nbatask $host >> jobs.log | echo $image1 $nitask $itask $nbatask $host >> jobs.log | ||
echo $image1 $nitask $itask $nbatask | mintegrate_par | echo $image1 $nitask $itask $nbatask | mintegrate_par</nowiki> | ||
</code> | </code> | ||