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HOWTOs/MXQ-Cluster.md

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The MXQ Cluster Environment Submitting Jobs Monitoring Killing Jobs Official Documentation Further Help
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The MXQ Cluster Environment

Currently there are about 1700 CPU nodes available in our cluster.

Submitting Jobs

To submit a job you use the mxqsub command:

mxqsub --threads=<n> --memory=<mem size> --runtime=<time> --stdout=<filename> --stderr=<filename>  <command + command line options>

Example:

mxqsub --threads=1 --memory=2G --runtime=60m --stdout=date.txt --stderr=/dev/null date +%H:%M

If you do not specify those options, very restrictive default values will be used. More options are available - run mxqsub -h to see them.

BEWARE: your job will be automatically killed if you try to allocate more memory than specified or your job runs longer than specified.

BEWARE: it is very well possible that hundreds of your jobs start up at the very same time. Loading the program or data over the network can slow down or even damage the network or hardware. Therefore do NOT access data in your home-dir or project-dir - instead use an appropriate dir in /scratch/cluster.

Monitoring

You can get information about your queued/running/finished jobs using mxqdump. See mxqdump -h for advanced options. A more readable page with all this information can be accessed here:

http://afk.molgen.mpg.de/mxq/mxq

and the load can be monitored here:

http://twiki.molgen.mpg.de/foswiki/Edv/LoadMXQ

Killing Jobs

If things go wrong and you have to kill jobs use the above web-site to find the corresponding group_id of your jobs and kill them with:

mxqkill -g <group_id>

At this time it is not possible to kill single jobs individually.

Official Documentation

The official documentation of the queueing system can be found here:

http://twiki.molgen.mpg.de/foswiki/Edv/MarIuX64ClusterHowTo

Further Help

If you need further help please contact: mailto:helpdesk@molgen.mpg.de