MXQ-Cluster.md

# 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