Submitting a job using multiple cores on the same compute server is done through the
-pe option that allows you to specify the
multicores parallel environment, as well as the desired number of cores:
$ qsub -pe multicores <number_of_cores> -q <QueueName> <script>
For example :
$ qsub -pe multicores 4 -q mc_long test.sh
The queues available for multi-core jobs are the following:
To know the queues limits please refer to the page Information on scheduling queues.
Access to all multi-core queues is restricted. You must contact your czar to access this type of resource. Restricted queues FAQ.
The higher the number of requested cores, the more likely the job will wait before executing. It is thus recommended not to ask more than 16 cores. 8 cores is a good compromise between job size and waiting.
Multi-core jobs must be properly configured to use the number of cores requested, accessible through the
$NSLOTS environment variable. The use of more cores than requested may impact the operation of the compute servers and the jobs of other users.
mc_highmem_huge give access to a machine dedicated to computations needing a high value of CPU. Please contact our user support to discuss your computing model.
The memory resource allocated when using the
-l option, such as
-l s_rss=4G, is the memory allocated for one core, and not for the whole job. For the latter, the total memory allocated is then the number of cores requested times the memory resource requested using that option.