Running jobs

FAQ

Frequently asked questions related to running jobs in the queue system on the HPC clusters (currently: Fram).

"srun: Warning: can't honor --ntasks-per-node set to X which doesn't match the requested tasks Y with the number of requested nodes Y. Ignoring --ntasks-per-node."

This warning appears when using the mpirun command with Intel MPI and specifying --ntasks-per-node for jobs in the normal partition on Fram. As far as we have seen, the job does not ignore the --ntasks-per-node, and will run the specified number of processes per node. You can test it with, e.g., mpirun hostname. Please let us know if you have an example where --ntasks-per-node is not honored!

So, if you get this when using mpirun with Intel MPI, our recommendation is currently that the warning can be ignored.

Job start gets postponed

Note: This is specific for Fram. If the estimated job start gets postponed again and again, one reason might be that the queue system cannot find idle nodes within the same "island" of Fram. The network on Fram is divided into four "islands", and the network is faster within the islands than between them. The queue system will by default delay a job with up to 7 days in order to be able to start it on a single island. This is most likely to happen for jobs asking for many nodes. It is possible to override this.

Things to avoid

Things you should not do or use when running jobs on the HPC clusters (currently: Fram).

#SBATCH --hint=nomultithread

Do not use this, at least not with Intel MPI jobs. If you do, the result is that all the tasks (ranks) will be bound to the first CPU core on each compute node.

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