Quick reference

Useful hints and short information on COSMOS resources and the SLURM batch system.

Installed software

To list all software available through the module system:

module spider

To check prerequisites for a specific package:

module spider <module_name/version>

To see currently loaded modules:

module list

To load a module:

module add <module_name>

To unload a module:

module del <module_name>

Resource allocation

Number of cores

Specify nodes and tasks per node in your job script:

#SBATCH -N <number_of_nodes>
#SBATCH --ntasks-per-node=<number_of_cores_per_node>

COSMOS has 48 cores per node. To allocate 192 cores across 4 nodes:

#SBATCH -N 4
#SBATCH --ntasks-per-node=48

Memory per core

#SBATCH --mem-per-cpu=<amount_in_MB>

COSMOS nodes have 256 GB of memory. The default allocation is 5300 MB per core, leaving headroom for the operating system. Requesting more than 5300 MB per core will leave some cores idle — your account is charged for those idle cores too.

File systems

Home directory

Your home directory on COSMOS is:

/home/<username>

Also accessible as $HOME.

Global working directory

Use your home directory for job submission. The old /lunarc/nobackup/users directory has been decommissioned.

Local working directory

Each compute node has a local scratch disk available during a job at $SNIC_TMP (also $TMPDIR). It is deleted when the job ends.

If a job is terminated early (e.g. walltime exceeded), files on the local disk are lost. To preserve specific files, list them in $SNIC_TMP/slurm_save_files — paths should be relative to $SNIC_TMP, separated by spaces or newlines. These files will be copied to the submission directory if at all possible.

Quotas

Disk quotas are set per user and filesystem. Your quota status is shown at login, or run:

snicquota

Quota increases are available on request.

Test queue

On COSMOS, short tests (maximum 1 hour, at most 2 nodes) can be given elevated priority:

#SBATCH --qos=test

Do not submit long series of jobs to the test queue.

Author: (LUNARC)

Last Updated: 2024-06-18