Rosetta
=======

The documentation for slurm commands can be found on the official Slurm_ website.
Of special note is the documentation of the sbatch_ command
Below is a reference table to be used as a comparison to our previously used SGE scheduler.

.. _Slurm: https://slurm.schedmd.com/man_index.html
.. _sbatch: https://slurm.schedmd.com/sbatch.html

+-----------------------+---------------------------------------------+-------------------------------------------------------+
| **User Commands**     | **SGE**                                     | **Slurm**                                             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job submission        | ``qsub [script_file]``                      | ``sbatch [script_file]``                              |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job deletion          | ``qdel [job_id]``                           | ``scancel [job_id]``                                  |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job status (by job)   | ``qstat -u \* [-j job_id]``                 | ``squeue [job_id]``                                   |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job status (by user)  | ``qstat [-u user_name]``                    | ``squeue -u [user_name]``                             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Queue list            | ``qconf -sql``                              | ``squeue``                                            |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Node list             | ``qhost``                                   | ``sinfo -N OR scontrol show nodes``                   |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Cluster status        | ``qhost -q``                                | ``sinfo``                                             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
|                       |                                             |                                                       |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| **Environment**       | **SGE**                                     | **Slurm**                                             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Script directive      | ``#$``                                      | ``#SBATCH``                                           |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Queue                 | ``-q [queue]``                              | ``-p [queue]``                                        |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Node Count            | N/A                                         | ``-N [min[-max]]``                                    |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| CPU Count             | ``-pe [PE] [count]``                        | ``-n [count]``                                        |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Wall Clock Limit      | ``-l h_rt=[seconds]``                       | ``-t [min] OR -t [days-hh:mm:ss]``                    |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Standard Output File  | ``-o [file_name]``                          | ``-o [file_name] OR --output=[file name]``            |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Standard Error File   | ``-e [file_name]``                          | ``-e [file_name] OR --error=[file name]``             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Combine stdout/stderr | ``-j yes``                                  | (use -o without -e)                                   |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Copy Environment      | ``-V``                                      | ``--export=[ALL | NONE | variables]``                 |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Event Notification    | ``-m abe``                                  | ``--mail-type=[events]``                              |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Email Address         | ``-M [address]``                            | ``--mail-user=[address]``                             |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job Name              | ``-N [name]``                               | ``--job-name=[name]``                                 |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job Restart           | ``-r [yes|no]``                             | ``--requeue OR --no-requeue``                         |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Working Directory     | ``-wd [directory]``                         | ``--workdir=[dir_name]``                              |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Resource Sharing      | ``-l exclusive``                            | ``--exclusive OR--shared``                            |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Memory Size           | ``-l mem_free=[memory][K|M|G]``             | ``--mem=[mem][M|G|T] OR --mem-per-cpu=[mem][M|G|T]``  |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Account to charge     | ``-A [account]``                            | ``--account=[account]``                               |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Tasks Per Node        | (Fixed allocation_rule in PE)               | ``--tasks-per-node=[count]``                          |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| CPUs Per Task         |                                             | ``--cpus-per-task=[count]``                           |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job Dependency        | ``-hold_jid [job_id | job_name]``           | ``--depend=[state:job_id]``                           |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job Project           | ``-P [name]``                               | ``--wckey=[name]``                                    |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Quality Of Service    |                                             | ``--qos=[name]``                                      |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Job Arrays            | ``-t [array_spec]``                         | ``--array=[array_spec]``                              |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Generic Resources     | ``-l [resource]=[value]``                   | ``--gres=[resource_spec]``                            |
+-----------------------+---------------------------------------------+-------------------------------------------------------+
| Licenses              | ``-l [license]=[count]``                    | ``--licenses=[license_spec]``                         |
+-----------------------+---------------------------------------------+-------------------------------------------------------+