Quick Reference (Cheat Sheet)
=============================

.. note::

   This page is a quick reference guide to be used once you are familiar 
   the HEC User Guide. Many entries contain a link to more detailed
   information on these commands

Login, filestore and data transfer
----------------------------------

.. list-table::
 
  * - *ssh USERNAME@wayland.hec.lancs.ac.uk*
    - :ref:`login<login>` from a linux desktop
  * - *gpfsquota*
    - show usage for for HEC :ref:`filestores<filestore>`
  * - *scp -r /path/to/my/directory USERNAME@wayland.hec.lancs.ac.uk*
    -  :ref:`upload<scp>` a directory to the HEC from a linux desktop 
  * - *scp -r /path/to/my/directory USERNAME@wayland.hec.lancs.ac.uk*
    - :ref:`upload<scp>` a directory to the HEC from a linux desktop
  * - *smbclient -k -D folder-path //luna/faculty-code*
    - :ref:`connect to a research folder<smbclient>` on LUNA. Use put and get to upload/download

Job Submission
--------------

.. list-table::

  * - *sbatch JOBSCRIPT*
    - submit file *JOBSCRIPT* as a :ref:`batch job<batch jobs>`
  * - *srun -\-pty bash -i*
    - submit an :ref:`interactive job<interactive jobs>`
  * - *scancel JOBID*
    - cancel job number JOBID

Job Monitoring
--------------

.. list-table::

  * - *squeue -\-me*
    - shows all :ref:`running and pending jobs<squeue>`
  * - *qcgtop -u USERNAME*
    - shows :ref:`CPU and memory usage summaries<qcgtop>` for all running jobs
  * - *qtop -u USERNAME*
    - shows :ref:`top-style information<qtop>` on all running jobs
  * - *qquota*
    - shows :ref:`job resource quotas<qquota>` (CPUs, memory and GPUs)
  * - *qacct -j JOBID*
    - shows :ref:`summary of completed<qacct>` job JOBID
  * - *qslots*
    - shows available CPU resource on the cluster
  * - *qgpuslots*
    - shows available GPU resource on the cluster


Enviroment Modules
------------------

.. list-table::

  * - *module avail*
    - show all :ref:`modules<envmods>`
  * - *module av PATTERN*
    - show available :ref:`modules<envmods>` matching PATTERN
  * - *module add MODULENAME*
    - add MODULENAME to the current shell environment
  * - *module rm MODULENAME*
    - remove MODULENAME from the current shell environment
  * - *module list*
    - show all :ref:`modules<envmods>` loaded into the current shell environment
  * - *module purge*
    - remove all :ref:`modules<envmods>` from the current environment

Job Type Templates
------------------

.. list-table::

  * - .. code-block:: console

         #SBATCH -p serial
         #SBATCH --mem=SIZE
    - a :ref:`serial job<serial job>` requesting *SIZE* memory (eg. 1G = 1 gigabyte)
  * - .. code-block:: console

         #SBATCH -p parallel
         #SBATCH --cpus-per-task=N
         #SBATCH --mem=SIZE
    -  a :ref:`single node parallel job<open mp>` with N cores on the same compute node, and SIZE memory
  * - .. code-block:: console

         #SBATCH -p parallel
         #SBATCH --nodes=N
         #SBATCH --exclusive
         #SBATCH -C node_type=X
    - a :ref:`multi node parallel job<mpi jobs>` requesting N nodes of compute node type :ref:`X<node types>`
  * - .. code-block:: console

         #SBATCH -p gpu-short
         #SBATCH --gres=gpu:1
         #SBATCH --mem=SIZE
         #SBATCH --cpus-per-task=N
    - submit a :ref:`gpu job<gpu jobs>` to the gpu-short queue, requesting N cores, SIZE memory and a single GPU
  * - .. code-block:: console

         #SBATCH --mail-type=END,FAIL
         #SBATCH --mail-user=youraddress@lancaster.ac.uk
    -  send an :ref:`email notification<email>` when a job finishes or fails
  * - .. code-block::

         #SBATCH -a x-y:z
    - turn the job into a :ref:`job array<job arrays>` running from task ID x through to y in steps of z