Merge pull request #66 from Danzelot/slurm

Slurm parameter overview section

index.rst

@@ -66,6 +66,7 @@ HPC-UiT Services User Documentation
    jobs/interactive
    jobs/monitoring
    jobs/running_mpi_jobs
+   jobs/slurm_parameter
    jobs/environment-variables
    jobs/torque_slurm_table
 

jobs/interactive.rst

@@ -1,4 +1,4 @@
-
+.. _interactive:
 
 Interactive jobs
 ================

jobs/slurm_parameter.rst

@@ -0,0 +1,81 @@
+.. _slurm_parameter:
+
+SLURM Workload Manager
+=======================
+
+SLURM is the workload manager and job scheduler used for Stallo.
+
+There are two ways of starting jobs with SLURM; either interactively with ``srun``
+or as a script with ``sbatch``.
+
+Interactive jobs are a good way to test your setup before you put it into a script
+or to work with interactive applications like MATLAB or python.
+You immediately see the results and can check if all parts behave as you expected.
+See :ref:`interactive` for more details.
+
+SLURM Parameter
+-----------------
+
+SLURM supports a multitude of different parameters.
+This enables you to effectivly tailor your script to your need when using Stallo
+but also means that is easy to get lost and waste your time and quota.
+
+The following parameters can be used as command line parameters with ``sbatch`` and
+``srun`` or in jobscript, see :ref:`job_script_examples`.
+To use it in a jobscript, start a newline with ``#SBTACH`` followed by the parameter.
+Replace <....> with the value you want, e.g. ``--job-name=test-job``.
+
+
+Basic settings:
++++++++++++++++
+
+=============================    ===============================================================================
+Parameter                        Function
+=============================    ===============================================================================
+--job-name=<name>                Job name to be displayed by for example ``squeue``
+--output=<path>                  | Path to the file where the job (error) output is written to 
+--mail-type=<type>               | Turn on mail notification; type can be one of BEGIN, END, FAIL, REQUEUE or ALL
+--mail-user=<email_address>      Email address to send notifications to
+=============================    ===============================================================================
+
+
+Requesting Resources
++++++++++++++++++++++
+
+=============================   ============================================================================================================================
+Parameter                       Function
+=============================   ============================================================================================================================
+--time=<d-hh:mm:ss>             Time limit for job. Job will be killed by SLURM after time has run out. Format days-hours:minutes:seconds
+--nodes=<num_nodes>             Number of nodes. Multiple nodes are only useful for jobs with distributed-memory (e.g. MPI).
+--mem=<MB>                      Memory (RAM) per node. Number followed by unit prefix, e.g. 16G
+--mem-per-cpu=<MB>              Memory (RAM) per requested CPU core
+--ntasks-per-node=<num_procs>   Number of (MPI) processes per node. More than one useful only for MPI jobs. Maximum number depends nodes (number of cores)
+--cpus-per-task=<num_threads>   CPU cores per task. For MPI use one. For parallelized applications benchmark this is the number of threads.
+--ntasks-per-core=1             Disables hyperthreading.
+--ntasks-per-core=2             Enables hyperthreading. Only useful in special circumstances.
+--exclusive                     Job will not share nodes with other running jobs. You will be charged for the complete nodes even if you asked for less.
+=============================   ============================================================================================================================
+
+
+Accounting
++++++++++++++++++++++
+See also :ref:`label_partitions`.
+
+==================      ==========================================================================================================
+Parameter               Function
+==================      ==========================================================================================================
+--account=<name>        Project (not user) account the job should be charged to.
+--partition=<name>      Partition/queue in which o run the job. 
+--qos=devel             On stallo the *devel* QOS (quality of servive) can be used to submit short jobs for testing and debugging.
+==================      ==========================================================================================================
+
+
+Advanced Job Control
++++++++++++++++++++++
+
+==========================   ==================================================================================================================================================================
+Parameter                    Function
+==========================   ==================================================================================================================================================================
+--array=<indexes>            Submit a collection of similar jobs, e.g. ``--array=1-10``. (sbatch command only). See official `SLURM documentation <https://slurm.schedmd.com/job_array.html>`_
+--dependency=<state:jobid>   Wait with the start of the job until specified dependencies have been satified. E.g. --dependency=afterok:123456
+==========================   ==================================================================================================================================================================

software/python_r_perl.rst

@@ -1,8 +1,8 @@
 .. _python_r_perl:
 
-*******************
+***************************
 Python, R, Matlab and Perl
-*******************
+***************************
 Scripting languages often support modules or libraries for additional functionality or convenience functions. We encourage users to install modules locally for only the current user.
 
 Python