================
Interactive jobs
================

.. tip::

   **Contact** `Secretariat System Administrators`_ **with HPC Questions!**

   +------------------+----------------+--------------------+
   | `Vijay Shankar`_ | `John Poole`_  | `Maria E. Adonay`_ |
   +------------------+----------------+--------------------+

   .. code-block:: text

      vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu

   .. raw:: html

      <hr>

   **Contact** `IHG Research Cores`_ **with Research Questions!**

   .. code-block:: text

      ihgcores@clemson.edu

----

.. attention:: When testing code on Secretariat, it is important that you **not** run your commands on the head node (*secretariat-master*).

When you follow the instructions on the `Logging in`_ page, you are connecting to the head node. To make sure that you are testing your code appropriately, please read the following.

srun
----

To create an *interactive session* on Secretariat, use ``srun``. 

.. attention:: You should use ``srun`` only to *test* your code. Once your code works, you should transfer it to a script. For more information on this, see the `Batch jobs`_ page.

Consider the *sbatch* header in the example script from the `Batch jobs`_ page:

.. code-block:: bash
   :linenos:

   #!/bin/bash
   #
   #SBATCH --job-name=fastp_ex
   #SBATCH --cpus-per-task=1
   #SBATCH --partition=compute
   #SBATCH --time=00:30:00
   #SBATCH --mem=2G
   #SBATCH --output=/opt/ohpc/pub/workshop/toyout/logs/fastp_ex.%j.out
   #SBATCH --error=/opt/ohpc/pub/workshop/toyout/logs/fastp_ex.%j.err
   
When initiating your session, you should specify your resource requests in your command. Make sure that you specify parameters for the options in lines 4-7, at least:

.. code-block:: bash

   srun --cpus-per-task=1 --partition=compute --time=00:30:00 --mem=2G --pty bash

where

	- ``--pty``: instructs ``srun`` to run in "pseudo terminal mode"
	- ``bash``: creates an "interactive bash shell"\

Every option that you could include in your *sbatch* header should be possible to include in an ``srun`` command. Please see the `Slurm documentation`_ for more details.

.. _Logging in: https://secretariat.readthedocs.io/en/latest/access/logging-in.html#logging-in
.. _Batch jobs: https://secretariat.readthedocs.io/en/latest/running-jobs/batch-jobs.html#batch-jobs
.. _Slurm documentation: https://slurm.schedmd.com/sbatch.html
.. _Vijay Shankar: https://scienceweb.clemson.edu/chg/dr-vijay-shankar-2/
.. _John Poole: https://scienceweb.clemson.edu/chg/dr-john-poole/
.. _Maria E. Adonay: https://scienceweb.clemson.edu/chg/maria-adonay/
.. _Secretariat System Administrators: https://scienceweb.clemson.edu/ihg/research-cores/bsc-core/
.. _IHG Research Cores: https://scienceweb.clemson.edu/ihg/research-cores/