Merge branch 'ENCCS:main' into main

Author: qianglise

content/setup.rst

@@ -1,21 +1,18 @@
 Installation and HPC access
 ===========================
 
+
 This page contains instructions for installing the required dependencies on a local computer 
 as well as instructions for logging into a EuroHPC system.
 
+
 Local installation
 ------------------
 
-If you already have a preferred way to manage Python versions and
-libraries, you can stick to that. If not, we recommend that you install
-Python3 and all libraries using
-`Miniforge <https://conda-forge.org/download/>`__, a free
-minimal installer for the package, dependency and environment manager
-`conda <https://docs.conda.io/en/latest/index.html>`__.
 
-Please follow the installation instructions on
-https://conda-forge.org/download/ to install Miniforge.
+If you already have a preferred way to manage Python versions and libraries, you can stick to that. If not, we recommend that you install Python3 and all libraries using `Miniforge <https://conda-forge.org/download/>`__, a free minimal installer for the package, dependency and environment manager `conda <https://docs.conda.io/en/latest/index.html>`__.
+
+Please follow the installation instructions on https://conda-forge.org/download/ to install Miniforge.
 
 Make sure that conda is correctly installed:
 
@@ -60,9 +57,56 @@ Finally, open Jupyter-Lab in your browser:
 LUMI
 ------------
 
-.. note::
 
-   .. todo::
-      Add Instructions for using this 
+Login to LUMI cluster
+^^^^^^^^^^^^^^^^^^^^^
+
+Follow practical instructions `HERE <https://enccs.se/tutorials/2024/02/log-in-to-lumi-cluster/>`_ to get your access to LUMI cluster.
+
+- On `Step 5 <https://enccs.se/tutorials/2024/02/log-in-to-lumi-cluster/>`_, you can login to LUMI cluster through terminal.
+- On `Step 6 <https://enccs.se/tutorials/2024/02/log-in-to-lumi-cluster/>`_, you can login to LUMI cluster from the web-interface.
+
+
+Running jobs on LUMI cluster
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you want to run an interactive job asking for 1 node, 1 GPU, and 1 hour:  
+
+.. code-block:: console
+
+   $ salloc -A project_465001310 -N 1 -t 1:00:00 -p standard-g --gpus-per-node=1
+   $ srun <some-command>
+
+Exit interactive allocation with ``exit``.
+
+Interacive terminal session on compute node:
+
+.. code-block:: console
+
+   $ srun --account=project_465001310 --partition=standard-g --nodes=1 --cpus-per-task=1 --ntasks-per-node=1 --gpus-per-node=1 --time=1:00:00 --pty bash
+   $ <some-command>
+
+
+You can also submit your job with a batch script ``submit.sh``:
+
+.. code-block:: bash
+
+   #!/bin/bash -l
+   #SBATCH --account=project_465001310
+   #SBATCH --job-name=example-job
+   #SBATCH --output=examplejob.o%j
+   #SBATCH --error=examplejob.e%j
+   #SBATCH --partition=standard-g
+   #SBATCH --nodes=1
+   #SBATCH --gpus-per-node=1
+   #SBATCH --ntasks-per-node=1
+   #SBATCH --time=1:00:00
+
+   srun <some_command> 
+
+
+Some useful commands are listed below:
 
-   Go to LUMI `open OnDemand portal <https://www.lumi.csc.fi/pun/sys/dashboard/>`__
+- Submit the job: ``sbatch submit.sh``
+- Monitor your job: ``squeue --me``
+- Kill job: ``scancel <JOB_ID>``