neuroinformatics-unit · niksirbi · Nov 24, 2023 · Sep 26, 2023 · Sep 26, 2023 · Sep 26, 2023
diff --git a/.github/workflows/docs_build_and_deploy.yml b/.github/workflows/docs_build_and_deploy.yml
@@ -1,4 +1,4 @@
-name: Build Sphinx docs and deploy to GitHub Pages
+name: Docs
 
 # Generate the documentation on all merges to main, all pull requests, or by
 # manual workflow dispatch. The build job can be used as a CI check that the

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -4,4 +4,5 @@ nbsphinx
 numpydoc
 pydata-sphinx-theme
 sphinx
+sphinx-copybutton
 sphinx-design
diff --git a/docs/source/_static/swc-wiki-warning.md b/docs/source/_static/swc-wiki-warning.md
@@ -2,4 +2,5 @@
 Some links within this document point to the
 [SWC internal wiki](https://wiki.ucl.ac.uk/display/SI/SWC+Intranet),
 which is only accessible from within the SWC network.
+We recommend opening these links in a new tab.
 :::
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -38,6 +38,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
     "sphinx_design",
+    "sphinx_copybutton",
     "myst_parser",
     "numpydoc",
     "nbsphinx",
@@ -134,3 +135,7 @@
 
 # Hide the "Show Source" button
 html_show_sourcelink = False
+
+# Configure the code block copy button
+# don't copy line numbers, prompts, or console outputs
+copybutton_exclude = ".linenos, .gp, .go"
diff --git a/docs/source/data_analysis/HPC-module-SLEAP.md b/docs/source/data_analysis/HPC-module-SLEAP.md
diff --git a/docs/source/data_analysis/index.md b/docs/source/data_analysis/index.md
@@ -5,4 +5,5 @@ Guides related to the analysis of neuroscientific data, spanning a wide range of
 ```{toctree}
 :maxdepth: 1
 
+HPC-module-SLEAP
 ```
diff --git a/docs/source/programming/SLURM-arguments.md b/docs/source/programming/SLURM-arguments.md
@@ -0,0 +1,148 @@
+(slurm-arguments-target)=
+# SLURM arguments primer
+
+```{include} ../_static/swc-wiki-warning.md
+```
+
+## Abbreviations
+| Acronym                                                         | Meaning                                      |
+| --------------------------------------------------------------- | -------------------------------------------- |
+| [SWC](https://www.sainsburywellcome.org/web/)                   | Sainsbury Wellcome Centre                    |
+| [HPC](https://en.wikipedia.org/wiki/High-performance_computing) | High Performance Computing                   |
+| [SLURM](https://slurm.schedmd.com/)                             | Simple Linux Utility for Resource Management |
+| [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface)  | Message Passing Interface                    |
+
+
+## Overview
+SLURM is a job scheduler and resource manager used on the SWC HPC cluster.
+It is responsible for allocating resources (e.g. CPU cores, GPUs, memory) to jobs submitted by users.
+When submitting a job to SLURM, you can specify various arguments to request the resources you need.
+These are called SLURM directives, and they are passed to SLURM via the `sbatch` or `srun` commands.
+
+These are often specified at the top of a SLURM job script,
+e.g. the lines that start with `#SBATCH` in the following example:
+
+```{code-block} bash
+#!/bin/bash
+
+#SBATCH -J my_job # job name
+#SBATCH -p gpu # partition (queue)
+#SBATCH -N 1   # number of nodes
+#SBATCH --mem 16G # memory pool for all cores
+#SBATCH -n 4 # number of cores
+#SBATCH -t 0-06:00 # time (D-HH:MM)
+#SBATCH --gres gpu:1 # request 1 GPU (of any kind)
+#SBATCH -o slurm.%x.%N.%j.out # STDOUT
+#SBATCH -e slurm.%x.%N.%j.err # STDERR
+#SBATCH --mail-type=ALL
+#SBATCH [email protected]
+#SBATCH --array=1-12%4 # job array index values
+
+# load modules
+...
+
+# execute commands
+...
+```
+This guide provides only a brief overview of the most important SLURM arguments,
+to demysify the above directives and help you get started with SLURM.
+For a more detailed description see the [SLURM documentation](https://slurm.schedmd.com/sbatch.html).
+
+##  Commonly used arguments
+
+### Partition (Queue)
+- *Name:* `--partition`
+- *Alias:* `-p`
+- *Description:* Specifies the partition (or queue) to submit the job to. To see a list of all partitions/queues, the nodes they contain and their respective time limits, type `sinfo` when logged in to the HPC cluster.
+- *Example values:* `gpu`, `cpu`, `fast`, `medium`
+
+### Job Name
+- *Name:* `--job-name`
+- *Alias:* `-J`
+- *Description:* Specifies a name for the job, which will appear in various SLURM commands and logs, making it easier to identify the job (especially when you have multiple jobs queued up)
+- *Example values:* `training_run_24`
+
+### Number of Nodes
+- *Name:* `--nodes`
+- *Alias:* `-N`
+- *Description:* Defines the number of nodes required for the job.
+- *Example values:* `1`
+
+:::{warning}
+This is usually `1` unless you're parallelising your code across multiple nodes with technologies such as MPI.
+:::
+
+### Number of Cores
+- *Name:* `--ntasks`
+- *Alias:* `-n`
+- *Description:* Defines the number of cores (or tasks) required for the job.
+- *Example values:* `1`, `5`, `20`
+
+### Memory Pool for All Cores
+- *Name:* `--mem`
+- *Description:* Specifies the total amount of memory (RAM) required for the job across all cores (per node)
+- *Example values:* `4G`, `32G`, `64G`
+
+### Time Limit
+- *Name:* `--time`
+- *Alias:* `-t`
+- *Description:* Sets the maximum time the job is allowed to run. The format is D-HH:MM, where D is days, HH is hours, and MM is minutes.
+- *Example values:* `0-01:00` (1 hour), `0-04:00` (4 hours), `1-00:00` (1 day).
+
+:::{warning}
+If the job exceeds the time limit, it will be terminated by SLURM.
+On the other hand, avoid requesting way more time than what your job needs,
+as this may delay its scheduling (depending on resource availability).
+
+If needed, the systems administrator can extend long-running jobs. 
+:::
+
+### Generic Resources (GPUs)
+- *Name:* `--gres`
+- *Description:* Requests generic resources, such as GPUs.
+- *Example values:* `gpu:1`, `gpu:rtx2080:1`, `gpu:rtx5000:1`, `gpu:a100_2g.10gb:1`
+
+:::{warning}
+No GPU will be allocated to you unless you specify it via the `--gres` argument (even if you are on the 'gpu' partition).
+To request 1 GPU of any kind, use `--gres gpu:1`. To request a specific GPU type, you have to include its name, e.g. `--gres gpu:rtx2080:1`.
+You can view the available GPU types on the [SWC internal wiki](https://wiki.ucl.ac.uk/display/SSC/CPU+and+GPU+Platform+architecture).
+:::
+
+### Standard Output File
+- *Name:* `--output`
+- *Alias:* `-o`
+- *Description:* Defines the file where the standard output (STDOUT) will be written. In the example script above, it's set to slurm.%x.%N.%j.out, where %x is the job name, %N is the node name and %j is the job ID.
+- *Example values:* `slurm.%x.%N.%j.out`, `slurm.MyAwesomeJob.out`
+
+:::{note}
+This file contains the output of the commands executed by the job (i.e. the messages that normally gets printed on the terminal).
+:::
+
+### Standard Error File
+- *Name:* `--error`
+- *Alias:* `-e`
+- *Description:* Specifies the file where the standard error (STDERR) will be written. In the example script above, it's set to slurm.%x.%N.%j.out, where %x is the job name, %N is the node name and %j is the job ID.
+- *Example values:* `slurm.%N.%j.err`, `slurm.MyAwesomeJob.err`
+
+:::{note}
+This file is very useful for debugging, as it contains all the error messages produced by the commands executed by the job.
+:::
+
+### Email Notifications
+- *Name:* `--mail-type`
+- *Description:* Defines the conditions under which the user will be notified by email.
+- *Example values:* `ALL`, `BEGIN`, `END`, `FAIL`
+
+### Email Address
+- *Name:* `--mail-user`
+- *Description:* Specifies the email address to which notifications will be sent.
+- *Example values:* `[email protected]`
+
+### Array jobs
+- *Name:* `--array`
+- *Description:* Job array index values (a list of integers in increasing order). The task index can be accessed via the `SLURM_ARRAY_TASK_ID` environment variable.
+- *Example values:* `--array=1-10` (10 jobs), `--array=1-100%5` (100 jobs, but only 5 of them will be allowed to run in parallel at any given time).
+
+:::{warning}
+If an array consists of many jobs, using the `%` syntax to limit the maximum number of parallel jobs is recommended to prevent overloading the cluster.
+:::
diff --git a/docs/source/programming/SSH-SWC-cluster.md b/docs/source/programming/SSH-SWC-cluster.md
@@ -1,3 +1,4 @@
+(ssh-cluster-target)=
 # Set up SSH for the SWC HPC cluster
 
 This guide explains how to connect to the SWC's HPC cluster via SSH.
@@ -9,14 +10,14 @@ This guide explains how to connect to the SWC's HPC cluster via SSH.
 ```
 
 ## Abbreviations
-| Acronym | Meaning |
-| --- | --- |
-| SWC | Sainsbury Wellcome Centre |
-| HPC | High Performance Computing |
-| SLURM | Simple Linux Utility for Resource Management |
-| SSH | Secure (Socket) Shell protocol |
-| IDE | Integrated Development Environment |
-| GUI | Graphical User Interface |
+| Acronym                                                                 | Meaning                                      |
+| ----------------------------------------------------------------------- | -------------------------------------------- |
+| [SWC](https://www.sainsburywellcome.org/web/)                           | Sainsbury Wellcome Centre                    |
+| [HPC](https://en.wikipedia.org/wiki/High-performance_computing)         | High Performance Computing                   |
+| [SLURM](https://slurm.schedmd.com/)                                     | Simple Linux Utility for Resource Management |
+| [SSH](https://en.wikipedia.org/wiki/Secure_Shell)                       | Secure (Socket) Shell protocol               |
+| [IDE](https://en.wikipedia.org/wiki/Integrated_development_environment) | Integrated Development Environment           |
+| [GUI](https://en.wikipedia.org/wiki/Graphical_user_interface)           | Graphical User Interface                     |
 
 ## Prerequisites
 - You have an SWC account and know your username and password.

diff --git a/docs/source/programming/index.md b/docs/source/programming/index.md
@@ -7,6 +7,7 @@ Small tips and tricks that do not warrant a long-form guide can be found in the
 ```{toctree}
 :maxdepth: 1
 
+SLURM-arguments
 SSH-SWC-cluster
 SSH-vscode
 Mount-ceph-ubuntu