Resolve conflicts

teaching/mlprojects24/slides/20240118-cluster.md

@@ -57,24 +57,6 @@ I am not an expert.
 
 ---
 
-## Why does all this matter?
-
-Because you will have access to computational resources from Calcul Québec for the development of your project, very kindly set up by .highligh1[Maxime Boissonneault], responsable des services à la recherche.
-
---
-
-Please take a few minutes to create an account to use the cluster from Calcul Québec. 
-
-.center[[https://mokey.ift6759.calculquebec.cloud/auth/signup](https://mokey.ift6759.calculquebec.cloud/auth/signup)]
-
-.highlight1[Important]: Please use your **first name**, **last name**, and **UdeM email** as it appears on StudiUM.
-
---
-
-Besides this cluster, computational resources are also available via Colab: [colab.research.google.com](https://colab.research.google.com/)
-
----
-
 ## What is HPC?
 
 .highlight1[High-performance computing (HPC)] typically refers to supercomputers, that is clusters of computers that provide access to computational resources. 
@@ -94,12 +76,12 @@ A .highlight1[cluster] is a set connected computers that work together such that
 
 ## The Alliance and Calcul Québec
 
-.highlight1[[The Digital Research Alliance of Canada](https://alliancecan.ca)], or _Alliance de recherche numérique du Canada_, or just the _Alliance_, and formerly known as _Compute Canada_, provides HPC to researchers in Canadian institutions and works closely with regional counterparts such as .highlight1[[Calcul Québec](https://www.calculquebec.ca/)].
+.highlight1[[The Digital Research Alliance of Canada](https://alliancecan.ca)], _Alliance de recherche numérique du Canada_, or simply _the Alliance_, formerly known as _Compute Canada_, provides HPC to researchers in Canadian institutions and works closely with regional counterparts such as .highlight1[[Calcul Québec](https://www.calculquebec.ca/)].
 
 Resources:
 
-* Compute Canada Wiki: [docs.alliancecan.ca](https://docs.alliancecan.ca)
-* Support email: `support@tech.alliancecan.ca`
+* The Alliance Wiki: [docs.alliancecan.ca](https://docs.alliancecan.ca)
+* Support email: `support@calculquebec.ca`
 
 ---
 
@@ -109,9 +91,9 @@ Resources:
 * Remote connection to the nodes (via SSH, see later).
 * Collectively shared.
 * Gateway into the cluster.
-* Important: not meant for heavy weight computing tasks.
 * Typical use: managing source code, environments and data.
 * Typical use: submitting jobs to the compute nodes.
+* .highlight1[Important]: not meant for heavy weight computing tasks.
 
 ---
 
@@ -167,7 +149,7 @@ $ salloc --time=1:00:00 --mem=2G
 ```
 
 .references[
-Source: [Compute Canada Wiki](https://docs.computecanada.ca/wiki/Running_jobs#Interactive_jobs)
+Source: [the Alliance Wiki](https://docs.alliancecan.ca/wiki/Running_jobs#Interactive_jobs)
 ]
 
 ---
@@ -206,7 +188,7 @@ echo "Bye!"
 ]
 
 .references[
-Source: [Compute Canada Wiki](https://docs.computecanada.ca/wiki/Running_jobs#Use_sbatch_to_submit_jobs)
+Source: [the Alliance Wiki](https://docs.alliancecan.ca/wiki/Running_jobs#Use_sbatch_to_submit_jobs)
 ]
 
 ---
@@ -254,18 +236,18 @@ Other useful Slurm tools are the following:
 ### Python: best practices
 
 * Load Python with `module load python/3.x[.y]`
-* Always use `venv` or `virtualenv`
+* Always use `virtualenv` or `venv`
 * Consider building the virtual environment in the compute node:
     * It improves I/O performance
     * Use pre-downloaded packages with `module`
 * Avoid Anaconda:
-    * It handles library management that should be left to Compute Canada admins
+    * It handles library management that should be left to the Alliance admins
     * It installs in `$HOME` by default and makes tons of files.
     * It is slower to install packages
     * It modifies `$HOME/.bashrc`
 
 .references[
-[Why avoiding Anaconda in the cluster and how to transition to virtualenv](https://docs.alliancecan.ca/wiki/Anaconda/en)
+Reference: [Why to avoid Anaconda (at least) in the cluster](https://docs.alliancecan.ca/wiki/Anaconda/en)
 ]
 
 ---
@@ -275,7 +257,7 @@ Other useful Slurm tools are the following:
 
 * Do not run code in the login nodes.
 * Try to not request more resources than you need and for more time you need.
-* Use archives (`.tar`, `.hdf5`, etc.): do not unpack gazillion files because it makes things slow.
+* Use archives (`.tar`, `.hdf5`, etc.): do not unpack a gazillion files because it makes things slow.
 * Profile your code.
 * Use `$SLURM_TMPDIR`:
     * To build your virtual environment whenever possible.
@@ -325,7 +307,7 @@ Alex Hernández-García (he/il/él)
 ## Connect to the cluster
 ### SSH
 
-The Secure Shell Protocol (SSH) is based on a client–server architecture, connecting an SSH client instance with an SSH server. We can use it to connect to our Calcul Québec cluster:
+The Secure Shell Protocol ([SSH](https://docs.alliancecan.ca/wiki/SSH)) is based on a client–server architecture, connecting an SSH client instance with an SSH server. We can use it to connect to our Calcul Québec cluster:
 
 ``` bash
 $ ssh <username>@ift6759.calculquebec.cloud
@@ -337,9 +319,33 @@ Lmod is automatically replacing "intel/2020.1.217" with "gcc/9.3.0".
 [<username>@login1 ~]$
 ```
 
-Configuring SSH keys for GitHub can take a while. These resources may help:
-* [Generating a new SSH key and adding it to the ssh-agent](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
+--
+
+It is convenient to [set up SSH keys](https://docs.alliancecan.ca/wiki/Using_SSH_keys_in_Linux) to log in password-less. [Here](https://mokey.ift6759.calculquebec.cloud/sshpubkey) you can add your SSH Public Keys for _our_ cluster: [mokey.ift6759.calculquebec.cloud/sshpubkey](https://mokey.ift6759.calculquebec.cloud/sshpubkey)
+
+.references[
+* [Configuring SSH keys for GitHub](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
 * [About `Error: Permission denied (publickey)`](https://docs.github.com/en/authentication/troubleshooting-ssh/error-permission-denied-publickey)
+]
+
+---
+
+## Connect to the cluster
+### SSH config
+
+It is also convenient to set up our SSH configuration. SSH configuration in Linux systems is usually stored in `~/.ssh/config`. The following is an example for our cluster:
+
+```
+# ML projects class
+Host mlprojects
+    User alexhg
+    Hostname ift6759.calculquebec.cloud
+
+# Common defaults
+Match all
+    ServerAliveInterval 60
+    ServerAliveCountMax 5
+```
 
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