v1.0 - First official release

01-Introduction.Rmd

@@ -0,0 +1,17 @@
+# Introduction
+The difficulty on finding instructional material that covers the complexities of 
+writing scientific code, and deploying it in High-Performance Computing (HPC) 
+environments led to the writing of this guide.
+
+This is a non-exhaustive work, but rather a reference one, in which the author 
+wishes to reduce the barriers of routine HPC workflows for Remote Sensing run at 
+the [McMaster University Remote Sensing Laboratory](https://remotesensing-mcmaster.org).
+
+These guidelines are provided without any guarantee, including of support, but 
+in a best effort to overcome the aforementioned barriers.
+
+I encourage users to suggest corrections, by clicking in the edit button 
+(available on the online version of this guide), and submitting a pull request.
+
+Other comments can be done though my [social media channels](http://about.me/ricardobarroslourenco/), or via 
+e-mail: barroslr mcmaster.ca

02-CC.Rmd → 03-CC.Rmd

@@ -2,13 +2,13 @@
 *Note*: This section is under heavy work. For now, please refer to Compute 
 Canada's [Wiki](https://docs.computecanada.ca/wiki/Compute_Canada_Documentation).
 
-### Setting up SSH on Compute Canada portal
+## Setting up SSH on Compute Canada portal
 From January 2022 forward, Compute Canada is enforcing that is mandatory to use 
 a key to use SSH with their premises (ex.: accessing login nodes). For this, you 
 need to create a public-private SSH key, and _drop_ the public key at the 
 Compute Canada user portal, under your account settings.
 
-#### Creating a SSH key
+### Creating a SSH key
 Some description of this is found at the Compute Canada documentation @CC_ssh_key . 
 Is good practice to read it, since it covers some specifics.
 
@@ -39,7 +39,7 @@ Once you hit the command, you should have on the folder you are running these tw
 *WARNING*: The private key is equal to a regular password to the system you are using it to access. Therefore, it is recommended that you assign a key password 
 (it will be requested when you are generating the key), to assure that if such key is lost/copied/etc, nobody would be able to access this system impersonating you. A series of good practices for ssh keys may be found at this [post](https://security.stackexchange.com/a/144044/275095).
 
-### Depositing the public key on Compute Canada
+## Depositing the public key on Compute Canada
 Once created the key pair, you need to deposit the *public key* on your Compute 
 Canada account. A main tutorial is provided [here](https://docs.computecanada.ca/wiki/SSH_Keys) 
 but you can proceed as follows:
@@ -66,7 +66,7 @@ To do so, you need to open your _.pub_ file with a simple text editor (ex.: Note
 
 - Then hit _Add Key_. This operation will put your public key on every machine of Compute Canada, and may take up to 30 minutes to be online.
 
-### Accessing a Compute Canada _login node_
+## Accessing a Compute Canada _login node_
 Once your public key is loaded and synchronized in all machines, you may login a compute node using a terminal (On Windows, you need to use PowerShell; on MacOS, Terminal; and on Linux, your preferred Shell, such as Bash):
 
 ```{bash, eval=FALSE}
@@ -88,7 +88,7 @@ The command opens a SSH terminal session with the following parameters:
 
 <!-- ### Basic Commands -->
 
-### Running batch jobs
+## Running batch jobs
 If you want to run a R-language batch job, please take a look on the 
 [CCrecipes repository](https://github.com/ricardobarroslourenco/CCrecipes). 
 
@@ -115,7 +115,6 @@ module load gcc/9.3.0 r/4.0.2
 #R install_script.R
 
 ### Export locally installed packages
-# TODO: check if this path holds
 export R_LIBS=~/local/R_libs/
 
 ### Run main_job.R - or any batch script necessary

04-RStudio.Rmd → 05-RStudio.Rmd

@@ -24,7 +24,8 @@ _From the cluster login node_ you can build it with the following steps (it is a
 module load apptainer
 ```
 
-Pick up the most recent version of it, and accept.
+Pick up the most recent version of it (please note that Docker Hub may have 
+different tags, with versioning for each), and accept.
 
 **2. Then run the build** (run this command at your _home_, _project_ or _scratch_ folder):
 ```{bash, eval=FALSE}
@@ -101,7 +102,7 @@ in your browser:
 localhost:9102
 ```
 
-## Finishing your Running session.
+## Finishing your Running session
 
 Do not forget saving your work in partitions that enable saving (ex.: `/home`, `/project`, `/scratch`), because **if you save in a folder within the container, it will not be saved**, after your session ends. Remember that `/scratch` is meant for temporary save, being automatically wiped by the cluster systems after 30 days.
 

05-Jupyter.Rmd → 06-Jupyter.Rmd

@@ -20,7 +20,7 @@ _From the cluster login node_ you can build it with the following steps (it is a
 module load apptainer
 ```
 
-Pick up the most recent version of it, and accept.
+Pick up the most recent version of it (note that there may be different tags, each one with its own versioning), and accept.
 
 **2. Then run the build** (run this command at your _home_, _project_ or _scratch_ folder):
 ```{bash, eval=FALSE}
@@ -165,7 +165,7 @@ http://127.0.0.1:8888/lab?token=XXXXXXXXXXXXXXXXXXXXXXX
 
 Remember that this is an example, so you need to get the token URL provided by JupyterLab once launching the session.
 
-## Finishing your Running session.
+## Finishing your Running session
 
 Do not forget saving your work in partitions that enable saving (ex.: `/home`, `/project`, `/scratch`), because **if you save in a folder within the container, it will not be saved**, after your session ends. Remember that `/scratch` is meant for temporary save, being automatically wiped by the cluster systems after 30 days.
 

07-Globus.Rmd

@@ -0,0 +1,11 @@
+# Globus
+Globus is currently a suite of products for Computational Science. 
+Initially defined as a tool that allowed the establishment of federations, 
+now it offers a platform that can do, among many features, distributed data 
+transfers. When referring in this guide to Globus, the author majorly means 
+Globus Transfer capabilities.
+
+## Documentation
+A full documentation of Globus is provided aat their website: https://docs.globus.org
+
+Additional information on how to create an account using the Compute Canada credentials can be found here: https://docs.alliancecan.ca/wiki/Globus