Posts

docs/HPC/jupyter.md

@@ -19,16 +19,16 @@ description: "Setting up Jupyter Notebook Over Tunneling on HPC."
 
 # Setting up Jupyter Notebook Over Tunneling on HPC.
 
-*Note: The procedure below will run the jupyter notebook on an interactive node in an HPC.*
+Below is an example protocol to run Jupyter notebook in an interactive node on a high-performance computer (HPCs). Most of the HPCs have their specialised way of interacting with them. Therefore, you may have to tweak this protocol as per your need. I would be happy to discuss and troubleshoot with you; contact me at [contact@rohitfarmer.dev](mailto:contact@rohitfarmer.dev). Any suggestions to augment this protocol with more advanced features are welcomed.
 
-1. Ssh to hpc (Locus).    
-2. Claim an interactive node with qrsh.   
-3. Note the node name.  
-4. Run jupyter on the claimed node by `jupyter notebook --no-browser --ip='0.0.0.0'` or create an alias in your bashrc for a shortcut `alias jup='jupyter notebook --no-browser --ip='0.0.0.0''`.  
-5. On your own computer start another ssh session with tunnelling using the node name as noted above `ssh user@host -L8888:nodeName:8888 -N`. *You will not see any message this time, but if it's not throwing any error then it's probably running just fine.*  
-6. To avoid writing the code in line 5 everytime you tunnel you can use the shell script below.
+1. SSH to the HPC.    
+2. Claim an interactive node (follow the standard procedure for your HPC, in my case it is `qrsh`).   
+3. Note the interactive node name.  
+4. Run Jupyter on the claimed interactive node by `jupyter notebook --no-browser --ip='0.0.0.0'` or create an alias in your bashrc for a shortcut. For example `alias jup='jupyter notebook --no-browser --ip='0.0.0.0''`.  
+5. On your computer start another SSH session with tunnelling using the interactive node name as noted above `ssh user@host -L8888:nodeName:8888 -N`. *The prompt probably won't return and you may also not see any message in your terminal, but as long as there is no error message, it's probably running fine.*  
+6. To avoid re-writing the code in step 5 every time you tunnel you can use the shell script below.  
 
-I named it as `jupssh`.  
+I named it `jupssh`.  
 ```
 #!/bin/sh
 
@@ -41,4 +41,5 @@ fi
 
 ssh user@host -L8888:$1:8888 -N
 ```
-7. Copy the URL that jupyter daemon generated in the step 4 and paste it in the browser on your own computer. URL should look something similar to `http://(nodeName or 127.0.0.1):8888/?token=3f7c3a8949b3fa1961c63653873fea075a93a29bffe373b5`. Choose either nodeName or 127.0.0.1 in the URL.
+
+* Copy the URL that the Jupyter daemon has generated in step 4 and paste it in the browser on your computer. URL should look something similar to `http://(nodeName or 127.0.0.1):8888/?token=3f7c3a8949b3fa1961c63653873fea075a93a29bffe373b5`. Choose either nodeName or 127.0.0.1 in the URL.

index.md

@@ -2,38 +2,13 @@
 layout: default
 title: Home
 nav_order: 1
-description: "Software documention website for CHI."
+description: "RF DOCS"
 permalink: /
 ---
 
-# Software Documentation for CHI's Computational Biology Group
-[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.niaid.nih.gov/chi/chi.github.niaid.nih.gov/commits/master) [![made-with-Markdown](https://img.shields.io/badge/Made%20with-Markdown-1f425f.svg)](http://commonmark.org) [![made-for-VSCode](https://img.shields.io/badge/Made%20for-VSCode-1f425f.svg)](https://code.visualstudio.com/) [![Open Source Love svg1](https://badges.frapsoft.com/os/v1/open-source.svg?v=103)](https://github.com/ellerbrock/open-source-badges/) [![powered by Jekyll](https://img.shields.io/badge/powered_by-Jekyll-yellow.svg)](https://jekyllrb.com)
-
-All the members of the CHI's GitHub organisation account have the write access to this repository. It is encouraged to post documentation page(s) for any software that you write or a trick or tweak that you have found that might be relevant to other members of the CHI here. Large documentation that are specifically written for a major development project may be kept in their repositories.
-
-For questions and suggestions please contact [Rohit Farmer](mailto:rohit.farmer@nih.gov).
-
-
-[Back to CHI GitHub](https://github.niaid.nih.gov/chi){: .btn .btn-green }
-
-## How-To Update CHI DOCS Website
-
-* Clone the repository to your workspace.
-```
-https://github.niaid.nih.gov/chi/chi.github.niaid.nih.gov.git
-```
-* Navigate to docs folder inside the cloned repository.
-```
-cd chi.github.niaid.nih.gov/docs
-```
-* Navigate to a parent folder related to your doc if it already exists.
-* Copy an existing .md file to a different name and change the contents accordingly.
-* If a parent folder is not already present, then please create a folder and place a .md file with the same name as the folder inside it. For ease copy the folder associated .md file from an existing folder and change the contents accordingly.
-* Update the repository with
-```
-git add .
-git commit -m "message"
-git push -u origin master
-```
+# Assorted & Ad Hoc Documentation for Some Commonly Used Software
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/rohitfarmer/docs/commits/master) [![made-with-Markdown](https://img.shields.io/badge/Made%20with-Markdown-1f425f.svg)](http://commonmark.org) [![made-for-VSCode](https://img.shields.io/badge/Made%20for-VSCode-1f425f.svg)](https://code.visualstudio.com/) [![Open Source Love svg1](https://badges.frapsoft.com/os/v1/open-source.svg?v=103)](https://github.com/ellerbrock/open-source-badges/) [![powered by Jekyll](https://img.shields.io/badge/powered_by-Jekyll-yellow.svg)](https://jekyllrb.com)
 
+Assorted documentation for some commonly used software.
 
+*Powered by [Just the Docs](https://github.com/pmarsceill/just-the-docs)*