draft HPC instruction with brown instructions

onboarding/hpc.md

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+# HPC Access
+
+## Lab computers 
+
+- medium compute in the lab computers 
+- request access on slack for lab computers
+- there is a default password there
+
+## URI HPC 
+
+
+- request URI access by e-mailing with Dr. Brown in cc
+- [HPC at URI]()
+
+
+## Unity
+
+
+
+## HPC Interactive Sessions with Jupyter Notebooks 
+
+Using Notebooks with CCV (Oscar) at Brown
+prereq: Get an account on Oscar from CCV
+
+log in to oscar:
+
+```
+ssh <username>@ssh.ccv.brown.edu
+```
+To use a notebook on oscar, you will need an interactive session. Get one with the following: see the above documentation
+
+```
+interact -t 01:00:00 -m 100g
+```
+that gives a time (-t)limit of 1 hour and (100Gb) of ram on one (default number) node
+
+1. load python 3.6. You can also add this to your auto load as described in the help on software
+
+    ```
+    module load python/3.6.6
+    ```
+1. (optional, recommended, cd to project folder) launch a notebook to be used remotely
+
+    ```
+    jupyter notebook --no-browser --ip=$(hostname -i) --port=8888
+    ```
+    the notebook will launch and the response will include the ip address and the token.
+    ```
+    http://172.20.204.32:8888/?token=a40dd28fc49f415b9e2f5c867c653ee9d458bb8c74432575
+    http://<ip-address>:<remote_port>/?token=<token>
+    ```
+1. in a new terminal window locally, ssh again to map the notebook to a local port
+
+    ```
+    ssh -N -L 8000:172.20.204.32:8888 <user>@ssh6.ccv.brown.edu
+    ```
+    enter your password and nothing will happen, but it will be working.
+1. point browser to localhost:8000 and enter the token to access the notebook server
+1. moving files to work locally if neeeded with:
+
+    ```
+    scp /path/to/source/file <username>@transfer.ccv.brown.edu:/path/to/destination/file
+    ```
+
+
+
+# Log into Unity account and run commands:
+
+- https://unity.uri.edu/panel/account.php
+- Either use Jupyter notebook for a more user interface-based experience. If preferred consol/CMD, add the SSH key to the local computer by following the following steps.
+- Generate the SSH key from the account. The key should begin with ssh-rsa… … …. 
+- Use the key to setup a configuration file to the local system. To do this, save the ssh key as a .key file. Notepad++ can be used for this. 
+- Save the .key file to a folder. Such as: C:\Users\pujag\.ssh\unity-privkey.key.
+- Then generate a configuration file to connect to Unity. 
+
+
+## The configuration file should be like the following:
+
+- “Host unity
+- HostName unity.rc.umass.edu
+- User puja_ghosh_uri_edu
+- IdentityFile C:\Users\pujag\.ssh\unity-privkey.key”
+
+- Save the file to C:\Users\pujag\.ssh\ as config file. This file should have no file extension. The file name should be only config. 
+
+- Now Unity can be launched by opening CMD and running the code “ssh unity”
+
+- The details are documented here https://docs.unity.uri.edu/connecting/ssh.html
+
+
+  ## Add Git to Unity with SSH:
+
+- To pull or clone any Git repository, Git does not use password anymore. It uses SSH key. To generate the key, go to account>settings>SSH..>generate a new key. 
+- Save the key to a secure location. This key replaces the password. Whenever the console asks for password, use this key instead.
+
+## To add Git account to the system, run the following command in the console:
+
+- ssh-keygen -t ed25519 -C "your_email@example.com"
+- Note: If you are using a legacy system that doesn't support the Ed25519 algorithm, use:
+ssh-keygen -t rsa -b 4096 -C “your_email@example.com”
+- when the command asks for a file name click enter to set it to default. The command should look like this “> Enter a file in which to save the key (/c/Users/YOU/.ssh/id_ALGORITHM):[Press enter]”
+- This will generate a .ssh folder in the home directory. This cannot be directly seen in the file browser as it is a hidden folder. To show hidden folders turn on show dot folders in https://ood.unity.rc.umass.edu/pun/sys/dashboard/files/fs//home/<user_name>
+- The folder now contains two key files privet and public. The id_rsa is the privet key and id_rsa.pub is the public key. 
+- Open the public key file, copy the key (the key starts with ssh-rsa) and add it to your git profile. Profile>settings>SSH…>add new key.
+- This will add the remote server to your account.
+- Now run “ssh -T git@github.com” to check if your username shows up in the console. This will confirm that the account has been added. 
+
+