Merge pull request #27 from flindersuni/develop

HPC Upgrade Documentation Release

docs/requirements.txt

@@ -5,7 +5,7 @@ docutils==0.14
 mock==1.0.1 
 pillow>=5.4.1 
 alabaster>=0.7,<0.8,!=0.7.5 
-commonmark==0.8.1 
+commonmark==0.9.1
 recommonmark==0.5.0 
 sphinx<2 
 sphinx-rtd-theme<0.5 

docs/source/Access/accessrequest.rst

@@ -0,0 +1,46 @@
+Access Requests for DeepThought HPC 
+====================================
+
+Getting access to the HPC is quick and easy process. Follow the steps below to get up and running.
+
+.. attention:: 
+    The HPC now has new URLs for access, specifically to the new web portals. 
+
+    1. deepthought.flinders.edu.au: SSH / Command Line Access
+    2. https://deepweb.flinders.edu.au/:  User Portal
+    3. https://deepweb.flinders.edu.au/jupyter: Jupyter Hub 
+
+
+VPN Requirements
++++++++++++++++++
+
+When **off campus** you must be connected to the Flinders VPN to access the HPC.
+
+
+Flinders Staff / HDR Students
+-----------------------------
+.. _ServiceOne: https://flindersuni.service-now.com/csp?id=sc_cat_item&sys_id=d95a633cdbf87810062472f5f39619f5 
+.. _(Linux & MacOS/X): unix.html 
+.. _Windows Sub-System for Linux: unix.html 
+.. _Windows: windows.html
+
+1. Create a `ServiceOne`_ Ticket asking for Access to the HPC
+
+    a. Currently the request is under the following path: Research Services -> Undertake Research -> Access to DeepThought HPC.
+
+2. Pick your Operating System for additional guidance:
+
+    a. `Windows`_
+    b. `Windows Sub-System For Linux`_
+    c. Unix Based Systems `(Linux & MacOS/X)`_  
+
+3. The HPC Team will send you an on-boarding email once your HPC account has been provisioned
+
+
+.. _HPC Support Team via Email: mailto:deepthought@flinders.edu.au
+
+Undergraduates 
+----------------
+Currently, the HPC is not open to Undergraduates on a general basis.
+Exceptions are made on a case-by-case basis - please talk to your project supervisor or Topic Coordinator first,
+then have them contact the `HPC Support Team via Email`_.

docs/source/Access/unix.rst

@@ -0,0 +1,44 @@
+Unix Connection Guide
+=========================
+
+MacOS / MacOSX shares a similar procedure to Unix/BSD Based system. 
+Unix/Linux & MacOS systems have native support for the SSH Protocol, 
+used to connect to the HPC.
+
+Windows Sub-System For Linux
++++++++++++++++++++++++++++++
+
+The windows Subsystem for Linux (WSL) allows you to run a Linux Distribution 
+as a sub-system inside the Windows Operating System. When following these 
+instructions, a 'terminal' is the same as starting your WSL Distribution. 
+
+Logging In on Unix 
++++++++++++++++++++
+The simplest manner is to open up a terminal windows and SSH into the HPC.
+
+.. figure:: ../_static/shellPasswordPromtImage.png
+    :align: center
+    :alt: SSH Login Prompt
+
+    SSH Login Prompt
+
+1. Your Username is your FAN
+2. Your Password is your FAN Password.
+
+
+These are the same credentials you use to login to OKTA. When successful, you will be logged into the system and presented with a screen 
+similar to the image below: 
+
+.. figure:: ../_static/loginOKImage.png
+    :align: center
+    :alt: Successful Login
+
+    Successful Login
+
+
+You are now connected to the DeepThought HPC and ready to go.
+
+SSH Keys on Unix
+------------------
+
+If you wish to setup password-less login via SSH Keys, you may do so.

docs/source/Access/windows.rst

@@ -0,0 +1,65 @@
+Windows Connection Guide 
+========================
+To connect to Deep Thought a SSH client such as PuTTy is required. 
+Below is a short list of the possible programs you can use as a client to connect to the HPC. 
+This guide will focus on Putty - but will be equally applicable to the other programs.
+
+
+Windows SSH Client Options
+----------------------------
+
+.. _Putty: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
+.. _KiTTY: http://www.9bis.net/kitty/#!pages/download.md
+.. _BitVise Client: https://www.bitvise.com/download-area
+.. _MobaXTerm: https://mobaxterm.mobatek.net/
+
+
+Windows SSH Connection Guide
+--------------------------------
+Open PuTTy, and you are presented with this screen:
+
+.. figure:: ../_static/puttyAccessImage.png
+    :align: center
+    :alt: PuTTY Connection Detail Screen 
+
+    PuTTY Connection Detail Screen 
+
+
+1. Fill in the hostname to be: deepthought.flinders.edu.au,
+2. Change the Connection Type to SSH
+3. Set the Port Number to 22
+4. Click Open
+
+
+Logging In on Windows
+++++++++++++++++++++++
+If all has gone well, you will be presented with a login prompt similar to the following image.
+
+.. figure:: ../_static/puttyLoginImage.png
+    :align: center
+    :alt: PuTTY Login Prompt
+
+    PuTTY Login Prompt
+
+
+1. Your Username is your FAN
+2. Your Password is your FAN Password.
+
+These are the same credentials you use to login to OKTA.
+
+When successful, you will be logged into the system and presented with a screen 
+similar to the image below: 
+
+.. figure:: ../_static/loginOKImage.png
+    :align: center
+    :alt: Successful Login
+
+    Successful Login
+
+
+You are now connected to the DeepThought HPC and ready to go.
+
+SSH Keys on Windows 
+*********************
+As with the Unix/Linux/MacOS system, you may also setup SSH Keys for password-less logins. 
+Be sure to follow the specific instructions for your client, as they will differ.

docs/source/FAQ/faq.rst

@@ -8,9 +8,9 @@ What are the SLURM Partitions?
 ===============================
 There are three at this point: 
 
-* hpc_general 
-* hpc_gpu
-* hpc_melfeu 
+* general 
+* gpu
+* melfeu 
 
 You can omit the 
 

docs/source/FileTransfers/FileTransfersIntro.md

@@ -2,7 +2,7 @@
 
 Transferring files to the HPC will change depending upon your OS. Thankfully, there are some excellent tools that take this from 'potentially-scary' to 'click a button or two'.  
 
-Before we start, ensure that you have read the [Storage Overview & Usage Guidelines](../Storage/storageusage.html).
+Before we start, ensure that you have read the [Storage Overview & Usage Guidelines](../storage/storageusage.html).
 
 ## Transferring Files
 
@@ -19,11 +19,9 @@ There is a critical difference between these two locations. The /scratch area is
 - /home/$FAN
 - /scratch/$FAN
 
-There following location is treated specially as it holds the older eRSA data and is slowly being phased out.
+### Where is the old r_drive? 
 
-- /r_drive/
-
-This location will surface specific mount points on request. If you have access to these locations, they auto-mount **on usage**. That is, simply try and touch or access the correct location that you have access to, and it will be handled automatically for you. For example, if you have access to a mount point called 'molecular_data', then the following command with surface that mount point to you - `cd /r_drive/molecular_data/`.
+The old /r_drive/ mount points where a legacy implementation left over from the eRSA Project. All the data from these drives has been migrated to a /RDrive/ share with the same name, and will appear automatically. 
 
 ### /Home