Merge pull request #3 from flindersuni/feature/access-docs

Feature/access docs
flindersuni · Jun 16, 2020 · 290b653 · 290b653
2 parents c3ee6bb + fa1769a
commit 290b653
Show file tree

Hide file tree

Showing 30 changed files with 552 additions and 325 deletions.
diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/DeepThoughtHPC-docs.iml b/.idea/DeepThoughtHPC-docs.iml
diff --git a/.idea/deployment.xml b/.idea/deployment.xml
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -3,7 +3,7 @@ Pygments==2.3.1
 setuptools==41.0.1 
 docutils==0.14 
 mock==1.0.1 
-pillow==5.4.1 
+pillow>=5.4.1 
 alabaster>=0.7,<0.8,!=0.7.5 
 commonmark==0.8.1 
 recommonmark==0.5.0 

diff --git a/docs/source/Access/GettingAccess.md b/docs/source/Access/GettingAccess.md
@@ -4,22 +4,86 @@ This page will guide you on the steps to get access and then connect to the HPC
 
 ## Flinders Staff / HDR Students
 
-1. Fire of an Assyst Ticket asking for Access to the HPC
+1. Fire of a ServiceOne Ticket asking for Access to the HPC
 
-2. Pick your Operating System
+2. Pick your Operating System ([Unix/Linux/MacOS](#unix-linux-macos) or [Windows](#windows) )
 
-3. Follow the more detailed guides for either:
+3. Read up on some basic [SLURM](../SLURM/SLURMIntro.md)
 
 ### Unix/Linux/MacOS
 
-MacOS / MacOSX shares a similar procedure to Unix/BSD Based system.
+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.
 
-[Link](Unix/UnixAccess.md) to unix page
+#### The Windows Sub-System for Linux
+
+The windows Subsystem for Linux (WSL) allows you to run a Linux Distribution as a sub-system in windows. When following these instructions, a 'terminal' is the same as starting your WSL Distribution.
+
+#### Getting Connected
+
+The simplest manner is to open up a terminal window and type in the following, substituting FAN for your FAN as needed.
+
+- ssh FAN@deepthought.flinders.edu.au
+
+If all is OK it will ask for your password. Enter the same password you use to login to OKTA.
+
+![SSHPasswordPrompt](../../_static/shellPasswordPromtImage.png)
+
+##### Success
+
+Upon a successful login, you should get a screen similar to this:
+
+![LoginOK](../../_static/loginOKImage.png)
+
+If so, you are now connected and ready to start using the HPC!
+
+#### SSH Keys
+
+If you wish to setup password-less login via SSH Keys, you may do so.
 
 ### Windows
 
-[Link](Windows/WindowsAccess.md) to Windows page
+To connect to Deep Thought a SSH application 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.
+
+#### The Windows Sub-System for Linux
+
+If you are using the Windows SubSystem for Linux (WSL), then go ahead and read the [Unix/Linux](#unix-linux-macos) instructions instead.
+
+#### 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)
+
+#### Getting Connected
+
+Open PuTTy, and you are presented with this screen:
+
+![](../../_static/puttyAccessImage.png)
+
+- Fill in the hostname to be: deepthought.flinders.edu.au,
+- Change the Connection Type to SSH
+- Set the Port Number to 22
+- Click Open
+
+#### Logging In
+
+If all has gone well, you will be presented with this screen:
+
+![](../../_static/puttyLoginImage.png)
+
+- Your Username is your FAN
+- Your Password is your FAN Password.
+
+These are the same credentials you use to login to OKTA.
+
+#### Success
+
+Upon a successful login, you should get a screen similar to this:
+
+![](../../_static/loginOKImage.png)
+
+If so, you are now connected and ready to start using the HPC!
 
-## For External Users
+#### SSH Keys 
 
-Sorry, but we aren't open for external users just yet. Check back soon!
+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! 
diff --git a/docs/source/Access/Mac/MacAccess.md b/docs/source/Access/Mac/MacAccess.md
diff --git a/docs/source/Access/Unix/UnixAccess.md b/docs/source/Access/Unix/UnixAccess.md
diff --git a/docs/source/Access/Windows/WindowsAccess.md b/docs/source/Access/Windows/WindowsAccess.md
diff --git a/docs/source/FAQ/faqandissues.rst b/docs/source/FAQ/faqandissues.rst
@@ -0,0 +1,29 @@
+*****
+FAQ 
+*****
+
+The always present 'We get asked these a lot' section. Currently, its empty!
+
+
+******************
+Known Issues
+******************
+
+Below are the 'known issues' with the documentation at this point.  This is not an issue tracker for the HPC, so please don't try and lodge an issue with Deepthought here!
+
+PDF Version
+==============
+
+Images are missing in some sections on the PDF Version 
+Alt-Text  appears when it should not in the PDF Version 
+
+EBPUB Version 
+================
+
+EPUB Version is missing some pages of content
+
+
+Web / ReadTheDocs / Online Version 
+====================================
+
+Occasionally, the Sidebar Mis-behaves when updating the Table of Contents 
diff --git a/docs/source/FileTransfers/FileTransfersIntro.md b/docs/source/FileTransfers/FileTransfersIntro.md
@@ -1,4 +1,4 @@
-# Transferring Files to the HPC
+# Transferring Files to Deepthought
 
 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'.
 
@@ -42,13 +42,78 @@ Here is a rough guide as to what should live in your /scratch/$FAN directory. In
 
 All file-transfers are done via Secure File Transfer Protocol (SFTP). As was the same with the 'Getting Access', pick your platform:
 
+### Linux/Unix File Transfers
 
-### Unix/Linux/MacOS
+Linux / Unix based systems share native support for the SFTP Protocol. The Secure Copy Protocol (SCP) is also widely accepted, which can sometimes offer an edge in transfer speed.
 
-[Link](Linux/LinuxFileTransfer.md) to unix page
+#### The Windows Sub-System for Linux
 
-MacOS / MacOSX shares a similar procedure to Linux/Unix Based system
+Since Windows 10 and Windows Server 2019, the windows Subsystem for Linux (WSL) allows you to run a Linux Distribution as a sub-system in windows. When following these instructions, a 'terminal' is the same as starting your WSL Distribution.
+
+#### Transferring Files to the HPC
+
+To upload files to DeepThought, the simplest method is to open a Terminal window.
+
+#### The Quick Version
+
+Substitute your filename, FAN and Password, type scp FILENAME FAN@deepthought.flinders.edu.au:/home/FAN then hit enter.
+Enter your password when prompted. This will put the file in your home directory on DeepThought. It looks (when substituted accordingly) similar to:
+
+![SCPExample](../../_static/SCPExampleImage.png)
+
+#### The Longer Version
+
+To download files from DeepThought, you simply need to invert that command to point to either:
+
+- A name of a Computer that Deepthough 'knows' about.
+- An IP Address that Deepthought can reach.
+
+#### Transfers By Computer Name
+
+If you know the hostname of the computer, you can substitute this to transfer files back to your machine. The command stays the same, mostly. You still follow the same idea, we just change where we are pointing it. This one assumed you are transferring it to a Linux/Unix based machine.
+
+The command will take this form:
+
+![SCPByHostname](../../_static/SCPByHostname.png)
+
+#### Transfer By IP Address
+
+If you don't know your computer IP, then the commands of:
+
+- ip addr
+- ifconfig
+
+Will be your friend to figure out what it is. Just like above, we slightly change the command, and sub-in an IP instead of a host-name.
+
+![SCPByIp](../../_static/SCPByIp.png)
 
 ### Windows
 
-[Link](Windows/WindowsFileTransfer.md) to Windows page
+Windows doesn't support the SFTP protocol in a native way. Thankfully, there are lots of clients written to do just this for us.
+
+#### Sub-System for Linux
+
+You can use the WSL for this - head on over to the [Linux](../Linux/LinuxFileTransfer.md) Guide.
+
+#### Potential Client List
+
+This is not an exhaustive list - feel free to use whatever you wish that supports the SFTP protocol.
+
+- [WinSCP](https://winscp.net/eng/index.php)
+- [FileZilla](https://filezilla-project.org/?AFFILIATE=6732&__c=1)
+
+This guide will focus on WinSCP.
+
+#### Getting Connected
+
+Open WinSCP, enter deepthought.flinders.edu.au as the host to connect to, and click Login. You should have a screen that looks like this.
+
+![WinSCPConnect](../../_static/WinSCPImage.png)
+
+The first time you connect up you will get a warning - this is fine, just click YES to continue on.
+
+![WinSCPSSHKeyNotice](../../_static/WinSCPSSHKeyNotice.png)
+
+A connection to Deep Thought will then be created - login using your FAN and password. If all goes well, you will be treated to this screen:
+
+![WinSCPConnected](../../_static/WinSCPConnected.png)