Windows: Use WinSCP, This is a GUI based scp client for MS Windows based computers that has a "drag and drop" facility and an inbuilt file editor

Download: http://winscp.net/eng/download.php

or if you have cygwin installed you can open a cygwin-terminal and then use ssh the same as Linux,Mac below.

Linux,Mac: Use the scp on the commandline

scp file-to-copy corvus.ersa.edu.au:

scp file-to-copy USERNAME@corvus.ersa.edu.au:FOLDER_IN_HOME_DIR/SUB_FOLDER/new-filename

(* copying the file to a SUB_FOLDER and renaming it to new-filename *)

For more info see: http://www.ersa.edu.au/corvus_guide

From Home:

Either , you first you need to connect to the UNI Network Via VPN (*see above*)

Or Alternatively there is a Webdisk and Webdav web based interface you can use from your interent web browser (eg Firefox, Chrome, Safari. Opera, IE)

https://adelaide.sasr.edu.au/webdav/adelaide/home/USERNAME
https://adelaide.sasr.edu.au/webdisk/base/adelaide/home/USERNAME

Videos:

https://www.eresearchsa.edu.au/sites/default/files/file/roadshowmovies/s...
https://www.eresearchsa.edu.au/sites/default/files/file/roadshowmovies/s...

How do I map my home directory on the HPC to my Desktop/Laptop ?:

Windows: You can mount this as a network share folder

                      https://www.ersa.edu.au/sasr_help
                      http://www.ersa.edu.au/sites/default/files/MappingSambaShares/index.html
                      http://www.ersa.edu.au/sites/default/files/file/roadshowmovies/sasr1-win...
                      https://www.eresearchsa.edu.au/sites/default/files/file/roadshowmovies/s...

   Linux (Ubunutu) :To use your home folder as if it was local to you desktop - open the location in your FilesBrowser and then save it a a bookmark.
                Open Top Level Menu: Places => Computer
                                 when Computer Window Opens Choose Go=>Location
                                   in the Location window enter:
                                  davs://adelaide.sasr.edu.au/webdav/adelaide/home/YOUR_USERNAME
           then Goto Bookmarks => Add BookMark
                                   From Now on it will look like another local folder on your desktop.

Now that I have connected to the HPC System - What do I do now ?:

You need to use the Linux Commandline.

Here are some cheat notes to get you started:
http://www.eresearchsa.edu.au/sites/default/files/unix-commands.html
http://www.eresearchsa.edu.au/sites/default/files/introductiontolinux.pdf

How do I Edit my Files on the HPC System ?

Use a commandline editor 'vi' or 'emacs'

Here are some cheat notes to get you started:
http://www.eresearchsa.edu.au/sites/default/files/vi-cheatsheet1.html
http://www.eresearchsa.edu.au/sites/default/files/vi-cheatsheet2.html

HPC User Guides - PBS submission scripts:

You will find template PBS submission scripts in your home directory under a folder called .templates. In here you will find a template for each of the HPC clusters (aquila,hydra,corvus)

ls -alr ~/.templates/
total 24
-rw-r--r-- 1 root root 676 Oct 23 2009 corvus.sub

Copy the one you require to your work folder and modify as required.

cd ~/WorkDir/WorkSubDir/

cp ~/templates/corvus.sub .

vi corvus.sub

*Note: you could modify the entry for Your-email-Address in the templates themselves so this part is already done*

### email address for user
#PBS -M Your-email-Address

See here for : PBS JOB Submission Script Flags

HPC User Guides - Corvus Upgrade Changes to PBS submission scripts:

Since the Upgrade to Corvus - some of the settings in your PBS submission script need to change.

See here for deatils : Corvus Upgrade Notes

What are different storage areas for (/home /data /scratch /tape etc)?

/home - Storage for your program code, submission scripts. This is network-based storage. (25GB / user)
/data - This is a storage area for application input and output files. This is network-based storage. (50GB / user)
/scratch - High performance storage used for storing temporary input and output files while a job is running. This is local node storage.

/home

Reading input or writing output files to /home is strictly prohibited.

/data

For MPI jobs please use /data.

ie /data/users/$USER

(* Note: you can use the linux shell to automagically substitute $USER for your USERNAME, or type it explicitly yourself *)

/scratch

For sequential jobs please make use of scratch storage. Scratch storage is much faster than network storage, so jobs will complete quicker.

You will the first time need to create a directory for yourself to use in /scratch

ie mkdir -p /scratch/$USER

What stops me using more than 25GB on home and 50GB on data?

Quotas.

What the heck is a Quota?
A quota is a restriction that is placed on the amount of data an account may use.
A quota consists of a soft/hard quota and a grace period.
A soft quota is a predetermined level where a warning email is sent out. This however does not prevent you writing more data until the grace period is reached.
A grace period is the amount of time you are allowed to go over the soft limit before the system blocks your ability to write more data.
A hard quota is a predetermined level where the system blocks your ability to write more data. You will still however be able to read your data.

Could I have an example of the Quota system?:
Scenario 1 -
I have 20GB of data in my home directory. I copy another 10GB to my home directory.
So I now have 30GB of data which means I'm 5GB over the soft limit. I receive an email stating I have gone over the quota.
A counter is now started on the server which is called the grace period.
I now have 7 days to reduce my data back down below 25GB (the soft limit). However I can still keep my data at 30GB safely for a week.

Scenario 2 -
I have 30GB of data in my home directory and I decide to copy another 25GB. As soon as I reach 50GB of usage on my home directory, the system stops me writing anymore data.
The copy / scp / rsync command would return an error "quota has been exceeded".

Scenario 3 -
I have 30GB of data in my home directory and I forget to reduce the data below 25G. The 7 day grace period then expires.
The 25GB soft limit now becomes a hard limit. I will be unable to write anymore data to my home directory until I reduce my usage below 25GB.

Screencasts:

*Note: If these play too fast for you via the web browser: Save the file to your PC and use your Media Player*

Windows: From A Windows PC to Corvus Cluster

Linux: From A Linux PC to Corvus Cluster

HPC: Running Jobs On The Clusters

Linux:
With Putty On Windows:

Quick Start Guide

Table Of Contents:

How do I login to the HPC Machines ?

How do I copy files/data to the HPC Machines ?