diff --git a/howTo/iridis.md b/howTo/iridis.md index 16d373e7116b843998db4d3e202744025c0be752..9679c569ab292b3ac130bde17262de0a9c35deb7 100644 --- a/howTo/iridis.md +++ b/howTo/iridis.md @@ -18,7 +18,7 @@ Fill in the form on the [iridis page](https://www.southampton.ac.uk/isolutions/s OK, so you are going to need to [get a bit friendly with unix](https://www.dummies.com/computers/operating-systems/unix/) because the Iridis service runs unix (linux). In general you will be interacting with it using a command line tool like terminal/console etc. Back to the good old days. -You can, possibly, get iridis to open an Xwindow on your PC nut that requires fancy ssh tunneling and stuff. +You can, possibly, get iridis to [open an Xwindow on your PC](https://hpc.soton.ac.uk/redmine/projects/iridis-4-support/wiki/Connecting_to_Iridis_4#Using-GUI-programs-through-SSH-connection) but that requires fancy ssh tunneling and stuff. Assuming you want iridis 4 to start with you can login to any of: @@ -31,7 +31,32 @@ To do this: * make sure you are running the UoS vpn * open a terminal/console window on your desktop - * type `ssh YourUsername@iridis4_a.soton.ac.uk` (or which ever you want). & hit return. YourUsername = your UoS username obvs + * type `ssh YourUsername@iridis4_a.soton.ac.uk` (or which ever you want) & hit return. YourUsername = your UoS username obvs * type `yes` to the fingerprint question (DO NOT PANIC!). This should only happen the first time you do this * type your UoS password & hit return * you're in! + * + +## Now what? + +You can interactively run R scripts by running R. Or you can run them non-interactively using the Rscript <yourScript.R> command. But you probably shouldn't. + +You should submit your commands (e.g. `Rscript myScript.R`) to the Iridis scheduling system so it can balance everyone's needs. You need to [learn how to do this](https://hpc.soton.ac.uk/redmine/projects/iridis-4-support/wiki/Job_submission)... + +## How to get your code on Iridis + +If you've set up a repo on git.soton it's easy - Iridis has git installed. You will have to use git at the command line but it's [not so bad](https://docs.gitlab.com/ee/gitlab-basics/start-using-git.html)... + +If you haven't then do so. + +## Where to put your data + +Sadly Iridis cannot see `J:\ or \\soton.ac.uk\resource\` so you you can't follow [usual advice](https://git.soton.ac.uk/SERG/workflow/-/blob/master/howTo/keepingData.md). You will need to copy the data you need to your home directory on Iridis. Do this using sftp - [CyberDuck](https://cyberduck.io/) works well on OSX, no doubt there are others for [Windoze](https://hpc.soton.ac.uk/redmine/projects/iridis-4-support/wiki/Transferring_files_to_and_from_Iridis_4). + +If you [run out of space](https://hpc.soton.ac.uk/redmine/projects/iridis-4-support/wiki/User_account_information_and_limits) in your home folder/directory (100 GB max) you can also put it in a scratch folder which will take 1 TB. But this is not backed-up - so data in there is at risk. + +## What you cannot do + +Run RStudio. Well OK, you can. But it needs the ssh tunneling and XWindow thing mentioned above. Yeahnah. + +