We followed the intro SCITAS Course to connect to the Clusters
Documentation is here:
https://scitas-data.epfl.ch/public/training/using_the_clusters.pdf
command id to know to which group you belong
https://scitas-data.epfl.ch/kb/File+systems to get some information on FIleSystem
=Structure of cluster =
`/home/username` your personal area, shared among all 3 clusters
`/work/ptbiop` where biop software are installed, shared among all 3 clusters
`/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to
=How to connect=
Type `ssh gasparlogin@clustername.epfl.ch` and give your password. For instance if Nico wants to connect to the deneb1 cluster (there's also deneb2 and fidis) : `ssh chiarutt@deneb1.epfl.ch`.
=How to transfer data into the server=
== Windows users ==
== Linux users ==
== Where ==
For temporary jobs, put to `\scratch\gasparlogin`. For instance Nico can type `cd \scratch\chiarutt` then `ls` to list the contents of this folder within a terminal.
=How to install software=
You can install either software (unix executable / java applications) into your folder.
=How to install software within your folder =
=How to install software within the BIOP work folder =
= Testing simple tasks on the cluster =
By default you are connected to the so-called login node, which is not a processing node. You can browse, copy files, do your stuff, even launch ImageJ / Ilastik / Whateve(r) , but this is not where you are supposed to do heavy processing!
Described below:
* how to launch process in the login node (in order to understand a bit about unix commands)
* how to launch a JOB, i.e. which is calling a request to launch a process.
== How to launch a process ==
== Example Ilastik Launch ==
`./run_ilastik.sh --headless --project=/scratch/chiarutt/ilps/MyProject.ilp /scratch/chiarutt/images_in/Vesicles.tif
`
== Example CellProfiler Launch ==
== Example Fiji Launch ==
= Software available =
In the work folder. Fiji is available. As several FIJI may be required depending on the configuration, the first one, which do not have any plugin installed, is the default one.
== DEFAULT FIJI ==
No update site installed. Just a raw updated fiji.
* Location folder: ` \work\DefaultFiji`
== Ilaslik ==