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
https://scitas-data.epfl.ch/kb/File+systems to get some information on FIleSystem
= Useful UNIX commands =
* `ls` list content of directory
* `id` returns all groups you belong to
* `pwd` displays current directory
* `mkdir` makes a folder
* `wget` download a web page
* `cat` displays the content of a file in the terminal
* `curl` (`curl www.perdu.com`) write the content of a web page ?
* `man` get help on a linux command `man wget` for instance
* `cd ~` goes to home directory
To execute a file:
* Add a point before the file : `.` (but why not required if using an absolute path ?)
= UNIX commands you can forget =
* `vi` not so modern torture method based on a text editor
=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=
[[ https://scitas-data.epfl.ch/kb/Connecting%2Bto%2Bthe%2Bclusters| Scitas documentation ]]
There are 3 clusters at EPFL named `deneb1`, `deneb2`, `fidis`.
* Linux: 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`.
* Windows:
** On windows 10, there's a ssh client: so execute `cmd.exe` and just type `ssh gasparlogin@deneb1.epfl.ch` in your windows terminal
** Alternative method: install and use [[ https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html | PuttY ]]
=How to transfer data into the server=
== Terminal command line ==
It can be useful to transfer directly from the internet :
* From the internet : `wget http://linkToMyFile.what` for instance to download ilastik: `wget http://files.ilastik.org/ilastik-1.3.0-Linux.tar.bz2`
* From a windows shared server (svfas6): `smbclient '//svfas6.epfl.ch/biop/c$' -c 'lcd /home/chiarutt/examples; cd public; get test.txt' -U intranet/chiarutt`. This rather unintuitive command copies the file `//svfas6.epfl.ch/biop/public/test.txt` to the folder `/home/chiarutt/examples`. You'll need to enter your gaspar password. Type `cat test.txt` in the correct folder to see that you've indeed downloaded this file.
== From your local computer with a Graphical User Interface ==
* Windows users: This can be done via [[ https://filezilla-project.org/ | FileZilla ]], but take care, this soft now installs unwanted software during the installation.
* Linux users: in nautilus, go to `ssh://gasparlogin@deneb1.epfl.ch`
== 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.
= 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.
== How to install new software ==
You can install either software (unix executable / java applications) into your folder or in the shared `/work/ptbiop/` folder. If you cannot execute it, be sure that the file is executable. For instance for Fiji, type `chmod +x ImageJ-linux64`.
== DEFAULT FIJI ==
No update site installed. Just a raw updated fiji.
* Location folder: ` /work/ptbiop/DefaultFiji/Fiji.app/`
* Fiji can be updated using command lines:
** Update FIJI using this command: `/work/ptbiop/DefaultFiji/Fiji.app/ImageJ-linux64 --update update`
== FIJI0 ==
Fiji0 is the fiji where update sites can be installed.
* Location folder: ` /work/ptbiop/Fiji0/Fiji.app/`
* Fiji can be updated using command lines:
** Update FIJI using this command: `/work/ptbiop/Fiji0/Fiji.app/ImageJ-linux64 --update update`
** To add an update site, see [[http://imagej.net/Updater#Command-line_usage | documentation]]
== Ilaslik ==
Ilastik is installed.
* Location folder: ` /work/ptbiop/Ilastik/ilastik-1.3.0-Linux/`
== CellProfiler ==
TODO, currently not installed.
= 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. Look at the [[https://scitas-data.epfl.ch/kb/Using%2Bthe%2Bclusters| Scitas documentation]] for detailed information
== Example simple Job on the CLUSTER ==
We will launch a job on the cluster. To do this, we need to encapsulate the command into a file which gives informations about how the job(s) should be launched and with which hardware. A simple file like this is given here:
`cat /work/ptbiop/jobs/samples/simplejob.sh`
Nano is used to display the file in the terminal. This job simply displays the name of the node it will be executed on.
* To launch this job, type:
** `sbatch /work/ptbiop/jobs/samples/simplejob.sh`
* To know the current status of the job:
** `Squeue`
* To retrieve info on recent job launches:
** `sacct`
* When the job is done, a file will appear in your current folder or in the working dir if it has been specified in the batch file by adding a line similar to `#SBATCH --workdir /scratch/chiarutt`. This file is of the form `slurm-jobid.out` and you can type `cat slurm-jobid.out`, which will display something similar to `hello from r06-node26`.
Congrats! You've launched a job on the cluster!
== Example Ilastik Launch - Login NODE ==
Headless ilastik operation documentation can be found here: `http://ilastik.org/documentation/basics/headless.html`
Launching ilastik, just for useless fun:
`/work/ptbiop/Ilastik/ilastik-1.3.0-Linux/run_ilastik.sh --headless`
Launching ilastik for a classification task, on the login node. There is an example project file on `/work/ptbiop/sampledata/ilastik/ilps/MyProject.ilp` which contains a classifier, and a sample image on `/work/ptbiop/sampledata/ilastik/image/Vesicles.tif`. To classify this image with the classifier contained in the project, type:
`/work/ptbiop/Ilastik/ilastik-1.3.0-Linux/run_ilastik.sh --headless --project=/work/ptbiop/sampledata/ilastik/ilps/MyProject.ilp /work/ptbiop/sampledata/ilastik/image/Vesicles.tif `
A file named `Vesicles_probabilities.h5` should have appear in the folder ``/work/ptbiop/sampledata/ilastik/image/`. You can delete this probabilities file, to be sure...
== Example Ilastik Job on the CLUSTER ==
TODO: launching Ilastik jobs on the cluster!
== Example Fiji Launch - Login NODE ==
To launch Fiji, just type:
` /work/ptbiop/DefaultFiji/Fiji.app/ImageJ-linux64 --ij2 --headless`
This launches a Fiji instance, which is doing nothing special. Some sparse documentation can be found on the ImageJ.net website:
* [[https://imagej.net/Headless | Headless ]]
* [[https://imagej.net/Scripting_Headless| Scripting Headless ]]
* [[http://imagej.net/Updater#Command-line_usage | Updating and update sites ]]
There is the possibility to run a simple script. For instance go to `/work/ptbiop/samplescripts/ij/` ant type `nano hello.py`. This script has one parameter and simply greets the user by its name. Type 'Ctrl+X' to exit nano, and then type:
` /work/ptbiop/DefaultFiji/Fiji.app/ImageJ-linux64 --ij2 --headless --run /work/ptbiop/samplescripts/ij/hello.py 'name="Patrick"' `
You've said Hello to Patrick with Fiji on the cluster. That's quite an achievement. Congrats!
However this was done on a login node node.
== Example ImageJ Job on the CLUSTER ==
TODO: launching ImageJ jobs on the cluster!
== Example CellProfiler Launch ==
TODO