We followed the intro SCITAS Course to How to connect How to install software How to install software at the BIOP account How to launch a job

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 * `nano filename` reasonably easy to use text editor * `echo $SCRATCH` print env variable To execute a file: * Add a point before the file : `.` (but why not required if using an absolute path ?) = UNIX commands you can forget = * `vi` not so modern torture method based on a text editor = Cluster Commands = * `sacct` retrieve info on recent job launches * `squeue` displays cluster queue (all users jobs) * `Squeue` displays cluster queue (your jobs) * `module purge` * `module load intel` * `module spider` displays lio * `module show` displays loaded modules * `scontrol -dd show job` =Structure of cluster = `/home/username` your personal area, shared among all 3 clusters `/work/ptbiop` where biop software are installed, shared among all 3 clusters `/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to =How to connect= [[ https://scitas-data.epfl.ch/kb/Connecting%2Bto%2Bthe%2Bclusters| Scitas documentation ]] There are 3 clusters at EPFL named `deneb1`, `deneb2`, `fidis`. * Linux: Type `ssh gasparlogin@clustername.epfl.ch` and give your password. For instance if Nico wants to connect to the deneb1 cluster (there's also deneb2 and fidis) : `ssh chiarutt@deneb1.epfl.ch`. * Windows: ** On windows 10, there's a ssh client: so execute `cmd.exe` and just type `ssh gasparlogin@deneb1.epfl.ch` in your windows terminal ** Alternative method: install and use [[ https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html | PuttY ]] =How to transfer data into the server= == Terminal command line == It can be useful to transfer directly from the internet : * From the internet : `wget http://linkToMyFile.what` for instance to download ilastik: `wget http://files.ilastik.org/ilastik-1.3.0-Linux.tar.bz2` * From a windows shared server (svraw1): `smbclient '//svraw1.epfl.ch/ptbiop/c$' -c 'lcd /home/chiarutt/examples; cd public; get test.txt' -U intranet/chiarutt`. This rather unintuitive command copies the file `//svraw1.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` 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 ]] == 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 == `sbatch /work/ptbiop/jobs/samples/ilastik.sh` Check with `Squeue` and `sacct`. == 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. 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 == `sbatch /work/ptbiop/jobs/samples/fiji.sh` Check with `Squeue` and `sacct`. == Example CellProfiler Launch == TODO

We followed the intro SCITAS Course to How to connect How to install software How to install software at the BIOP account How to launch a jobWe 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 * `nano filename` reasonably easy to use text editor * `echo $SCRATCH` print env variable To execute a file: * Add a point before the file : `.` (but why not required if using an absolute path ?) = UNIX commands you can forget = * `vi` not so modern torture method based on a text editor = Cluster Commands = * `sacct` retrieve info on recent job launches * `squeue` displays cluster queue (all users jobs) * `Squeue` displays cluster queue (your jobs) * `module purge` * `module load intel` * `module spider` displays lio * `module show` displays loaded modules * `scontrol -dd show job` =Structure of cluster = `/home/username` your personal area, shared among all 3 clusters `/work/ptbiop` where biop software are installed, shared among all 3 clusters `/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to =How to connect= [[ https://scitas-data.epfl.ch/kb/Connecting%2Bto%2Bthe%2Bclusters| Scitas documentation ]] There are 3 clusters at EPFL named `deneb1`, `deneb2`, `fidis`. * Linux: Type `ssh gasparlogin@clustername.epfl.ch` and give your password. For instance if Nico wants to connect to the deneb1 cluster (there's also deneb2 and fidis) : `ssh chiarutt@deneb1.epfl.ch`. * Windows: ** On windows 10, there's a ssh client: so execute `cmd.exe` and just type `ssh gasparlogin@deneb1.epfl.ch` in your windows terminal ** Alternative method: install and use [[ https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html | PuttY ]] =How to transfer data into the server= == Terminal command line == It can be useful to transfer directly from the internet : * From the internet : `wget http://linkToMyFile.what` for instance to download ilastik: `wget http://files.ilastik.org/ilastik-1.3.0-Linux.tar.bz2` * From a windows shared server (svraw1): `smbclient '//svraw1.epfl.ch/ptbiop/c$' -c 'lcd /home/chiarutt/examples; cd public; get test.txt' -U intranet/chiarutt`. This rather unintuitive command copies the file `//svraw1.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` 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 ]] == 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 == `sbatch /work/ptbiop/jobs/samples/ilastik.sh` Check with `Squeue` and `sacct`. == 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. 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 == `sbatch /work/ptbiop/jobs/samples/fiji.sh` Check with `Squeue` and `sacct`. == Example CellProfiler Launch == TODO