## Basic UNIX commands (reminder)

Connecting to the front-end machines of the Vital-IT clusters:

• ssh <userName>@dev.vital-it.ch      (UNIL development machine)

Copying files from a local machine to the Vital-IT cluster:

• scp <fileName> <userName>@frt.vital-it.ch:~  (this will copy the file into your home on the cluster)
• On windows machines, use an external program such as FileZilla (https://filezilla-project.org) or WinSCP (http://winscp.net).

Simple text editors available on all Vital-IT machines:

• nano
• vim

Create a new work directory on the cluster in /scratch/cluster/weekly:

• Important: remember that any files older than 1 week are deleted from /scratch/cluster/weekly. Make sure to backup any file you with to keep to a different location (e.g. your home on Vital-it, if you have one).

UNIX documentation (background info in case you need help with UNIX): http://edu.isb-sib.ch/course/view.php?id=82

Hint: you can also directly copy the example files to your current folder on prd.vital-it.ch with the following command: wget ftp://ftp.vital-it.ch/edu/HPC/examples-files.tar.gz

Important:

• We recommend that you create a folder in /scratch/cluster/weekly/ and that you perform all the exercises there. At the end of the workshop, you can copy the files you want to keep on your local machine.

1. Login to the cluster front-end.
Open a command line terminal on your local machine (a UNIX shell on Mac/Linux or putty on Windows), then log in to the Vital-IT (UNIL) cluster front-end machine using the following command:

• pwd (prints current working directory so you can see where you are)

2. Create a directory in /scratch/cluster/weekly/ and move into it.

• cd /scratch/cluster/weekly/

• wget ftp://ftp.vital-it.ch/edu/HPC/HPCexercises.tar.gz
• list the content of the compressed file: tar -ztvf HPCexercises.tar.gz  (the 't' lists the content of the archive. Notice the dates of the files.)
• Extract the content of the compressed file: tar -zxvmf HPCexercises.tar.gz  (the 'm' preceeding the f - for 'modification-time' will set the current date and time to the files. Why could this be important?)
4. Download a DNA sequence from www.ebi.ac.uk to your local computer and then copy it to the cluster.
 # 1) login to cluster front-end# ssh @dev.vital-it.ch# pwd # 2) Create a directory in /scratch/cluster/weekly/# you can use your username instead of the command: whoamicd /scratch/cluster/weekly/mkdir whoamicd whoami # 3) Download a copy of the example files to your current folderwget ftp://ftp.vital-it.ch/edu/HPC/HPCexercises.tar.gztar -ztvf HPCexercises.tar.gztar -zxvmf HPCexercises.tar.gzrm HPCexercises.tar.gzcd HPCexercisescp /db/HPC-course/slides/thio_rat.dna exercise7/