Setting up your working environment

Basic UNIX commands (reminder)

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

• ssh <userName>@frt.vital-it.ch        (UNIL front-end)
• ssh <userName>@devfrt.vital-it.ch      (UNIL development machine)
• ssh <userName>@frt.el.vital-it.ch    (EPFL front-end)
• ssh <userName>@frt.ug.vital-it.ch   (UNIGE front-end)
• Note: replace <userName> with your actual user name.

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:

• mkdir /scratch/cluster/weekly/<userName>
• Note: replace <userName> with your actual user name.
• 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): https://edu.sib.swiss/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.

Setting-up your environment

Note: do not forget to replace <userName> in the following examples with your actual username!

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:

• ssh <userName>@devfrt.vital-it.ch
• 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/
• mkdir <userName>
• cd <userName>

3. Download a copy of the HPC course exercise files to your current working directory.

• 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?)

• On your local machine, go to: http://www.ebi.ac.uk/ena/data/view/AF311055&display=fasta
• Save the file as 'AF311055' on your laptop.
• Copy 'AF311055' from your local machine to the Vital-IT cluster:
  

• Rename the file "thio_rat.dna":