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>@dev.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): 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.

  

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>@dev.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?)
4. Download a DNA sequence from www.ebi.ac.uk to your local computer and then copy it to the cluster.
on mac/linux: scp AF311055 <userName>@dev.vital-it.ch:/scratch/cluster/weekly/<userName>/HPCexercises/exercise7/
on windows: use an external program such as FileZilla or WinSCP (see basic unix commands section above), or the Ubuntu on Windows shell.
  • Rename the file "thio_rat.dna":
          cd /scratch/cluster/weekly/<userName>/HPCexercises
          mv exercise7/AF311055 exercise7/thio_rat.dna



Commands shortcut for steps 2-3:
# 1) login to cluster front-end
# ssh <userName>@dev.vital-it.ch
# pwd
# 2) Create a directory in /scratch/cluster/weekly/
# you can use your username instead of the command: `whoami`
cd /scratch/cluster/weekly/
mkdir `whoami`
cd `whoami`

# 3) Download a copy of the example files to your current folder
wget ftp://ftp.vital-it.ch/edu/HPC/HPCexercises.tar.gz
tar -ztvf HPCexercises.tar.gz
tar -zxvmf
HPCexercises.tar.gz
rm HPCexercises.tar.gz
cd HPCexercises
cp /db/HPC-course/slides/thio_rat.dna exercise7
/

Last modified: Tuesday, 29 August 2017, 10:13 AM