Quick start

From IBERS Bioinformatics and HPC Wiki
Jump to: navigation, search

Logging into Bert, the HPC solution in IBERS

Once you have your login details from the administrator, you will be able to access Bert.

In GNU/Linux, UNIX or Mac OSX

At the command line simply type into your terminal;

   ssh username@bert.ibers.aber.ac.uk

This will give you a shell on the login node. From here you can submit jobs and write programs.

Unix ssh.png

In Windows

For Windows Operating Systems you will need to download PuTTY SSH [1].

Enter username@bert.ibers.aber.ac.uk into the hostname dialogue box. This will bring up a black screen prompting you for your password. Once entered this will give you a shell on the login node. From here you can submit jobs and write programs.

Putty pic1.jpg

Accessing files on Bert

In GNU/Linux, UNIX or Mac OSX

To send a single file to bert, type the following into the terminal on your local machine;

   scp filename username@bert.ibers.aber.ac.uk:

If you wish to send a folder, type;

   scp -r foldername username@bert.ibers.aber.ac.uk:

To copy a file back from bert to your local machine, type;

   scp username@bert.ibers.aber.ac.uk:filename .

or if you wish to copy a whole folder, type;

   scp -r username@bert.ibers.aber.ac.uk:foldername .

For more information about the scp command in GNU/Linux, read the man pages [2] or see more examples [3]

In Windows

Download WinSCP [4] (other file manager clients are available). If you do not have admin rights on your local computer you may have to change the default install location during the installation process, otherwise the install may quit with an error message. If this happens, select an install location that is in your home folder, or anywhere you have permission to create and modify files.

Once installed, double click on the WinSCP icon on your desktop (or find it in the programs on the start bar) and enter the hostname and user information into the WinSCP login screen.

Winscp3 pic1.png

This will then bring up the program allowing you to access files on both your local machine (left) and the machine you've logged onto (right).

Winscp3 pic2.png

With this you can navigate the file structure of both your local machine, and the HPC machine so that you can 'drop and drag' files and folders. You can also edit text files which is useful when creating scripts to work with SGE.