Getting started
Here you will find the basics to work with Scicluster.
Get an account
If you are associated with the Faculty of Science, Ferdowsi University of Mashhad, you may apply locally, otherwise please contact us.
Connect to Scicluster
Please connect to the VPN address provided to you. Then you may connect to Scicluster login/head/frontend node via SSH into the login-node.
This means that on Gnu/Linux and OSX you may directly connect by opening a terminal and writing ssh your_username@login-node.
From Windows, you may connect via termius PuTTY or MobaXterm software. X-forwarding for graphical applications is also possible.
Please see the login section for details.
On nodes and files
When you login, you will be on the frontend node. Please do not run any long-lasting programs here. The frontend should only be used for job preparation (see below), internet access and simple file operations.
You will also be in your home directory /home/username. Here, you have ~ 4.5 GB at your disposal with everyday backup.
For actual work, please use the work area at /work8. It is better to make a directory with your username (if it is not made by admin for you) as
The quota for /work8 is 375 GB. This space is not backed up, but it has a good performance. Please remove old files regularly (see the storage section). There are also two high performance storages fortitude8 and gratitude8 that you must contact administrator to apply for.
To move files from your computer to Scicluster or vice versa, you may use any tool that works with ssh. On Linux and OSX, these are scp, rsync, or similar programs. On Windows, you may use WinSCP. You can also use our web portal.
Run a program
There are many programs and libraries pre-installed. You may get a list of all programs by typing module avail.
When you find your program of choice, you may load it using module load. You can also compile your own software, if necessary (see the module and compile sections).
To eventually run the program, you have to write a job script. In this script, you can define how long the job (i.e. the program) will run and how much memory and compute cores it needs. For the actual computation, you need to learn at least the basics of Linux shell scripting.
When you wrote the job script, you can start it with sbatch jobscript.sh.
This will put the script in the queue, where it will wait until an appropriate compute node is available.
You can see the status of your job with squeue -u $USER. Please see Batch and Job script examples sections.
Get help
Do you need help with Scicluster? Contact us via [email protected]. You can also request new software (either an update or entirely new software), suggest changes to this documentation, or send us any other suggestions or issues concerning Scicluster to that email address. Please also read the rest of this documentation.
Happy computing!