Getting started

This page is meant to get you started on our resources and briefly list the essentials. In the menu on the left you will then find more in-depth documentation on these topics.

Getting access

To get access you need two things:

Information on available CPU hours and disk space

This will list your available projects and the remaining CPU hours (see also Projects and accounting):

$ cost

This will give you information about your disk Usage and quota:

$ dusage

Logging in

Logging into the machines involves the use of Secure Shell (SSH) protocol, either in a terminal shell or through a graphical tool using this protocol under the hood. SSH login is available natively to Linux or macOS. Also on Windows a number of good tools for this exists.

For more information and examples see SSH.

$ ssh <username>@<machinename>

Replace <username> with your registered username and <machinename> with the specific machine name.

The machine names are:

Transferring files

To copy files from your machine to the HPC machines, use SSH file transfer Protocol (SFTP) or Secure Copy (SCP). They are available as command-line tools for Linux and MacOS X but Windows users need to download a separate SCP or FTP client, such as WinSCP or MobaXterm.

For example, to copy projectfiles.tar.gz from your local home directory to the remote home directory of myusername on Fram, type (the colon at the end is important):

$ scp projectfiles.tar.gz myusername@fram.sigma2.no:

For more information please see our page on File transfer.

Remote desktop

The Fram and Saga systems provide a Remote desktop service.

Quickstart: Use a VNC client to log into desktop.fram.sigma2.no:5901 or desktop.saga.sigma2.no:5901. A web based remote desktop service is also available https://desktop.fram.sigma2.no:6080. Access to these services are blocked outside the Norwegian research network, e.g. only accessible from UNINETT and partner institutions.

Modules

To keep track of the large number of different pieces of software that is typically available on a shared HPC cluster, we use something called a software module system. This allows us to have many different versions of compilers, libraries, and applications available for different users at the same time without conflicting each other.

By default when you log in to the cluster you will get a clean environment with nothing but standard system compilers and libraries. In order to make your favourite software application available to you, you need to load its module into your environment, which is done using the module command

$ module <options> <modulename>

Some of the more common options include:

  • avail - list the available modules

  • list - list the currently loaded modules

  • load <modulename> - load the module called modulename

  • unload <modulename> - unload the module called modulename

  • show <modulename> - display configuration settings for modulename

For more details please see Software module scheme.

Running applications

The HPC machines provide compute nodes for executing applications. To ensure fair access to the resources, the HPC machines run applications as jobs in a queue system, which schedules the tasks and process to run on compute nodes. All systems use the Slurm queue system.

A job is described by a batch script, which is a shell script (a text file) with SBATCH options to specify the needed resources and commands to perform the calculations. All batch scripts must contain at least the following two SBATCH options (on Saga you also need to indicate maximum memory):

#!/bin/bash -l

# account name
#SBATCH --account=nnXXXXk

# max running time in d-hh:mm:ss
# this helps the scheduler to assess priorities and tasks
#SBATCH --time=0-00:05:00

For more details please see Running jobs.