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 and possibly you have these already:
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.
Replace <username> with your registered username and <machinename> with the
specific machine name:
$ ssh <username>@<machinename>
The machine names are:
The Fram and Saga systems also provide a Remote Desktop service.
Learning about the Linux command line
Learning the basics about the Linux command line (shell) navigation and shell scripting will make your daily work easier and more efficient.
If you are new to command line, go through some Linux tutorials on the subject first. Here are some useful pages you can look into: shell novice or Effective shell. O therwise consult your local IT resources for help.
However, do not be afraid to contact support if you are not an expert or have knowledge of this. We will try our best to help you.
Transferring files
We recommend to use rsync to transfer files. It is often faster and safer (in
terms of overwriting files) than using scp. On Windows we recommend to use
rsync through Windows Subsystem for Linux
(WSL). Read more
on our page about File transfer.
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.
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 Storage quota:
$ dusage
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 moduleslist- list the currently loaded modulesload <modulename>- load the module calledmodulenameunload <modulename>- unload the module calledmodulenameshow <modulename>- display configuration settings formodulename
For more details please see Software module scheme.
How to get the most out of your allocation
We want to support researchers in getting the most out of the high-performance computing services. When supporting users, we see that these problems are very frequent:
Reusing outdated scripts from colleagues without adapting them to optimal parameters for the cluster at hand and thus leaving few cores idle. Please check at least how many cores there are on a particular cluster node.
Requesting too much memory which leads to longer queuing and less resource usage. Please check How to choose the right amount of memory.
Requesting more cores than the application can effectively use without studying the scaling of the application. You will get charged more than needed and others cannot run jobs. If others do this, your own jobs queue.
Submitting jobs to the wrong queue and then queuing longer than needed. Please take some time to study the different Job Types.
If you are unsure about these, please contact us via support@nris.no and we will help you to use your allocated resources more efficiently so that you get your research results faster.