Abacus 2.0 User's Guide
This user's guide is intended to provide enough information to enable a new user to use our system. As almost all supercomputer/HPC centres around the world Abacus 2.0 is running Linux, and the user is assumed to be familiar with Linux like systems.
Let us know if you find anything that you think should be covered in the guide or if you find something that should be clarified.
Also note the Getting help section further below.
DeIC National HPC Centre, SDU
Further information about the hardware available at Abacus, can be found here.
To get access to Abacus you need to be associated with a project. You can find further information on how to apply for access at the Get Access Page.
Many users (in particular post docs, PhD students, and other students) get access via a project applied for by their research group leader, i.e., they should not apply themselves.
In all cases you get a project token which is a string of the form
12345-67890-abcde-54321. The project token enables you to sign
in at our admin home page using WAYF:
As part of the setup process at the page you must choose your own username. Furthermore, you are required to upload an SSH key enabling you to use ssh to login to our system. See the next section for further information.
Please note that you should expect up to 15 minutes delay for any change on our admin home to take effect.
Connecting to Abacus 2.0 using Secure Shell (SSH)
Secure Shell (SSH) is a way to login to remote computers securely (encrypted). SSH keys is an even more secure way to do this without involving any password exchange between the local and remote computer. SSH using SSH keys is the only way to get remote access to Abacus. For further information on SSH, we refer to our two guides on how to setup SSH:
After your SSH key has been uploaded, you can connect to Abacus using
ssh as shown below. Replace
testuser with the user name
you selected on our admin home page.
peter@laptop:~$ ssh email@example.com _ _ ____ ___ / \ | |__ __ _ ___ _ _ ___ |___ \ / _ \ / _ \ | '_ \ / _` |/ __| | | / __| __) || | | | / ___ \| |_) | (_| | (__| |_| \__ \ / __/ | |_| | /_/ \_\_.__/ \__,_|\___|\__,_|___/ |_____(_)___/ Welcome to DeIC National HPC Centre, SDU ... testuser@fe1:~$
To copy files to and from Abacus you can use direct
sftp to the frontend nodes,
fe.deic.sdu.dk. Note that you
in all cases must use the SSH key you uploaded earlier.
For further information, look at our SSH setup guides.
IMPORTANT: It is your own responsibility as a user of Abacus to
backup all your data yourself. We only guarantee daily snapshots of
the contents in
/home (a week back in time) and weekly disaster
recovery backup of
For further information on the file systems available at the cluster, look at our Storage page.
To see how much available disk space you have, run the command
testuser@fe1:~$ abc-quota ... Available disk space ==================== Filesystem | Quota Avail | Used Use % | IUsed IUsed% ---------------- + -------- -------- + -------- -------- + -------- -------- /home/testuser * | 10G 10G | 100M 1 % | 2.3K 2 % /scratch/test00 | 10G 10G | 1G 10 % | 1.2K 1 % /work/test00 | 250G 235G | 16G 7 % | 146K 2 %
Software via Modules Environment
At Abacus we maintain a short list of standard software available for our users. A few software packages are only available for some research groups.
Users are not limited to using the software installed by us. You are
welcome to install your own software either in your home directory or
in your project's
Running jobs using Slurm
Accounts - how many node hours are available?
To see which accounts are available to you, including how many node
hours are available, use the command
testuser@fe1:~$ abc-quota Available node hours per account/user ===================================== Account/user | Quota Avail | UsedPeriod % of Qt | UsedMonth ------------ + ------- ------- + ---------- --------- + --------- test00_gpu | 2,000 1,220 | 780 39.4 % | 650 otheruser | | 80 4.4 % | 50 testuser * | | 700 35.0 % | 600 ...
In this case,
testuser can use the account
test00_gpu. Within this accounting period, the user
testuser has used 700 node hours, and the
account has used in total used 780 hours. 1,220 node hours are still
available. As shown in the column
UsedMonth most node hours
have been used during this month.
For further information, we refer to our Slurm help pages.
If you have questions or have run into an issue with a program, you are welcome to send us an email to the address firstname.lastname@example.org.
If possible (and relevant), please always include all necessary information to reproduce the issue. This makes it easier to determine what the problem is and to later confirm that the problem has been fixed.
A list of possible things to include in your email
- Your user name and the name of the account you are using
- The name and version of the program in question
- Further description of the problem, including in particular the steps necessary to reproduce the problem, the response/result you got, and the response/result you expected
- Time and date of when the problem appeared
- If possible, job id and the location of the job script and any other files necessary to rerun the script
Frequently asked questions
A list of frequently asked questions can be found on our FAQ page.