User guide

Abacus 2.0 User's Guide

Introduction

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

System overview

Further information about the hardware available at Abacus, can be found here.

Getting access

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:

https://deic-adm.sdu.dk/admin/.

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 testuser@fe.deic.sdu.dk
    _    _                            ____    ___
   / \  | |__   __ _  ___ _   _ ___  |___ \  / _ \
  / _ \ | '_ \ / _` |/ __| | | / __|   __) || | | |
 / ___ \| |_) | (_| | (__| |_| \__ \  / __/ | |_| |
/_/   \_\_.__/ \__,_|\___|\__,_|___/ |_____(_)___/

Welcome to DeIC National HPC Centre, SDU
...
testuser@fe1:~$

Data transfer

To copy files to and from Abacus you can use direct scp or 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.

File systems

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 /home.

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 abc-quota.

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 /work/project/ folder.

For further information, look at our page on Modules. You can also get further information on the available software.

Running jobs using Slurm

At Abacus we use Slurm for batch job scheduling. For further information on Slurm, we refer to our Slurm help pages.

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 abc-quota:

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 test00_gpu 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.

Getting help

If you have questions or have run into an issue with a program, you are welcome to send us an email to the address support@escience.sdu.dk.

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

  1. Your user name and the name of the account you are using
  2. The name and version of the program in question
  3. 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
  4. Time and date of when the problem appeared
  5. 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.