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ALICE User Documentation Wiki

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Welcome to the ALICE HPC user documentation.

ALICE is a computing facility for state-of-the-art research and education of Leiden University. With ALICE you have the world of computing at your fingertips. On this wiki, you can find the information you'll need to get started and become more skilled in using computing to support your research and education.

We appreciate any questions or comments on the content of the documentation so that we can improve the range of information that we supply here.

If you are unsure about where to go next, have a look below.

What is ALICE?

Please check out the About ALICE pages to get some background information, a quick overview and see how to acknowledge it.

How can I get an account?

The page Getting an Account has all the information you need on how to request an account on ALICE.

What's new with ALICE?

To get information about updates, upgrades, events, planned maintenance and more, have a look at the News page.

Here are the most recent news:

Latest News

  • 29 Mar. 2021 - ALICE User Survey 2021 out: The ALICE User Survey 2021 is online. All users should have received a link and password. If you are a user and you have not received a link, please contact the ALICE Helpdesk. We hope that you take the time to fill it out and help us improve ALICE: We are looking forward to your responses.
  • 29 Mar. 2021 - MATLAB 2020b available: We have updated MATLAB to version 2020b and changed the license server configuration so that ALICE can now make use of the MATLAB campus license. If you still need version 2019b, please contact the ALICE Helpdesk.
  • 8 Mar. 2021 - Maintenance was successful: Login node 02 has been expanded with an NVIDIA Tesla T4. The new GPU will be tested by us in the next few weeks. So, for now please do not use the GPU. After testing has been completed, we will release the GPU for general use and provide more information.
  • 25 Feb. 2021 - Next major maintenance window on 08 March 2021: Please have a look at the maintenance page for details on our planned work and how it affects you.
  • 12 Feb. 2021 (Update 22 Feb. 2021) - SSH Connection Stability: If you recently started experiencing that your ssh connection is breaking up after a few minutes of being idle, please check the settings below for you ssh configuration for ALICE. If this does not solve the issue, please contact the ALICE Helpdesk.
    • for Linux, MacOS, Windows using OpenSSH command line connection: Make sure you use "ServerAliveInterval 60" and "ServerAliveCountMax 3" to your ssh config settings.
    • MobaXterm: Go to Settings -> SSH -> SSH settings and enable "SSH keepalive"
    • PuTTY: Go to Settings -> Connection -> Set a non-0 value in "Settings between keepalives" (e.g., 60)

Just Getting Started?

If you're new to ALICE, please check out the User Guide.

What more can I do with ALICE?

If you already have experience with ALICE and/or HPC, have a look at the Advanced Guide pages. Please note that many of the pages here are still under construction and subject to change.

What else is there about ALICE?

If you need more information on general topics, such as hardware, storage, and policies, please take a look at the Documentation pages. Please note that many of the pages here are still under construction and subject to change.

Have a question or feedback on ALICE?

If you have a question about ALICE, need help with using it or want to give us some feedback, please see the Support page to know how you can connect with us.

Status of ALICE?

Would you like to know how busy ALICE is and if all nodes are up, then please have a look at the Current Status Overview.

This is a quick overview:

ALICE node status

Login nodes: OK
CPU nodes: OK
GPU nodes: OK
High-memory nodes: OK

Current Issues

  • E-Mail notifications not always working:
    • We discovered an issue with e-mail notificaitions from ALICE. It seems that sometimes e-mails a not delivered to the recipient. However, most notifications are still being send properly. If you think that you have been affected by this issue, please contact the ALICE Helpdesk.
    • Status: Work in progress
    • Last Updated: 16 Mar 2021, 12:49 CET
  • SSH connection breaking up after a few minutes
    • We have received several reports that since last week ssh connections to ALICE are getting closed after a few minutes of being idle. This has not been the case before the 1 Feb.
    • Changes to the ssh gateway require the client to keep SSH connection alive. This can be achieved by using the ServerAliveInterval setting (e.g., "ServerAliveInterval 60") in your ssh config settings for ALICE.
    • Status: Solved
    • Last Updated: 16 Mar 2021, 12:48 CET
  • Slurm issue with ssh to compute nodes when more than one job is running:
    • The current slurm version has a bug which prevents users from logging into the compute node on which their job is running if two or more jobs are running on the node. We are looking into this.
    • If you try to log into a node which has more than job running you will see this error message: "Access denied by pam_slurm_adopt: you have no active jobs on this node Authentication failed."
    • If your job is the only one running on the node, ssh to the node should work without a problem.