ALICE User Documentation Wiki

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Welcome to the ALICE HPC user documentation.

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

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

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

What is ALICE?

The About ALICE pages give some background information, a quick overview and how to acknowledge ALICE in your publications.

How can I get an account?

The page Getting an Account explains 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 is the most recent news:

Latest News

  • 01 Jun 2022 - Disabled access to old scratch storage: As previously announced, we have disabled access to the old scratch storage. We will keep the data available until 30 June 2022. Afterwards, we will start to delete data so that we can repurpose the storage within ALICE. You can request temporary access by contacting the ALICE Helpdesk. See also the wiki page: Data Storage.
  • 25 May 2022 - Security update of Slurm: Because of recently disclosed critical vulnerabilities in Slurm, we had to update Slurm to 20.11.9 today. The vulnerabilities were severe enough that they required immediate action from us.
  • 02 May 2022 - Old shared scratch space: We have extended the availability of the old shared scratch space on /data until 31 May 2022. If you have not done yet, please move your data to the new scratch space. If you need assistance, please contact the ALICE Helpdesk. After this date, we will disable access to it. See also the wiki page: Data Storage.
  • 21 Apr 2022 - ALICE-SHARK User Meeting 2022 - Second Announcement and reminder about contributions: It is still possible to register for the first joined meeting of the user communities of the ALICE HPC cluster (Leiden Univeristy) and the SHARK HPC cluster (LUMC). The deadline for submitting a title/abstract for a talk is 25 Apr 2022 at 23:59 CEST. For more information, please see here: ALICE-SHARK User Meeting 2022
  • 29 Mar 2022 - ALICE-SHARK User Meeting 2022 - Announcement and Registration open: The first joined meeting of users of the ALICE HPC cluster at Leiden University and the SHARK HPC cluster at the Leiden University Medical Center will take place on 18 May 2022 from 09:00 - 13:00. The meeting will provide an opportunity for users to connect with each other and the support teams behind the clusters. The meeting will feature an overview and update for both clusters, a selection of talks from users on past, ongoing or upcoming projects and aa Q&A session with the support team of both clusters. Registration is now open and mandatory. You can find more information here: ALICE-SHARK User Meeting 2022
  • 24 Mar. 2022 - New scratch storage available to all users: We are excited to announce that the new scratch storage on ALICE is available for you to use from now on. It is a BeeGFS-powered parallel file system storage with a total capacity of 370TB. We have created a user directories for all ALICE users on the new scratch storage: /data1/$USER with a link in your home directory/home/$USER/data1. By default, you have a quota of 5TB which can be extended upon request. We ask all users to migrate their data to the new storage and adjust their workflows accordingly. See also the wiki page: Data Storage. We will keep the old scratch storage available for you to use until 30 April 2022. Then, we will disable access to it and you will have to contact us to gain access. Another two months later, we will start to remove any remaining data on the old scratch storage. Project directories on the old shared scratch have also been set up on the new scratch storage in /data1/projects/, but links in home directories of project team members have not been changed in order to avoid breaking existing workflows. We ask PIs to also start migrating the data in their project directories. After the migration has been completed, we will change links in the home directories of team members. If you have any questions or need assistance for migrating your data and workflow, please do not hesitate to the ALICE helpdesk.
  • 09 Mar. 2022 - New short partition amd-short for all users So far node802 has been exclusive to researchers of MI. In agreement with the PI of node802, we are making parts of the resources of this node available to all users now. This will be facilitated through a specific partition called "amd-short" that can run jobs up to 4h using up to 64 cores and up to 1TB of memory. Node802 is somewhat different than all other nodes on ALICE which is you should go through the section "Important information about amd-short" before you start using the new partition.

Next Maintenance

To be announced

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, 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, 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 have a look at the Current Status Overview.

This is a quick overview:

ALICE node status

Gateway: UP
Head node: UP
Login nodes: UP
GPU nodes: UP
CPU nodes: Up
High memory nodes: UP
Storage: UP
Network: UP

Current Issues

  • No access to ALICE - SSH gateway failure:
    • The ssh gateway is currently not working.
    • Access to ALICE is not possible. The cluster itself is not affected and processing continues.
    • The gateway is working again. Access is possible
    • Status: SOLVED
    • Last Updated: 02 Jun 2022, 19:45 CET
  • Copying data to the shared scratch via sftp:
    • There is currently an issue on the sftp gateway which does prevents users from copying data to their shared scratch directory, i.e., /home/<username>/data
    • A current work-around is to use scp or sftp via the ssh gateway and the login nodes.
    • Status: Work in Progress
    • Last Updated: 30 Nov 2021, 14:56 CET

See here for other recently solved issues: Solved Issues