Services

High Performance Computing for Research

The cluster of the Faculty of Mathematics and Physics, is a virtually interconnected infrastructure comprising the Chimera cluster located in Troja and the Parlab cluster from Malá Strana. Users can run computational jobs across these resources using the SLURM resource manager.

Teaching & Education

You can use the cluster to support your coursework in any subject requiring computational resources.

Virtual Lecture Rooms:

There are currently three virtual lecture rooms available in SIS, which correspond to specific cluster nodes:

  • HPC01, HPC02: Correspond to nodes mff-a2-01, mff-a2-02.
  • HPC03: Corresponds to a specialized GPU node mff-a2-19.

Reservation Procedure:

The nodes can be reserved just like any physical lecture room.

  1. One-time reservations: These are made via SIS Schedule NG by selecting "Lecture room," choosing the desired HPC room, and providing a description including the course code.
  2. Repeated reservations: These must be performed by the departmental scientific secretary (tajemník) in SIS, and the cluster administrator should be contacted via email or Mattermost to guarantee resource availability.

  3. Approval: Once approved, the admin will provide a Reservation code, and an account named after the course code will be created in SLURM.

  4. JupyterHUB Integration: For a more accessible teaching environment, teachers offten take advantage of the JupyterHUB environment in combination with reservation of the computing resources.

Course Accounts and Directories:

A user is identified by his/her login. Account is a billing entity: we won't charge you for using our clusters but each user must be assigned to at least one account. Accounts have access to certain partitions.

  • Account Management: Lecturers are appointed as account coordinators, allowing them to manage student access. Students can be added using the command sacctmgr add user <user_name> account=<account_name> or via the sadd_list_to_account script for bulk additions.
  • Directories: Teachers can request a dedicated course folder, typically located at /home/teaching/<course_code>/, where permissions are restricted to course members.

Detailed instructions for reserving the virtual lecture rooms

Virtual lecture rooms are a collection of computing hardware which you can use to support your teaching. You can reserve them as you would reserve any other lecture room. The reserved resources can be shared by your students so make sure you reserve enough resources (at least one physical core per student).

We have (for now) 3 lecture rooms in SIS corresponding to three different cluster nodes. HPC[01-02] correspond to mff-a2-[01-02] and HPC03 corresponds to a specialized GPU node mff-a2-19.

Lecture room CPU Sockets Cores Threads available RAM [GB] Max users GPU
HPC01 AMD EPYC 7543 2 32 2 496 64 T600 can be used only by one user
HPC02 AMD EPYC 7543 2 32 2 496 64 T600 can be used only by one user
HPC03 AMD EPYC 7543 2 32 2 496 64 L40 can be used by multiple users via mps.
For example 10% of GPU can be requested by entering --gress=mps:10 into Other SLURM options

1. Reserve the virtual lecture room via SIS

A. One time reservation

Make reservation request: - start by selecting New reservation and then Lecture room in Schedule NG lecture rooms in SIS

  • select which room you want to request reservation for lecture rooms in SIS

  • select month and start time for the reservation request lecture rooms in SIS

  • fill end time, name and description - if it is for the lecture, please indicate lecture code there.

  • wait for approval and email from cluster admin.

B. Repeated reservation

  • can be done only by the departmental scientific secretary (tajemník) in SIS - there is no approval system for repeated reservations.
  • in this case please contact cluster administrator via email or mattermost. Without it, making a reservation on the cluster is not guaranteed.

When making the reservation, you have to specify in the Description the code of the course or the group name which the reservation is for, e.g. NOFY056. The cluster admin will approve your reservation, create an account in SLURM with the name of the course code and add you (the lecturer) as the coordinator for the account. This will enable you to add all his/her students to the account, see gitlab for details. More user friendly tools (scripts) to do this will be provided soon.

2. Using the reservation in your lectures

When the reservation is approved, the admin will provide you with the code of the Reservation. Reservation are usually magnetic - they will be used automatically if the job satisfy requirements. This usually means you only need to specify account (usually course code) when selecting the computing resources. If you have to specify reservation you can do this by adding the option --reservation reservation_name in the field Other SLURM resources.

You will be also account coordinator for corresponding account. With this you can add and remove users from it.

You can add users to the account using SLURM command sacctmgr add user user_name account=account_name.

If you have list of user names in a file (one line per user name) you can also use script sadd_list_to_account account_name file_with_user_names. This will add all user names to the account or report errors if there are problems (like account does not exist on the cluster).

To display the list of users associated with the subject account use sacctmgr show association account=account_name | grep chimera.

3. Sharing files with students

Ask the admin to create a folder on the cluster associated with your course. This will be most likely in the /home/ partition, e.g. /home/teaching/course_code/. The permissions will be set so only members of the course can access this folder.