Access to Chimera Cluster

The following university units and groups of users have access to the cluster.

Faculty/University unit Employees Students
Faculty of Mathematics and Physics (MFF) Yes Yes
Faculty of Arts Yes Yes
Second Faculty of Medicine Yes Yes
Faculty of Medicine in Pilsen Yes Yes
Faculty of Science Yes No
Charles University Environment centre Yes No
First Faculty of Medicine Yes No
Central Library Yes No
The Center for Economic Research and Graduate Education (CERGE) Yes No
Faculty of Humanities Yes No

If your section of the university and/or a user group is not in the list, but requires access, please write an email to the cluster administrator.

How to login for the first time

  • Users from Faculty of Mathematics and Physics can use either SSH Access or JupyterHUB Access.
  • Users from other faculties must use JupyterHUB Access for the first time. Following that SSH Access can be enabled as explained below.

1. SSH Access

  • Chimera: ssh <CASlogin>@hpc.troja.mff.cuni.cz.
  • Parlab: ssh -p 42222 <CASlogin>@parlab.ms.mff.cuni.cz.
  • Gpulab: ssh -p 42222 <CASlogin>@gpulab.ms.mff.cuni.cz.
  • Credentials: Use lower-case CAS usernames (not the numeric CAS ID) and the same password as in SIS. If you are not affiliated with Faculty of Mathematics and Physic, the access using login / password is available only via JupyterHUB.

If you are an MFF user with a fresh account you need to change your password at least once at CAS UK before attempting to use it on the cluster. The default password received with a fresh MFF account does not work for reasons outside of our control.

SSH Keys

For MFF users SSH Keys are optional, for non-MFF users SSH keys must be used for terminal access. To set up:

  1. You will need a pair of private/public SSH keys. You can generate them on your local machine: ssh-keygen -t ed25519, set the file name and passphrase (password to protect the local private key on your local machine or leave it blank). It creates a private ~/.ssh/id_ed25519 and public ~/.ssh/id_ed25519.pub keys. If you're connecting to the cluster from OpenWebUI via ChimeraMCP, then ask OpenWebUI to generate the public key for you.
  2. Sign into JupyterHUB, open the Terminal app and follow these steps on the command line:
mkdir -p ~/.ssh
chmod 700 ~/.ssh
echo "YOUR_PUBLIC_KEY" >> ~/.ssh/authorized_keys
chmod 600 ~/.ssh/authorized_keys

Replace the string YOUR_PUBLIC_KEY with the contents of ~/.ssh/id_ed25519.pub or with the key supplied by OpenWebUI.

2. JupyterHUB Access

JupyterHUB provides a web interface for Chimera. It also gives access to various applications that need a graphical interface and it is often used for teaching. Visit the JupyterHUB section for detailed instructions for use.

Running jobs on the cluster

Chimera uses the SLURM scheduling system to launch your calculations on the servers (nodes). To run jobs on Chimera, you need to be assigned to a SLURM account. Following the first login, you will have been assigned to the default account.

  • If you want/need specific SLURM account association, send an email that includes your CAS username and affiliation in the message to the cluster admin or to your account coordinator.

SLURM jobs can be run either manually or using natural language input and LLMs via the ChimeraMCP connector.

SLURM Essentials

  • Terminology: A cluster consists of nodes, which are grouped into partitions. Users submit jobs (which may include multiple tasks - parallel processes) to a scheduling queue.
  • GRES (Generic Resources): Used to request specialized hardware like GPUs. Use --gpus=count or --gres=gpu:type:count in submission commands.
  • Fair Share Priority: Users who have used the cluster less in recent weeks receive higher priority. The priority half-life is 14 days.
  • Preemption: Low-priority jobs in partitions like ffa-preempt can be interrupted by high-priority jobs in two different ways, depending on the queue
    • REQUEUE: The job is killed and requeued; Slurm sends a signal one minute before termination.
    • SUSPEND: The job is paused, releasing CPUs but not memory.
  • Checkpointing: Used to ensure continuation of a preempted job. Use the scheckpoint command or the DMTCP system.
  • Important Commands: sinfo (status), squeue (queue info), srun (interactive), sbatch (batch), scancel (terminate job), seff (efficiency statistics).

Access for users from institutions outside of Charles University

Sometimes collaborators from external institutions (typically students, former colleagues) need access to the cluster. It is certainly possible to give them access to the cluster and for that reason the faculty has approved a new mechanism for generating accounts called External user of services (Externí uživatel služeb), see below, which can be used to setup an account for a non-faculty user.

External user of services

The account called External user of services can be setup for your colleague by your departmental admin of the Amoeba system. This is a standard CAS account although with limited access rights and will be enabled for the period of one year. Two weeks before its expiry the Amoeba system will generate a notification e-mail for the departmental admins of the Amoeba system. The admins can then extend the account lifetime by another year. If the account is not extended a three month grace period applies in which the external user can continue accessing the cluster as usual. After that access will be blocked unless the CAS account is revived by the Amoeba admin. In any case the user data on the cluster will not be automatically deleted. An alternative to the External user of services would be the status of an External collaborator but this type of account is a higher-level since those users appear in the official listing of departmental members on the faculty website. You need to decide which level of access is more appropriate for your collaborator.