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Research Zernike (ZIAM) Theoretical Chemistry

TheoChem cluster

The TheoChem cluster is the property of the Theroretical Chemistry group.

Request account

The TheoChem cluster is accessible to all members of the TheoChem group. Please send an email to your PI to request for an account


The CIT offers a beginners course for using the Habrok cluster. The Habrok cluster in priniciple works the same as the TheoChem cluster. More information can be found on the course page.

The cluster consists of these nodes

  • 10 Standard Nodes (node01 to node10)

    • 2 CPUs (18 Cores each/36 Threads per CPU)

    • 1 TB Disk
    • 128 GB ram

The nodes are coupled using an 56 Gb/s Infiniband network. This network has both a high bandwidth (large amounts of data per second) and a low latency (minimal amount of time needed for sending small messages). This makes this network especially suited for tasks using more than one machine.

Disk space and management

  • The drive /home contain 500 Gb of space of which 10 GB is assigned to each user.

  • The drive /data contain 36 TB of space of which 1 TB is assigned to each user.

The /home drive is intended for location of important files, scripts, and own programs for development. The /data drive is intended for all data files.

To check your use of quota use quota -vs

It is recommended that you check your disk quota (with the 'quota' command) before submitting any job to make sure that the output fits. You should also regularly check the available disk space with the 'df -h' command to check that the disk systems are not full.

Full disks result in crashing jobs.

When you clean up your directories, you may find the 'du -sh' command as it lets you find out how much space you have in a particular folder specified.

Additional disk space can be assigned to high priority Berendsen Center project upon approval by the center PIs.

System Administration

The system administration is performed by Jaap Aikema (

Last modified:21 June 2023 3.19 p.m.