Hpc on C&CZ

Compute Cluster Maintenance

Simon Oosthoek — Fri, 28 Aug 2026 00:00:00 +0000

To ensure the stability and security of our compute clusters, C&CZ performs regular maintenance.

Info

cluster node maintenance

Simon Oosthoek — Fri, 05 Jun 2026 00:00:00 +0200

We will reboot clusternodes and possibly upgrade them from older ubuntu versions to ubuntu 24.04 in the last week of August 2026.

If you have clusternodes and would like to plan for an upgrade from ubuntu 22.04 to ubuntu 24.04, please let us know

Update: the (first) reboot should take place between 10:00 and 11:00, if subsequent reboots are needed we will try to keep it within the same day timeframe.

Slurm and High Performance Computing

Ben Polman — Tue, 25 Nov 2025 12:30:42 +0000

Computer cluster architecture

The clusternodes that we manage for the various departments are all connected to the network, but not all are in the same subnet/vlan. We strive to keep the nodes of a single group in the same vlan to optimise internal network traffic. Connectivity with the storage servers for shares and homedirectories is always routed through the firewall, thus it is less performant than a local server and much less performant than local (within the server) storage on /scratch.

High Performance Computing

Simon Oosthoek — Tue, 05 Nov 2024 00:00:00 +0100

At the faculty of science, C&CZ manages a number of compute clusters and we have our own computer room with a few dozen racks for server hardware and also some racks in the Forum computer room.

Managed clusters

The largest cn-cluster is heterogeneous: it holds nodes purchased by individual departments as well as a number of nodes purchased by C&CZ, which FNWI departments may use after approval. The cn-cluster includes nodes with a GPU with CUDA cores. All nodes use SLURM as cluster software; regular maintenance is performed according to the Compute Cluster Maintenance policy.

Module command for optional software versions

Fri, 25 Aug 2023 00:00:00 +0200

On C&CZ managed Ubuntu hosts, the “module” command is available. This makes it easy to use specific versions of available software.

To view which modules are available, use:

module avail

and to use Matlab-R2023a:

module add Matlab-R2023a`

For more info, see the Environment Modules website.

JupyterHub

Malte Rösner — Wed, 31 Aug 2022 06:38:28 +0000

JupyterHub is a multi-user Hub that spawns, manages, and proxies multiple instances of the single-user Jupyter notebook server. It can offer notebook servers to a class of students, a scientific research project, or a high-performance computing group.

Please contact C&CZ if you plan to use or are interested in using the JupyterHub for your course or project.

The JupyterHub is available via https://jupyterhub22.science.ru.nl and you can login with your Science username / password combination.

Nbgrader

Malte Rösner — Tue, 30 Aug 2022 07:17:33 +0000

NBGrader is a system for assigning and grading Jupyter notebooks.

Student Interface

Using the assignment list extension within the JupyterHub, students may conveniently view, fetch, submit, and validate their assignments.

For details see: https://nbgrader.readthedocs.io/en/stable/user_guide/highlights.html#student-interface

Instructor Interface

The NBGrader services guide the instructor and teaching assistants through assignment and grading tasks using the familiar JupyterHub environment.

For details see: https://nbgrader.readthedocs.io/en/stable/user_guide/highlights.html#instructor-interface

Crest

Fri, 24 Jun 2022 12:18:55 +0000

Prerequisities

Same as for gaussian
set-up environment (check gaussian)

General topics

General topics like queue handling, queues and similar are covered in the gaussian wiki entry.

Submitting jobs

Basic syntax of crest submission script is following:

cnorris@lilo7:~$ Crest structure.xyz

where structure.xyz is the structure which you want to submit.

More advanced syntax looks like this:

cnorris@lilo7:~$ Crest structure.xyz -chrg 1 -uhf 0 -quick

Here I’ve added quick keyword which makes the screening less in-depth but it goes much quicker. I also added chrg keyword to define charge and uhf keyword to define spin state. For more detailed description and full list of keywords, please refer to crest command line arguments documentation.

Gaussian

Mon, 13 Dec 2021 09:44:20 +0000

Prerequisities

Science (CNCZ) account.
Being member of the qm, qmorgchem or qmteaching and gaussian groups (ask Jan for access).
Vpn (when working from home).
SSH client (linux usually has OpenSSH, windows - for instance MobaXterm or Putty).
X11 client (linux usually has OpenSSH, windows - for instance MobaXterm
(optional) WinSCP

Video guides

GUIDE how to setup environment for Gaussian calculations in windows.

Setting-up the environment (to be done once)

To submit calculations easily you need to set-up the environment first.

Hpc on C&CZ

Compute Cluster Maintenance

cluster node maintenance

Slurm and High Performance Computing

Computer cluster architecture

High Performance Computing

Managed clusters

Module command for optional software versions

JupyterHub

Login

Nbgrader

Student Interface

Instructor Interface

Crest

Prerequisities

General topics

Submitting jobs

Gaussian

Prerequisities

Video guides

Setting-up the environment (to be done once)