Hpc

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

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. ...

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. ...

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

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

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. ...

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. ...