Howto on C&CZ News

Contact

Bram Daams — Wed, 02 Nov 2022 10:08:04 +0100

For all ICT related questions and problems within FNWI please contact C&CZ.

Helpdesk & Sysadmin

phone	room	mail
+31 24 36 20000	`HG00.051`	helpdesk@science.ru.nl

Visiting address

We are located on in the front part of wing 5, ground floor of the Huygens Building (rooms HG00.051, HG00.509 and HG00.545). The helpdesk is available during office hours (8:30 - 17:00). During that time the office is staffed.

Full address: Huygens Building, HG00.051, Heyendaalseweg 135, 6525 AJ Nijmegen

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.

WWW Service

Simon Oosthoek — Mon, 27 Oct 2025 09:05:18 +0000

Starting a new WWW service

This document gives a short description which decisions have to be made before a new WWWW service within the Science Faculty can be started.

Contact Communications

C&CZ is not the communications department, officially all communication and therefore websites should be provided and endorsed by the communication department.

However, sometimes a website is actually an application with a web interface and this can usually not be provided via the official communication website.

Servers

Simon Oosthoek — Wed, 22 Oct 2025 12:38:00 +0000

Servers and Workstations

C&CZ manages about 400 Linux servers and hundreds of Linux workstations and a few servers with MS-Windows, primarily in the domain science.ru.nl. Dual boot Windows/Linux machines are counted twice. The servers are distributed over three datacenters.

Workstations

C&CZ manages (for departments) workstations with Ubuntu Linux. There are also workstations in the PC-rooms for general use by anybody with a Science login, but also by all RU employees and students and guests with a temporary login. Almost all those machines are dual boot, the user can choose to boot Ubuntu Linux or MS-Windows.

Login

Bram Daams — Tue, 26 Aug 2025 17:03:10 +0000

A Science login provides faculty students and employees access to services like networked storage, computer labs, JupyterHub, clusternodes and GitLab & Mattermost.

A Science login usually resembles your name and does not contain periods, capital letters or an at sign (@). For example johndoe.

All settings related to your Science login, like setting your password, MFA, storage, groups and email aliases can be managed in DIY. See the DIY howto for more information.

For Students & Employees

To create your Science login:

Data storage

Bram Daams — Thu, 13 Mar 2025 12:36:19 +0000

Introduction

In our Faculty, different types of data storage are offered:

Storage class	Description	Risk for data loss
Home directories	Small (several GB), reliable, backed up storage for individuals	low
Network shares	Larger (1-200 TB), reliable, backed up storage for individuals or groups	low
Local storage	Not backed up storage on desktop computers and cluster nodes, likely to be lost in case of a hardware problem or when the machine gets reinstalled	high

Home directories

Your Science login comes with a home directory of 5GB at no costs. This is a safe place to store you work related documents. Home directories are stored on reliable hardware and backupped automatically. If you need more than 5GB of storage, and you can’t clean up some data, it can be enlarged on request.

Operations, Helpdesk, User support

Simon Oosthoek — Thu, 20 Feb 2025 15:29:55 +0000

location

Operations/helpdesk is located in room HG00.051.

Type of help available

User support for students and staff (General IT questions)
Installation and maintenance of hardware available for students, especially the computer labs and public workstations
General support of computer equipment in research departments
Assistance for, or advice with respect to,
- PC installation and software
- repairing PC’s and laptops

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.

Financial model

The faculty in general doesn’t own (m)any compute nodes, departments purchase their own servers (we can help configure these), which we install and manage during their lifetime. All clusternodes can be integrated in our SLURM cluster management.

ZFS Volumes

Miek Gieben — Fri, 12 Jan 2024 15:12:45 +0000

A new storage option has been developed by C&CZ. This page will show the technical details and properties of this storage, which will hopefully help you make a decision if this is something you want. Any storage we handout we call a “volume”. For these ZFS volumes:

Size: Storage size can be as large as you want, but smaller than the amount we can put in a single machine. Currently (2024+) we can buy machines with roughly 140-200 TB storage.
Snapshots: On this we enable snapshots, so that you can retrieve (deleted) files your self.
Backup: Each volume will be back upped to local S3 storage. This should be thought of as disaster recovery, and restoring from the cloud should (hopefully) be rarely needed.

All of these volumes are visible in DIY in the “Storage” section if you have access to them. How to order such storage can be seen here.

Cleanup disk space

Bram Daams — Fri, 24 Nov 2023 12:17:00 +0000

You might have received an email that your personal or group network disk is almost full. This articles describes some tools to identify large files/directories and cleanup disk space.

Finding large files / directories with WinDirStat (graphical, Windows)

WinDirStat is a disk cleanup tool for Windows that provides a visual representation of disk space usage. It helps you to quickly identify and understand which files and folders are consuming the most space. The program offers detailed information about each file, including type, last modified date, and file path. In addition to visualization, WinDirStat includes built-in cleanup options, enabling you to directly delete or move files within the program.

Carbon Connects

Eric Lieffers — Thu, 02 Nov 2023 15:03:10 +0000

Project: Carbon Connects

Funding Party NW Europe

Link to official website: https://sites.google.com/view/c-toolbox/home

Disk quota

Ben Polman — Wed, 13 Sep 2023 17:07:00 +0000

Your personal quota only determine the amount of disk space your own data may occupy and the number of files and folders you may have on your Windows U:\ disk or Linux home directory. Quotas may be active on other disks as well, however not all disks have quotas. The mail servers also use quotas to limit the disk space of each user’s mailbox.

Windows

On Windows desktops where the home directory is available as U: or H: disk right click on the disk, then choose Properties to view the amounts of used and available personal disk space in kbytes.

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.

Snapshots with ZFS

Miek Gieben — Wed, 05 Jul 2023 15:12:45 +0000

Network shares with ZFS as file system have the ability (which C&CZ switches on by default) to make snapshots.

A snapshot is a read-only copy of the share, made at a specific point in time. Such snapshots allow you to find previous versions of your files. On most shares, snapshots go back 45 days. After that period they are removed.

Tip

Remote Assistance

Simon Oosthoek — Fri, 27 Jan 2023 00:00:00 +0100

C&CZ helpdesk can assist you by taking over your screen using TeamViewer. In case you are requested to download TeamViewer, use the following link:

https://get.teamviewer.com/ischelpdesk

Mounting a network share

Bram Daams — Mon, 16 Jan 2023 15:12:45 +0000

What path to mount?

The storage page describes the paths for your home directory and network shares. Once you know what network share to mount, follow the steps for your operating system below.

Info

Work from Home - FNWI

Bram Daams — Wed, 11 Jan 2023 09:28:26 +0000

Also see the working from home page provided by the central IT Service Centre.

Email

User webmail or your local e-mail client.

Library

How to get access to the University Library (when you are off-campus).

BASS

BASS can only be accessed directly from the campus network or through VPN from any Internet location. Note however that from a small part of the subnets at the Faculty of Science, direct access to BASS is not possible. These subnets are the ones with servers that can be accessed from the Internet.

SSH

Wed, 21 Dec 2022 13:20:00 +0000

SSH Secure Shell

SSH is used to get a secure terminal-connection to a login server. All Linux loginservers can be reached with SSH client software.

NB: as of December 2022, not all science logins are allowed to login on the login servers anymore. Should you have trouble logging in on our loginservers, please contact postmaster.

Recommended SSH client software

Windows:
- MobaXterm. From the MobaXterm website: “MobaXterm is an enhanced terminal for Windows with an X11 server, a tabbed SSH client and several other network tools for remote computing (VNC, RDP, telnet, rlogin). MobaXterm brings all the essential Unix commands to Windows desktop, in a single portable exe file which works out of the box.” The support of OpenGL could also be a reason to start using MobaXterm. If you use it professionally, you should consider subscribing to MobaXterm Professional Edition. MobaXterm is available on the S-disc.
- Mosh (mobile Shell) when roaming and intermittent connections.
- PuTTY.
- The OpenSSH client provided by Cygwin.
Linux: Your computer should have ssh installed by default. Otherwise, install the openssh-client package. Install Mosh (mobile Shell) when roaming or having intermittent connections.
OS X: the ssh client should be available on your Mac. For graphical/X11 functionality one can install XQuartz. Install Mosh (mobile Shell) when roaming or having intermittent connections.
Android: JuiceSSH or ConnectBot. Install Mosh (mobile Shell) when roaming or having intermittent connections.

Recommended software for filetransfer

Windows: MobaXterm or WinSCP
Linux: scp
OS X and Windows: Cyberduck

SSH keys

ssh can use login and password to authenticate with the server, but you can also use ssh keys as an alternative authentication method. ssh keys are public-private key pairs that you can generate using the ssh-keygen command on linux. Read the manpage man ssh-keygen to learn more. You can set a password on the private key, to prevent it from being copied and used by someone else to impersonate you.

About Phishing via e-mail

Simon Oosthoek — Fri, 16 Dec 2022 00:00:00 +0100

Phishing

Trying to acquire useful data, ie login credentials, for abusing someone else’s ICT infrastructure.

Methods of phishing

In general, phishing works by send a clickable link surrounded by an important message about Salary, payment or a prize, a punishment or fee. This distracts your rational mind and ensures your emotional response controls your mouse-clicking finger.

Tip

OriginLab

Tue, 08 Nov 2022 16:37:04 +0000

OriginLab

Origin by Originlab is scientific graphing and data analysis software.

License

C&CZ acquired a network license for FNWI for the use of OriginPro. One can get the software and installation/licensing keys of OriginPro from C&CZ system administration.

The network license can only be used by computers on the Internet. For standalone use, there are home-use licenses included. The current support contract ends August 2026.

If you get a message that the license will expire soon and you are using a standalone version you can update the license by clicking on Activate in the Help menu.

System Development

Tue, 08 Nov 2022 09:49:45 +0100

System Development and Administration

System development and administration is located in room HG00.545.

Who are they?

Remco Aalbers
Bram Daams
Miek Gieben
Alexander Greefhorst
Wim Janssen
Eric Lieffers
Simon Oosthoek
Ben Polman
Arnoud Thörig
Erik Visser

What do they do?

System Administration takes care of

Management of the servers of the faculty and of various departments.
Back-up and restore of the data on the servers.
Management of workstations in the departments and in the computer labs and publicly available workstations: Managed PC’s with MS-Windows and/or Ubuntu Linux.

For all other computers (hundreds of MS-Windows PCs and tens of Linux PCs and MACs, not managed by C&CZ) it is understood that the owner (department) takes care of the systems management. For these systems, C&CZ system administration can try to answer questions.

X on Windows

Thu, 27 Oct 2022 15:25:24 +0000

Using X applications from your Windows PC

MobaXterm is software which is available on the S-disc. From the MobaXterm website: “MobaXterm is an enhanced terminal for Windows with an X11 server, a tabbed SSH client and several other network tools for remote computing (VNC, RDP, telnet, rlogin). MobaXterm brings all the essential Unix commands to Windows desktop, in a single portable exe file which works out of the box.” The support of OpenGL could also be a reason to start using MobaXterm. If you use it professionally, you should consider subscribing to [MobaXterm Professional Edition.

Data sharing

Simon Oosthoek — Sat, 22 Oct 2022 00:00:00 +0200

Often people want to share data, choosing the right method can be complex.

This page hopes to help you choose the right solution.

Options:

https (previously ftp)
e-mail
surfdrive
surf filesender
physical transfer
custom solution
Microsoft Teams

Situations:

one to few people
one to many people
share with public
co-authoring
moving datasets between institutions

Whenever you are sharing documents or files, be aware that restrictions apply when sharing personal information and all involved parties must explicitly accept responsibility for keeping within the legal boundaries.

Electronic Lab Journals

Simon Oosthoek — Thu, 20 Oct 2022 00:00:00 +0200

Availability of Elab software

ElabFTW

Chemotion

TODO

Mailman lists

Bram Daams — Sat, 15 Oct 2022 00:00:00 +0200

Mailing lists

Mailman lists are highly configurable and moderatable mailman mailing lists, e.g. the list of FNWI-employees or the list of FNWI-students. Usually one can add oneself to or remove oneself from such a mailman mailing list. Every mailman mailing list has a moderator, who can approve or reject messages to the mailman mailing list. For mailman list admins: To filter spam one can choose in the Privacy options... under Spam filters as Spam filter regexp:

Email

Bram Daams — Fri, 14 Oct 2022 00:00:00 +0200

Tip

LimeSurvey

Bram Daams — Sat, 08 Oct 2022 12:38:24 +0000

Introduction to LimeSurvey

Online surveys can be used for any type of data collection, not just for marketing purposes. Possible uses of surveys are sign-up forms for conferences, questionnaires for research projects, order forms, etc. For students and employees of the beta-faculty, C&CZ offers a survey service based on LimeSurvey.

LimeSurvey is an open source web application. It currently offers:

Sending of invitations, reminders and tokens by email
Multilingual surveys
Conditions for questions depending on earlier answers (Skip Logic / Branching)
Integration of pictures and movies into a survey

Logging in

The admin login page is located at:

EmailCodes

Bram Daams — Fri, 23 Sep 2022 07:16:08 +0000

Email codes overview

ALICE-1

This is an email in which students are requested to participate in the digital course evaluation.

Recipients? All students that are registered in OSIRIS for the exam of the corresponding course.
When? Typically on the day of the exam (around 17:00).

ALICE-2

This is an email reminder in which students are requested once again to participate in the digital course evaluation.

Recipients? All students that are registered in OSIRIS for the exam of the corresponding course.
When? Five days after the ALICE-1 email, so typically five days after the exam.

ALICE-3

This is an email in which the feedback of the course are sent to the students.

Netwerk draadloos

Bram Daams — Mon, 19 Sep 2022 16:30:58 +0000

Wireless network

The wireless network that we advise to use, is eduroam. Authentication is done in one of the following ways:

Firstname.Lastname@ru.nl and RU password
Science-loginname@science.ru.nl and Science password

Employees of Science-departments can request Eduroam Visitor Access accounts, that give visitors access to a separate part of the wireless network. through C&CZ-Operations, tel. 20000. Every employee of Radboud University can provide a guest with access for the rest of the day, by providing the guest a day code (keyword). That code can be found on the the RU portal. For more information, see the ILS website. Guests can also get access through the Library of Science.

Matlab

Bram Daams — Mon, 19 Sep 2022 16:29:14 +0000

Matlab

Matlab, a “matrix laboratory” for interactive scientific calculations of The Mathworks Inc. is an integrated software package, it combines numeric calculations, data visualization and a programming language.

License

A number of departments in the university have bought shares in the network license that C&CZ has arranged for the use of Matlab. When one has bought a share, one can get the software and installation/licensing keys of Matlab for either Linux, Mac or MS-Windows, also for older versions of Matlab, from C&CZ system administration.

Installeren werkplek

Bram Daams — Mon, 19 Sep 2022 16:27:01 +0000

Installing a PC

When installing a new PC you have several options.

If the PC is not connected to the network, C&CZ can offer little or no help to install your PC. You can borrow DVD/CD’s with a Windows Operating system and application software like MS-Office, etc from C&CZ .
If the PC is connected to the network via a (PXE enabled) network interface, a fully automated installation of Windows with standard applications is possible. In this case your PC becomes a beheerde werkplek PC.
Also it is possible to install, fully automated, Ubuntu Linux with standard applications on the PC.
In both cases contact C&CZ to register your PC.

Network time (ntp)

Bram Daams — Mon, 19 Sep 2022 16:26:21 +0000

The system clocks on C&CZ managed Linux machines are being kept up to date by using the Network Time Protocol (ntp). Each machine checks at regular intervals its system clock with several designated machines on the network and adjusts their system clock when needed. Whenever the difference between the local system clock compared to the system clock of other servers gets bigger than half a second the clock will be adjusted. If the difference is smaller, the system clock will be adjusted in small steps by slowing down or accelerating a little, to avoid multiple large time adjustments. Because all systems adjust their system clock to the same ntp servers, all system clocks will eventually become synchronized. The local servers are ntp1.science.ru.nl and ntp2.science.ru.nl.

Disposal

Bram Daams — Mon, 19 Sep 2022 16:23:09 +0000

Disposal

Safe disposal of IT equipment and data carriers
The FNWI Housing & Logistics (HL) department manages a contract with an external specialized company for the secure destruction/shredding of data carriers on location. The secure metal container that is used as a temporary cache, can be found at C&CZ as of September 2022. Employees and students of the Faculty of Science can put data carriers with sensitive data in the container themselves at C&CZ. The C&CZ helpdesk can help recognizing and removing data carriers from desktops, laptops etc.

Terminal-rooms

Bram Daams — Mon, 19 Sep 2022 16:12:50 +0000

C&CZ manages a large number of machines that anybody with an Science-account can use. Students can also login to the PC’s in the computer labs, the study area and the library with their S-number and RU-password, in the RU-domain on MS-Windows. All computer labs are dual boot: during startup of the PC one can choose to boot Linux (Ubuntu) or Windows.

Available computer labs

The Science Faculty provides the following computer labs:

Thunderbird

Bram Daams — Mon, 19 Sep 2022 16:07:13 +0000

Mozilla Thunderbird is free and open-source email client software. Below are instructions to configure Thunderbird for RU MS365 mail and for Science mail.

Configure Thunderbird for RU MS365 mail.

The RU MS365 instructions do not mention Thunderbird, but there is a RU created set of instructions (pictures in Dutch).

Configure Thunderbird for Science mail.

NB: For a self managed pc after installing Thunderbird you’ll have to uncheck Launch Mozilla Thunderbird now and click Finish.

Last installation dialog screen

Thunderbird Tags

Bram Daams — Mon, 19 Sep 2022 16:05:54 +0000

Thunderbird tags

In Thunderbird you can tag a message with one or more tags by clicking on the message with the right mouse button and choosing Tag. There are five standard tags with descriptions Important, Work, etc. If the mail server is an imap server like post.science.ru.nl, then the tags are stored on the server, which means that every Thunderbird will show the tags.

It is somewhat more complicated for new tags that you can create. Thse are also stored on the imap server, but will initialy not be visible in other Thunderbird programs. One can make a new tag by clicking with the right mouse button on a message and choosing Tag -> New Tag… or using the menu Tools -> Options… -> Display -> Tags -> Add. The tag name will be used both as internal tag name and as visible description. If you alter the tag name later on, then the internal tag name will remain the same. The internal tag name (i.e. the initial tag name) will be used as tag on the imap server. A new tag will only be visible in another Thunderbird if a tag with the same internal tag name exists. So it is important the choose the right initial tag name. In particular one has to agree on a tag name if the mailbox is shared. After that everyone can change the colour and tag name, without consequences for the visibility of the tags.

Faq unix

Bram Daams — Mon, 19 Sep 2022 14:08:15 +0000

C&CZ’s Not Frequently Enough asked questions

with answers!

Last modified: 2018-03-21

For questions, contact us.

About this FAQ

Contributors

Patrick Atoon patricka@cs.kun.nl
Kees Keijzers keesk@science.ru.nl
Jos Alsters josal@science.ru.nl
Peter van Campen Peter.vanCampen@science.ru.nl
Simon Oosthoek S.Oosthoek@science.ru.nl

Linux shells

What is a shell?

The shell is a program that interprets the user’s commands and executes them on the Operating System. There are many kinds of shells, which have different interpreted languages in which to write commands.

FoxIt PDF Reader

Mon, 12 Sep 2022 06:31:56 +0000

The program FoxIt PDF Reader can be used as an alternative to Adobe Reader, it is a free program to view or print PDF files.

One reason to sometimes not use Adobe Reader is that Adobe Reader 8 produces PostScript that HP4250/HP4350 printers can’t handle, not even after a firmware upgrade. Therefore C&CZ switched to using the (slower) PCL-driver for almost all HP4250/HP4350 printers.

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

Netwerk ethergids

Tue, 05 Jul 2022 11:29:47 +0000

C&CZ Ethernet guide

All network info is, mainly automatically, saved in a database. Some info can be looked up below by searching on MAC address, IP address, room number, outlet number or hostname.

FNWI Ethergids

Did you find an inaccuracy? Please contact us[contact us].

Reparaties

Tue, 28 Jun 2022 14:59:09 +0000

The repair procedure depends on the firm that sold the machine. Whether the repair is free of charge or not, depends on the precise terms of warranty (and whether the repair is within the period of warranty or not).

Normally, PC’s sold by standard PC supplier Dustin have a warranty period of 3 years. But: be aware that this does not hold for all machines. Read the website of Dustin (formerly CentralPoint) carefully when ordering.
For other suppliers and products, a different warranty period may be applicable.

Repairs can be ordered through C&CZ: within as well as outside of the period of warranty. We can also advise when a defect is suspected.

Huisleverancier PC's

Tue, 28 Jun 2022 14:57:16 +0000

Standard supplier: Dustin (formerly CentralPoint/Scholten Awater)

The standard supplier of pc’s for Radboud University is Dustin (formerly CentralPoint/Scholten Awater since March, 2006, after several European tenders.

Limited selection

The ISC picks a limited selection of tested products with often a favourable price. These can be seen via BASS at CentralPoint in “Mijn assortiment” as RU-laptop, RU-desktop etc.

Website

From within the purchasing system BASS you can reach the website of CentralPoint with RU pricing.

Website

Fri, 24 Jun 2022 12:55:42 +0000

There are three major types of web sites in use at the Faculty of Science:

LAMP (Linux, Apache, MySQL, PHP/Perl/Python) and MediaWiki based general purpose web servers (possibly offering some high level content management system). These sites are hosted, managed and supported by C&CZ. All content management tasks are performed by the respective web site owners: institutes and scientific departments, student organisations, service departments, etc. Please contact C&CZ for more information about WWW_Services.
Externally hosted web sites (including sites hosted by ILS) for which custom management and support agreements may be in place.
Web sites based on the Radboud University’s Content Management System (CMS) (also known as IPROX, which is the name of the management software suite).

Faculty telephone and email guide

Fri, 24 Jun 2022 12:54:04 +0000

Telephone and email guide

You can search this guide for (part of the) name, phone number, room, department etc. If you are calling from outside The Netherlands first dial +31 24 36 and then the internal phone number.

RBS

Departments within the Faculty of Science can enter or adjust their guide entries themselves via RBS. All telephone contact persons have a login to edit directory data directly in RBS.

The telephone contact person also receives the telephone cost specifications, can request or cancel changes and subscriptions and, if there is reason to do so, receives information from ILS about the telephony facilities within the RU (eg rate changes, malfunctions, maintenance).

Software licences

Fri, 24 Jun 2022 12:45:46 +0000

Science software licences negotiated by C&CZ

All info can be found on the Science licenses pages. Questions: please contact C&CZ.

Most software can be found on the install share. On a PC with MS-Windows (or a Linux “Samba client”), one can connect to the service:

\install.z.science.ru.nl\install

RU software licences negotiated by ILS

ILS negotiated license agreements for the RU for a number of software packages. This makes that software relatively cheap (bulk license) or even free (campus license) for use by students and employees.

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.

Address

Fri, 24 Jun 2022 12:17:55 +0000

Visiting address

C&CZ is situated in the Huygens building, ground floor, next to the entrance of wing 5. The room number is HG00.051, the systematics behind the room numbers is explained on the website of the [housing & logistics department HL](http://www.ru.nl/fnwi/ihz https://www.radboudnet.nl/science/faculty-services/faculty-services-d-tot-en-met-k/housing-logistics-hl/).

C&CZ, FNWI, Radboud University Nijmegen
HG00.051
Heyendaalseweg 135
6525 AJ Nijmegen

Postal address

Radboud Universiteit Nijmegen
Faculty of Science
C&CZ
Postbus 9010
6500 GL Nijmegen

Further questions or information contact C&CZ.

Printing workarounds

Wed, 25 May 2022 13:44:50 +0000

Info

Labservant

Luuk Van Summeren — Thu, 19 May 2022 12:05:09 +0000

General

Account

The procedure below only works for employees with an U-number. For access with an E-number account please contact labservant@science.ru.nl

All employees and guests who need to access to labservant can obtain an account using the following steps:

Request labservant access via the secretariat of your department, they can grand labservant access via RBS.
After labservant access is granted in RBS, login to labservant using your RU account (https://labservant.science.ru.nl)
During your first logon an account is created based on your personal data in RBS
After a successful login (you should see the Labservant home screen), the lab-manager of your department can grant you the authorizations needed.

When the message “Logged in but no verified check” is displayed after logon, try to login again using a capital letter in your user name (U-number). If the message persists the most probable cause is that labservant access was not granted in RBS by your department’s secretariat.

ChemDraw Prime / ChemBioOffice

Ben Polman — Tue, 05 Apr 2022 11:52:47 +0000

Starting December 2022 the ChemOffice+ license is being replaced by a ChemDraw Prime campus license.

ChemDraw Prime is a complete “entry-level” drawing program that provides all the tools you need to quickly create chemically intelligent, publication-ready chemical structures and reactions, laboratory notes and experiment write-ups. As well as a full set of chemical structure essentials such as rings, bonds, chains, atoms and functional groups, ChemDraw Prime includes chemical and lab equipment templates and handy TLC and Gel Electrophoresis Plate drawing tools.

LabVIEW

Fri, 18 Mar 2022 13:43:09 +0000

C&CZ administers the licenses for the use of LabVIEW within FNWI. LabVIEW by NI is a graphical programming environment engineers use to develop automated research, validation, and production test systems.

From version 2022Q3 LabVIEW no longer works standalone and unlimited in terms of time. C&CZ manages a LabVIEW license server with a small number of licenses that have to be renewed every year. Users of this license must be registered on the license server.

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.

Mathematica

Sun, 05 Dec 2021 23:34:06 +0000

Mathematica is a mathematical software package made by Wolfram Research.

C&CZ manages the network license for the concurrent use of Mathematica within Radboud University.

The license for a small number, ca. 20, of concurrent users of Mathematica, is paid for by C&CZ and may be used freely by students and staff of the Faculty of Science. Until the end of 2023, there temporarily was an unlimited license for all RU staff and students. Users/departments from other parts of the campus can use Mathematica for a yearly reimbursement of the license costs.

Maple

Sun, 05 Dec 2021 23:25:59 +0000

Maple by Waterloo Maple’s Maplesoft is an interactive computer-algebra system, for which C&CZ has acquired a license.

The license of Maple is a 4-user concurrent license in 2023 and a 2-user in 2024.

GitLab

Bram Daams — Fri, 03 Dec 2021 16:33:36 +0000

About GitLab

“GitLab is an incredibly powerful open source code collaboration platform, git repository manager, issue tracker and code reviewer.” Quoted from the GitLab website

Logging in

Info

VPN

Wim Janssen — Fri, 24 Sep 2021 10:55:58 +0000

VPN

A VPN makes it possible to get secure access to the internet or to the campus network from anywhere. The computer at home (or anywhere on the internet) in the latter case becomes part of the campus network. In this way you can get access to services that are normally only accessible from computers on campus. The most common of such services are connecting to disk shares or to special servers.

Printing

Wim Janssen — Mon, 10 May 2021 19:13:27 +0000

Printing

Through the Radboud University printing system, students and employees are able to print, scan, and copy anywhere on campus, regardless of the location or building at which they study or work. When printing, you send your print job to a print queue instead of a specific printer. The next step is to simply retrieve your print job from any printer. Read more…

Printing from own laptop.

In case printing does not work on self managed devices, documents can be uploaded to https://peage.ru.nl. Other workarounds are described here.

MestreNova

Luuk Van Summeren — Mon, 26 Apr 2021 15:31:55 +0000

Mnova is a multivendor software suite designed for processing data from NMR, LC-MS, GC-MS, and Electronic & Vibrational Spectroscopic techniques (UV-VIS, FT-IR etc.).

Mnova is available for installation on Windows, Linux, and MacOS machines. Employees and students from the Faculty of Science can install mestreNova under the university site licence on their personal computer.

Currently the faculty holds a site license for MNova 15. Installation & license files can be found on the install share in \install\science\MestreNova.

Laptop pool

Fri, 14 Aug 2020 08:36:14 +0000

Lending laptop pool

General remarks

The Faculty of Science has a pool of 60 RU-standard laptops that can be lent by employees and students of the Faculty. These are standard-RU laptops. They are almost identical in use to the pc’s in the computer labs. The main difference is that reservation is not through Housing & Logistics.

The reservation of the laptops is administered by the Library of Science. Use for FNWI education has precedence.

CourseFiles

Tue, 23 Jun 2020 16:22:15 +0000

How can I access my course file?

The course files is an network disk that can be attached on campus. Off-campus, VPN must be used to attach this network disk. More info on how to attach a network disk and on using VPN is available. Linux users have the alternative to login with ‘ssh’ on the Science loginserver lilo, followed by a cd to /vol/cursusdossiers.

Windows:

At ‘File Explorer’, choose the option ‘Map Network Drive’, and type in file://cursusdossiers-srv.science.ru.nl/cursusdossiers and pick your drive letter of choice. By doing so, you will link up the network disk to your local computer. The next options are also possible to get a more limited set of courses:

Intel compilers

Thu, 26 Sep 2019 15:40:21 +0000

New Intel compilers (Intel OneAPI Base and HPC Toolkits)

The newest versions of the Intel compilers, available under the name Intel OneAPI, do no longer require a license, they are freely available. The 2023.2 version has been installed on C&CZ managed Ubuntu systems. When they are available, the module command

module avail

will list among others “compiler/latest”, so e.g. the Intel C (icc) and Fortran (ifort) compilers can be used after typing

Internet studenten

Fri, 06 Sep 2019 16:16:30 +0000

students

WWW by students

All student associations of the Science Faculty have their own WWW service. These are

Thalia (Computer Science), 1
Desda (Mathematics), 2
Sigma (Chemistry), 3
Marie Curie (Physics), 4
BeeVee (Biology), 5
Leonardo (Sciences), 6

Students who would like to start their own www service are advised to contact their association using the association’s website or by sending a mail to one of the mail addresses.

If that doesn’t work out you can always visit C&CZ and talk to one of the system administrators to see if it is possible to start a new WWW service.

Informatiebeveiliging

Ben Polman — Wed, 13 Feb 2019 15:38:54 +0000

Information security

European directives and Dutch law prohibit the storage of personal data (persoonsgegevens) outside the European Economic Area (EEA). Most of the well known cloud services are US based: Dropbox, all Google services such as Gmail and Google+, Hotmail, iCloud. This implies that (data collections containing) personal data may not be stored on these cloud services. In addition to the law, Radboud University has issued an internal security policy that prohibits the storage of data that is classified as critical (this includes all personal data) on any (public) cloud service, even those which are EEA based. However, RU considers SURFnet’s SURFdrive, SURFfilesender and edugroepen as safe community cloud services for data exchange between RU employees, students, and external parties.

Proquota

Tue, 27 Nov 2018 09:41:23 +0000

ProQuota, what does it do ?

When you log in on a managed PC, your private settings (Profile) of Windows and the applications are copied from the network to your current PC. During the session, these copied settings on the PC are used and changed if necessary. At logout, the (altered) settings are copied back to the network. When you log in, at a later point in time, on a different managed PC, these settings are copied to the new PC and your own settings are available again. You may locate these settings under C:\Documents and Settings\<loginname>.

Email sieve

Wed, 27 Jun 2018 05:42:46 +0000

Sieve

If one wants incoming mail to be sorted into folders automatically or to be filtered in some special way, one can use “Sieve” if one has the IMAP-server post.science.ru.nl as incoming mailserver.
To put the sieve script on the mail server and activate it, use a mail program which supports sieve. The filter settings can be managed quite easily in Roundcube webmail with Settings -> Filters. It is also possible with e.g. KMail or Thunderbird with the sieve addon.
On lilo4 you get with the command sieve-connect postvak.science.ru.nl an interactive commandline where you can use the command put to upload a sieve script.
The Sieve language is described in RFC3028.

Install share

Wed, 10 Jan 2018 15:14:49 +0000

Most licensed software that can be freely used by students and staff of the Science faculty can be found in the install network share.

You can connect the install share in MS Windows using the path:

\\install-srv.science.ru.nl\install

Info

Netwerk mutaties

Fri, 03 Mar 2017 10:51:40 +0000

NOT_YET_TRANSLATED

Medewerkers latexbrief

Wed, 21 Sep 2016 08:20:41 +0000

RU Corporate Identity Information

Starting September 1, 2004, a new corporate identity has been introduced in which the name and logo of the university changed, but also the layout of all printed material. For MS-Word, templates and manuals have been centrally developed. Information can be found elsewhere. For LaTeX C&CZ developed a new letter layout.

RU letter layout for LaTeX

The new version supports an English and a colored version of the logo.

Subversion

Simon Oosthoek — Wed, 01 Jun 2016 07:34:28 +0000

Info

Network profile

Wed, 25 Nov 2015 14:12:31 +0000

Manual for the BW-PC for students

How to log in faster and not lose data.

Introduction

Regularly students complain about the time it takes to log into and out from PC’s in the computer labs. This manual explains the reason behind it and what you can do about it yourself.

Working with the C&CZ Profile and Home-disk (H:\)

In order to have your own settings (your “profile”), C&CZ uses three central computers, the so-called “Domain Controllers”. Your profile consists of all kind of user-specific stuff like desktop background, shortcuts on your desktop and all kinds of user-specific settings of programs (e.g.: recently opened documents in Word, recently typed commands in Matlab etc.). You can find these settings in “C:’‘/Documents and Settings/<inlognaam>/”. All of this profile is copied when you login, from the Domain Controller to your local computer because Windows needs these settings often and fast to run your prograns fast. When you logout, all changes are copied back to the Domain Controller, in order to have an up-to-date copy that is needed when you login to a different PC. Next to your profile disk space (30 MB) every user also has a Home-disk (home-directory, H:\, ’My Documenst’) for large documents, reports, pictures etc. This drive is usually at least 200 MB large. This home-directory is *not* being copied when you log in or out, it is part of a central C&CZ server that is reachable through the network as (H:\ , ‘\\manus\<inlognaam>’ of ‘\\pluri\<inlognaam>’).

T-schijf

Fri, 14 Nov 2014 11:44:26 +0000

T-disk

On pc’s in computer labs which are managed by C&CZ, not only the S-disk is available but also the T-disk (a network share). On this network share, a large number of programs for a large number of courses is available that can be run directly from this share (no local installation on the pc necessary). Lecturers can manage the course software themselves. These programs may also be used on pc’s that are not managed by C&CZ.

S-schijf

Fri, 14 Nov 2014 11:32:29 +0000

S-disk

On pc’s managed by C&CZ the S-disk (a network share) is available by default. On this share a large number of programs is available that can be run directly form this share (no local installation needed). These programs can also be used on pc’s not managed by C&CZ.

Attach the network share as \\software-srv.science.ru.nl\software using Drive letter S because some software might depend on the driveletter S.

Pine

Fri, 14 Nov 2014 09:31:06 +0000

Pine

Use ‘S’ for SETUP and then’C" for Config and fill in:

  smtp-server    = smtp.science.ru.nl/user=...
  inbox-path     = {post.science.ru.nl/ssl/user=...}INBOX

where … should be replaced by your login name

To see the other IMAP folders, use ‘S" for SETUP and then ’C’ for Config and change:

  [ Folder Preferences ]
            [X]  combined-folder-display
            [X]  expanded-view-of-folders
            [X]  quell-empty-directories

Ook nog binnen SETUP: kies ‘L’ voor collectionLists en maak met ‘A’ twee nieuwe collection lists:

Hardware werkplekken

Fri, 17 Aug 2012 14:33:34 +0000

PC workstation

Everyone interested in buying a PC will be interested in reading the information about the default supplier of PCs. C&CZ can help with the installation or do this completely. One can choose between MS-Windows and Ubuntu Linux. Information about the repair procedure is also available.

Thunderbird Add-ons

Wed, 09 Apr 2008 22:21:43 +0000

abcTajpu
- Copy Sent to Current
- Folderpane Tools
- GMailUI
- Lightning
- Provider for Google Calendar
- New Mail Icon
- Nostalgy
- Quicktext
- Signature Switch
- ThunderBrowse
- Xnote
- MailClassifier
- Tag bar
- Priority Switcher
- MailTweak
- Mail Redirect
- View Headers Toggle Button
- Display Mail User Agent Extension
- FolderFlags

More add-ons can be found at addons.mozilla.org.

Email vakantie

Wed, 09 Apr 2008 22:19:36 +0000

Automatically respond to incoming email

The settings to automatically respond to incoming email can be changed at the Do-It-Yourself website.

If a (vacation) message is sent for incoming email, each sender of a mail that is directly sent to you (no BCC:), gets only once a mail with the text you have specified.

If one does not want to send automatic replies anymore, the (vacation) message is saved for later use.

Mon, 01 Jan 0001 00:00:00 +0000

Institute/Service	Department	Lab Manager(s)
Donders Centre for Neuroscience
DCN	Section Neurobiology	Debbie Tilburg-Ouwens
DCN	Section Neurophysics	Debbie Tilburg-Ouwens
High Field Magnet Laboratory & FELIX
HFML/FELIX	FELIX Facility	Jonathan Martens Britta Redlich
HFML/FELIX	High Field Magnet Laboratory	Hans Engelkamp
Institute for Molecules and Materials
IMM	Analytical Chemistry & Chemometrics	Joris Meurs
IMM	Applied Materials Science	Peter Mulder
IMM	Biophysical Chemistry	Frank Nelissen Amrah Weijn
IMM	Biomolecular Chemistry	Amrah Weijn Frank Nelissen
IMM	Molecular and Laser Physics	Andre van Roij
IMM	Molecular Chemistry Cluster	Samuel Bosma Jan Dommerholt
IMM	NMR Research Centre	Ruud Aspers
IMM	Physical Chemistry of Soft Matter	Ruth Croters
IMM	Scanning Probe Microscopy	Henning von Allwörden
IMM	Solid State Chemistry	Erik de Ronde Paul Tinnemans
IMM	Spectroscopy of Cold Molecules	Andre van Roij
IMM	Utlrafast Spectroscopy of Correlated Materials	Chris Berkhout
Radboud Institute for Biological and Environmental Sciences
RIBES	Ecology	Niels Wagemaker Annemiek Tiekstra
RIBES	Environmental Sciences	Martien Graumans Katinka van de Pas-Schoonen
RIBES	Experimental Garden and Genebank	...
RIBES	Microbiology	Katinka van de Pas-Schoonen Rob de Graaf
RIBES	Plant & Animal Biology	Jan Zethof Daan van den Brink
RIBES	RIBES Radio Lab	Jan Zethof
Educational Institutes
OBW	Education Labs Biosciences	Lydia Ketelaars Guus Middelbeek
OMW	Education Labs Molecular Sciences	Tom Bloemberg Luuk van Summeren
ONS	Education Labs Physics	Luuk van Summeren
Radboud Institute for Molcular Life Sciences
RIMLS	Molecular Biology	Anita Kaan
RIMLS	Molecular Developmental Biology	Siebe van Genesen
RIMLS	Proteomics and Chromatin Biology	Pascal Jansen
Supporting Services
GI	General Instrumentation	Sebastian Krosse
Housing & Logistics	Logistics Centre	Ruud Patings Patrick van de Vooren Nicky Boschman
TeCe	Techno Centre	Luuk van Summeren

Howto on C&CZ News

Contact

Helpdesk & Sysadmin

Visiting address

Slurm and High Performance Computing

Computer cluster architecture

WWW Service

Starting a new WWW service

Contact Communications

Servers

Servers and Workstations

Workstations

Login

Science login

For Students & Employees

Data storage

Introduction

Home directories

Operations, Helpdesk, User support

location

Type of help available

High Performance Computing

Financial model

ZFS Volumes

Cleanup disk space

Finding large files / directories with WinDirStat (graphical, Windows)

Carbon Connects

Project: Carbon Connects

Funding Party NW Europe

Disk quota

Windows

Module command for optional software versions

Snapshots with ZFS

Remote Assistance

Mounting a network share

What path to mount?

Work from Home - FNWI

Email

Library

BASS

SSH

SSH Secure Shell

Recommended SSH client software

Recommended software for filetransfer

SSH keys

About Phishing via e-mail

Phishing

Methods of phishing

OriginLab

OriginLab

License

System Development

System Development and Administration

Who are they?

What do they do?

X on Windows

Using X applications from your Windows PC

Data sharing

GDPR (Dutch: AVG)

Electronic Lab Journals

Availability of Elab software

ElabFTW

Chemotion

Mailman lists

Mailing lists

Email

LimeSurvey

Introduction to LimeSurvey

Logging in

EmailCodes

Email codes overview

ALICE-1

ALICE-2

ALICE-3

Netwerk draadloos

Wireless network

Matlab

Matlab

License

Installeren werkplek