Ubuntu computer room facilities

Important changes

Ubuntu software image in computer rooms will be phased out by the end of 2021

After extensive communication with all current users (teachers) of the Ubuntu software image, we have decided to phase out this service at the end of 2021. Almost no courses are using the Ubuntu OS and software, for those that do we will find an acceptable alternative. Please let us know if you don't have an alternative yet. Please contact: s.holleman@uu.nl Below you find an excerpt of the communication:

It's been almost a year since we were able to use the UU computer rooms (and Linux software) for education. In this year we have developed X2Go (remote Linux desktop) as a flexible alternative for off campus software use. In the end only one course made use of this facility, all others have found different alternatives for running Linux software. We intend to phase out X2Go and the linux image in the UU computer rooms because of increasing demand for flexibility in booking education rooms and frankly: there is no future for this setup in the long run (security, maintenance, flexibility). Based on this year's experience there are quite a number of alternatives: Jupyter notebooks setup, CoCalc, local install and remote desktop to name a few. Based on this years' experience, you probably already found an alternative, otherwise we would like to help you find it for your future educational setup. Our aim is to have this done by the end of 2021.

Alternatives to on campus computer room (CLZ) usage

Following the extended closure of the Utrecht Science Parc you may encounter additional challenges to provide for your courses that make use of software.

In general: UU computer rooms were already using https://myworkplace.uu.nl, so all software is available to students online in the same way as before in the computer rooms. In preperation to using myworkplace, you could point out to students once more what needs to be setup on a laptop, but this should be commonplace by now: https://students.uu.nl/myworkplace

Linux/Ubuntu software is unfortunately not completely available online. We are looking into alternatives, but as each courses’ setup is tailor made, this is not an easy task. Here are some suggestions for alternatives we can think of:

- Linux software that doesn’t require graphics intensive calculations may be performed on the Gemini server (all students already have a Gemini account) https://ict.science.uu.nl/index.php/Gemini_FAQ

- In case of graphics intensive software, you could consider creating Python code which students can run locally on their laptops.

Other alternatives we can think of (but may not apply to your specific situation):

- Virtualization under VirtualBox or likewise (https://www.virtualbox.org)

- Windows (10) subsystem for Linux: provides an application called Bash.exe that, when started, opens a Windows console running the Bash shell. Using Bash, you can run command-line Linux tools and apps. (https://docs.microsoft.com/en-us/windows/wsl/about)

- CoCalc environment (https://cocalc.science.uu.nl, about: https://doc.cocalc.com )

- MyWorkplace (some comparable software is available, for an overview of software: https://students.uu.nl/sites/default/files/myworkplace_applicaties_feb2020_website_v5.00.pdf)

All questions for support can be directed through TopDesk: https://uu.topdesk.net This also includes help in setting up any of the alternative environments. We will assist you to our best abilities.

Changes with Ubuntu 18.04 LTS to clz image: 08-07-2019

Home directory

You now have a local home directory in /nethome/"solis-id"

Your Bèta home directory ( S drive ) is not mounted by default anymore!

In the near future your home directory will be available as /science/users/"solis-id"

Mounting your old home directory staff/students

Open Nautilus filemanager from Dash sidebar ( Archive icon )

Select Other Locations

Connect to server smb://storage3.science.uu.nl/"solis-id"

Connect

Bookmark specific folders in Nautilus filemanager

Open Nautilus filemanager from Dash sidebar ( Archive icon )

Select Other Locations

Click on Computer

Browse to the folder you want

Press ctrl - D to bookmark this folder

On the left side of Nautilus an icon represent your current selection

This bookmark will continue to exist for subsequent logins

To remove this bookmark

Right click bookmark and select Remove

Users with a migrated / new home directory can bookmark their user directory

/science/users/"solis-id"

Mounting solis U drive

Mount your U-drive with the script: udrive It will ask for your solis password.

Your solis U-drive data are now accessable via /udrive and will be disconnected on logout.

Check diskspace

Check yourself if the local system disk is getting low on diskspace with the following terminal command:

 df -h /

See value at Use% column.

Make regularly a backup of important data to your home directory or U-drive.

Project space

General project folders are now mounted via: /science/projects/"project name"

Specific folders for education, like; aw, bio-binf, molmod and structbiol are mounted via /science/projects/clz-local/"project name"

Info for teachers

              For those of you with write permission.
              The project spaces /science/projects/clz-local/"project name" are also
              accessable via gemini.science.uu.nl and can be used to update your
              software and documentation yourself.

Applications

The icon Show Applications (9 dots icon, lower left corner on Dash sidebar ) displays the most important user applications. Select all to see all applications.

Environment setup for specific applications

First open a terminal window ( ctrl alt t )

Using root package: go to a directory with write permissions and

                         source /science/projects/clz-local/apps/root/bin/thisroot.sh

Using crystallography programs:

                         go to a directory with write permissions and
                         source /science/projects/clz-local/apps/kristal/setup_env.sh

You can read this text again with the program changes-clz (top icon in Dash sidebar)

Exchange files

Use Filezilla to exchange data with other netwerk storage.

HowTo

Click Filezilla icon from Show Applications (9 dots icon, lower left corner on Dash sidebar ) to start the program

- Open Site Manager from File menu

- Select New Site

Fill in some fields:

Host: gemini.science.uu.nl Protocol: SFTP - SSH File Transfer Profocol Logon Type: Ask for pasword

- Connect

 Remember passwords?

- Do not save passwords

 OK

Enter username and password

 OK

Unknown host key

 OK

Now your files should appear in Remote site window pane.

To exchange data just drag and drop file from Local site to Remote site or visa versa.

Disconnect from currently visible server by selecting icon with red cross in toolbar.

Log out from Ubuntu desktop

Select Power off / Down arrow from top right corner desktop Select your account and logout

Shutdown or restart PC

After log out select Power off icon again and select shutdown or restart.

Automatic reboot

At 11 pm this PC will shutdown from Linux and reboot to allow installing MSWindows updates.