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# Cubbli Linux
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Cubbli (**C**ommon **Ub**untu **B**ased **Li**nux) is the official Linux distribution of University of Helsinki.
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The current version of Cubbli Linux (Cubbli 22) is based mostly on Ubuntu 22.04. Cubbli 20 will receive updates until further notice. Cubbli 18, which is based on Ubuntu 18.04, is still getting security updates until April 2023 but will no longer receive software updates. If you wish to have the newest available software you should [upgrade your Cubbli version](https://wiki.helsinki.fi/display/it4sci/Upgrading+or+reseting+a+Cubbli+installation).
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Cubbli Linux comes preconfigured to the University's environment, which means that accessing University's network services, like printers, file shares, virtual desktops, remote accessible Linux machines, High-performance computation (HPC) clusters and Virtual private networks (VPNs) should be easy.
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If your computer is using any other older Linux distribution, including older Cubbli Linux distributions, you should contact cubbli-upgrade(at)helsinki.fi to get an upgrade. In most situations the update can be done remotely and shouldn't take more than 1-2 hours. [You can also do the upgrade yourself](https://wiki.helsinki.fi/display/it4sci/Upgrading+or+reseting+a+Cubbli+installation).
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For seeing the version of a specific software installed in the computer, you can, for example (from the command line):
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<table>
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<tr>
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<td>
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<pre>
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\# list everything
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$ dpkg --list
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\# check specific package, for example Zoom version
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$ dpkg --list | grep zoom
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ii zoom 5.9.3.1911 amd64 Zoom Cloud Meetings
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\# check availability of a package with apt
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$ apt list zoom zoom/stable,stable,now 5.9.3.1911 amd64 \\\[installed\\\]
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</pre></td>
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</tr>
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</table>
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## Different Cubbli Linux flavors
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* Classroom installations use shared network home directories. They are mostly located in publicly accessible spaces where there are multiple potential users, like classrooms and lecture halls.
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* Remotely accessible VDI (Virtual Desktop Infrastructure) hosts share network home directories and default to Mate desktop environment, since 3D hardware accelerated graphics is not available in our current VDI environment.
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* Workstation installations have local home directories, but network file shares are available by default. These are mostly staff's personal computers and can have multiple hard drives (a fast SSD drive and a slower but larger spinning hard drive) and sometimes GPUs for scientific computation.
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* Personal laptop installations don't have network home directories available (mounted) by default. These include staff's laptops, but also freshmen (fuksi) laptops.
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* Remotely accessible with `ssh` (or `mosh`) interactive multi user Cubbli hosts, which use shared network home directories. Currently these are **melkinpaasi.cs.helsinki.fi**, **melkinkari.cs.helsinki.fi**, **melkki.cs.helsinki.fi** and **pangolin.it.helsinki.fi**. These hosts can also be used as a gateway host to other Linux hosts which provide SSH access, but are not visible outside University's firewall. They also listen for SSH connections in HTTPS port 443 to circumvent 3rd party firewalls.
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## Home Directories
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In a perfect world users would have only one home directory. However, we aren't living in a perfect world:
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* Laptop and workstation Cubbli Linuxes use local home directories with a home directory path `/home/local/user` or sometimes just `/home/user`. **By default no backups are made of local home directories**, since we don't have enough shared disk space (or network capacity) to maintain them.
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* Classroom, interactive and VDI Cubbli Linuxes use shared NFS **lxhome** directory with path `/home/ad/lxhome/u/user/Linux`_._ This home directory has a default quota of 50 gigabytes, but it is regularly backed up and you can access snapshots of older versions of files from a hidden `.snapshot` sub directory.
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* Computer Science department CS home directory `/home/fs/user` is available to Computer Science department's staff and students. It has a much larger quota than the default **lxhome** directory. You can use the command line tool `cubbli-home-dir` to change your default Cubbli home directory to CS home directory instead of `lxhome`.
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* Z-drive is the default IT department home directory for Windows hosts and is available for Linux users too. It is available from path `/home/ad/home/u/user`_._ If you are using classroom, VDI or interactive Linux, then _Desktop, Download and Documents_ subdirectories in `lxhome` are symlinks pointing to your Z-drive to enable easy document and space sharing with Windows installations.
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* Physics department's home, group and scratch directories are available from path `/home/phys-data/`
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* If you had a home directory in the old and now defunct Unix servers (Kruuna, Klaava, Myntti, Cedi), the home directory is now available from path: `/home/ad/lxhome/u/user/HY-Unix`
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## Group Directories
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* University's P-drive group directories are available from path `/home/ad/dfs/group` in workstations and classroom installations. Laptop users can use command `mount /home/ad/dfs/group` to mount it when they are inside University's network. Outside University's network you can use Pangolin and SFTP with path [`sftp://`](sftp://pangolin.it.helsinki.fi/home/ad/dfs/group)`pangolin.it.helsinki.fi/home/ad/dfs/group` .
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* Computer Science Department's group directories are available from path `/home/group/` in workstations and classroom installations. In laptop installations you can mount the group directory with the command `mount /cs/group` but remember to unmount it before suspending the laptop or moving outside University's network (NFS is likely to crash the Linux hosts if NFS server gets lost).
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## Desktop
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The desktop environments available by default include:
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* Cinnamon
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* Mate
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* Unity
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* Gnome
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* KDE
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* XFCE
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And also some windows managers which aren't available directly from the login screen.
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Dropbox, Google Chrome, Skype (MS beta package), Spotify local client and Open Broadcast Streaming (https://obsproject.com/) are available by default.
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## Programming
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We try to have all open source and freely available Linux programming languages and programming environments installed by default (this is why default Cubbli installation needs about 50G of disk space). The programming languages include GNU C, C++, Perl, Python, OpenJDK, Oracle JDK, Haskell and Rust. Unlike in University's Windows environments, you are free to compile, install and run your own software (from your home directory). Node.js, Heroku and npm are installed.
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If we have missed some useful programming languages, environments or utilities, please make an issue here or contact helpdesk@helsinki.fi so that we know that it should be installed.
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Nvidia CUDA drivers and programming environment with the NVIDIA CUDA® Deep Neural Network library is installed by default in Cubbli Linux hosts which have the required Nvidia GPU (including VDI GPU hosts).
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## Scientific Software
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Cubbli includes lots of software intended for scientific usage, including some commercially licensed software using University's licenses (this list is not complete).
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* R project for statistic computing version: https://www.r-project.org/
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* RStudio Desktop open source version.
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* GNU Octave Scientific Programming Language https://www.gnu.org/software/octave/
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* Julia, [high-level, high-performance dynamic programming language for numerical computing](https://julialang.org/)
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* Matlab
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* IDL [Interactive Data Language](https://www.harrisgeospatial.com/SoftwareTechnology/IDL.aspx)
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* SPSS
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* Qgis Open Source Geographic Information System
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* NoMachine Enterprise client
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Some software packages are too large to be installed in the default installation, but are however packaged and configured to work with Cubbli Linux. These include:
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* FreeSurfer open source software suite for processing and analyzing (human) brain MRI images. https://surfer.nmr.mgh.harvard.edu/
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* Mathematica
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* SPSS
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* VMD Visual Molecular Dynamics: [http://www.ks.uiuc.edu/Research/vmd/](http://www.ks.uiuc.edu/Research/vmd/%EF%BF%BC)
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Cubbli Linux is maintained by [IT Center's IT for Science group. ](https://wiki.helsinki.fi/display/it4sci/Cubbli+Linuxonhttps://wiki.helsinki.fi/display/it4sci/Cubbli+Linuxon)
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Copypasted from https://wiki.helsinki.fi/display/it4sci/Cubbli+Linux on 5.9.2022. |
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