Wiki source code of User documentation
Last modified by Mikko Halmela on 2024/03/18 13:24
Show last authors
| author | version | line-number | content |
|---|---|---|---|
| 1 | The current version of Cubbli Linux (Cubbli 22) is based mostly on Ubuntu 22.04. Cubbli 20 and Cubbli 18, which are based on older Ubuntu versions are still getting security updates until April 2023, but will no longer under active development. If you wish to have the newest available software you should upgrade your Cubbli version (see link below). | ||
| 2 | |||
| 3 | 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. | ||
| 4 | |||
| 5 | 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 s ituations the update can be done remotely and shouldn't take more than 1-2 hours. You can also do the upgrade yourself. | ||
| 6 | |||
| 7 | [[Instructions for upgrading Cubbli yourself is found here>>https://wiki.helsinki.fi/xwiki/bin/view/Cubbli/User%20documentation/Upgrading%20or%20reseting%20a%20Cubbli%20installation/||shape="rect"]] | ||
| 8 | |||
| 9 | |||
| 10 | For seeing the version of a specific software installed in the computer, you can, for example (from the command line): | ||
| 11 | |||
| 12 | {{code language="bash"}} | ||
| 13 | # list everything | ||
| 14 | $ dpkg -l | ||
| 15 | |||
| 16 | # check specific package, for example Zoom version | ||
| 17 | $ dpkg -l | grep zoom | ||
| 18 | ii zoom 5.9.3.1911 amd64 Zoom Cloud Meetings | ||
| 19 | |||
| 20 | # check availability of a package with apt | ||
| 21 | $ apt list zoom | ||
| 22 | zoom/stable,stable,now 5.9.3.1911 amd64 [installed] | ||
| 23 | |||
| 24 | |||
| 25 | {{/code}} | ||
| 26 | |||
| 27 | {{expand title="Click here for older news"}} | ||
| 28 | |||
| 29 | |||
| 30 | 2021-09-06: R updated to version 4.4.1. R Studio updated to version 1.4.1717. Nextcloud updated to version 3.3.3. | ||
| 31 | |||
| 32 | 2021-09-03: Updated sofware: atom-1.58, qgis-3.20.2, Zoom-5.7.31792.0820, Nextcloud 3.3.1, vmware-horizon-client 2106-8.3.0-1 | ||
| 33 | |||
| 34 | 2021-06-07: Updated software: qgis 3.18.2, atom-1.57.0, Zoom 5.6.20278.0524 and Nextcloud 3.2.2 | ||
| 35 | |||
| 36 | 2021-05-06: Updated irssi to irssi-1.2.3 | ||
| 37 | |||
| 38 | 2021-04-28: [[Short instructions to printing>>doc:Cubbli.User documentation.Printing.WebHome]] added to wiki. | ||
| 39 | |||
| 40 | 2021-04-19: Nvidia CUDA 11-3 has been installed. | ||
| 41 | |||
| 42 | 2021-04-19: Qgis version 3.18.2 | ||
| 43 | |||
| 44 | 2021-04-15: Featherpad editor added to default applications. | ||
| 45 | |||
| 46 | 2021-04-13: Solaar version 1.0.4 supports Logitech lightspeed receivers in addition to Nano and Unified receivers. | ||
| 47 | |||
| 48 | 2021-04-12: [[Nextcloud>>url:https://nextcloud.com/||shape="rect"]] upgraded to version 3.2.0 | ||
| 49 | |||
| 50 | 2021-04-06: Fix chromium browser problems by removing the snap package and installing deb-package instead. | ||
| 51 | |||
| 52 | 2021-04-06: Update [[Cinnamon Desktop>>url:https://en.wikipedia.org/wiki/Cinnamon_(desktop_environment)||shape="rect"]] to version 4.8.1 (supports non integer HIDPI scaling). | ||
| 53 | |||
| 54 | 2021-04-06: Updates: Zoom 5.6.13632.0328, Cryptomator 1.5.14 | ||
| 55 | |||
| 56 | 2021-03-26: [[xournal++ >>url:https://github.com/xournalpp/xournalpp||shape="rect"]]added to default installation. | ||
| 57 | |||
| 58 | 2021-03-26: [[No Machine clients>>url:https://www.nomachine.com/||shape="rect"]] updated to version 7.3.2. | ||
| 59 | |||
| 60 | 2021-03-23: Some new instuctions for [[MS Teams users>>doc:Cubbli.User documentation.Microsoft Teams.WebHome]]. | ||
| 61 | |||
| 62 | 2021-03-22: Qgis updated to version 3.18.1. | ||
| 63 | |||
| 64 | 2021-03-18: [[melkinpaasi.cs.helsinki.fi>>url:http://melkinpaasi.cs.helsinki.fi||shape="rect"]] remote accessible ssh host has been upgraded to Cubbli 20 / Ubuntu 20.04- | ||
| 65 | |||
| 66 | Matlab 2020b release 5 is now installed by default in Cubbli 20. | ||
| 67 | |||
| 68 | [[Cubbli version 20>>doc:Cubbli.User documentation.Archived pages.Cubbli 20\.04 project.WebHome]] based on [[Ubuntu 20.04>>url:https://ubuntu.com/blog/whats-new-in-ubuntu-desktop-20-04-lts||shape="rect"]] is now in production use. | ||
| 69 | |||
| 70 | |||
| 71 | 2020-08-20: Zoom has been updated to version 5.2.446620.0816. SSO and GUI scaling bugs have been fixed. | ||
| 72 | 2020-07-20: Atom text editor updated to version 1.49.0. | ||
| 73 | 2020-07-20: Rstudio updated to version 1.3.1056 | ||
| 74 | 2020-07-20: Zoom has been updated to version 5.1.422789.0705 | ||
| 75 | 2020-07-20: Nodejs has been updated to version 12.18.2. | ||
| 76 | 2020-07-20: R has been updated to version 3.6.3. | ||
| 77 | 2020-07-06: Zoom desktop client updated yet again to version 5.1.418436.0628. Release notes here. | ||
| 78 | 2020-06-12: Zoom desktop client upgraded to version 5.0.418682.0603. | ||
| 79 | 2020-06-01: Zoom desktop client upgraded to version 5.0.413237.0524. | ||
| 80 | 2020-05-13: Fish shell has been added to defautl installations. Instructions about how to use other shells has been added to wiki. | ||
| 81 | 2020-05-12: File share ~\~\[[ad.helsinki.fi>>url:http://ad.helsinki.fi||shape="rect"]]\dept (Departments' own file servers) is now available from path /home/ad/dept. | ||
| 82 | 2020-05-12: Zoom desktop client upgraded to version 5.0.399860.0429 | ||
| 83 | 2020-04-28: Zoom desktop client upgraded to version 5.0.398100.0427. | ||
| 84 | 2020-04-24: Freesurfer 6.0 is available in VDI hosts and Pultti. | ||
| 85 | 2020-04-15: Added tig, surfraw and mstmp to default installation. | ||
| 86 | 2020-04-07: Stata updated to version 16. | ||
| 87 | 2020-03-26: Instructions for OneDrive access are now available. | ||
| 88 | 2020-03-23: Zoom updated to version 3.5.361976.0301 | ||
| 89 | 2020-03-23: Rclone versio 1.51 added. | ||
| 90 | 2020-03-20: New OpenVPN configuration options available. | ||
| 91 | 2020-02-27: Matlab R2019b release 4. | ||
| 92 | 2020-02-17: Zotero has been updated to version 5.0.82. | ||
| 93 | 2020-01-29: Mendeley Desktop is now part of default installation. | ||
| 94 | 2020-01-27: Qgis has been updates to version 3.10.2 | ||
| 95 | 2020-01-27: Putty and MS Teams added to default intallation. | ||
| 96 | 2020-01-14: R has been upgraded to version 3.6.2 and RStudio to version 1.2.5033. | ||
| 97 | 2020-01-14: Nextcloud client has been updated to version 2.6.1 | ||
| 98 | 2020-01-14: ida2 command line tools for [[https:~~/~~/www.fairdata.fi/en/>>url:https://www.fairdata.fi/en/||shape="rect"]] have been installed. | ||
| 99 | {{/expand}} | ||
| 100 | |||
| 101 | |||
| 102 | == Different Cubbli Linux flavors == | ||
| 103 | |||
| 104 | * 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. | ||
| 105 | * 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. | ||
| 106 | * 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. | ||
| 107 | * Personal laptop installations don't have network home directories available (mounted) by default. These include staff's laptops, but also freshmen (fuksi) laptops. | ||
| 108 | * 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. | ||
| 109 | |||
| 110 | == Home Directories == | ||
| 111 | |||
| 112 | In a perfect world users would have only one home directory. However, we aren't living in a perfect world: | ||
| 113 | |||
| 114 | * 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. | ||
| 115 | * 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. | ||
| 116 | * 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. | ||
| 117 | * 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. | ||
| 118 | * Physics department's home, group and scratch directories are available from path ///home/phys-data/// | ||
| 119 | * 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// | ||
| 120 | |||
| 121 | == Group Directories == | ||
| 122 | |||
| 123 | * 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:~~/~~/pangolin.it.helsinki.fi/home/ad/dfs/group>>url:sftp://pangolin.it.helsinki.fi/home/ad/dfs/group||shape="rect"]] . | ||
| 124 | * 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). | ||
| 125 | |||
| 126 | == Desktop == | ||
| 127 | |||
| 128 | The desktop environments available by default include: | ||
| 129 | |||
| 130 | * Cinnamon | ||
| 131 | * Mate | ||
| 132 | * Unity | ||
| 133 | * Gnome | ||
| 134 | * KDE | ||
| 135 | * XFCE | ||
| 136 | |||
| 137 | (% style="text-align: left;" %) | ||
| 138 | And also some windows managers which aren't available directly from the login screen. | ||
| 139 | |||
| 140 | (% style="text-align: left;" %) | ||
| 141 | Dropbox, Google Chrome, Skype (MS beta package), Spotify local client and Open Broadcast Streaming ([[https:~~/~~/obsproject.com/>>url:https://obsproject.com/||shape="rect"]]) are available by default. | ||
| 142 | |||
| 143 | == Programming == | ||
| 144 | |||
| 145 | 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. Unlike in University's Windows environments, you are free to compile, install and run your own software (from your home directory). Nodejs, heroku and npm are installed. | ||
| 146 | |||
| 147 | If we have missed some useful programming languages, environments or utilities, please contact [[helpdesk@helsinki.fi>>mailto:helpdesk@helsinki.fi||shape="rect"]] so that we know that it should be installed. | ||
| 148 | |||
| 149 | 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). | ||
| 150 | |||
| 151 | == Scientific Software == | ||
| 152 | |||
| 153 | Cubbli includes lots of software intended for scientific usage, including some commercially licensed software using University's licenses (this list is not complete). | ||
| 154 | |||
| 155 | (% style="list-style-type:square" %) | ||
| 156 | * R project for statistic computing version: [[https:~~/~~/www.r-project.org/>>url:https://www.r-project.org/||shape="rect"]] | ||
| 157 | * RStudio Desktop open source version. | ||
| 158 | * GNU Octave Scientific Programming Language h[[ttps:~~/~~/www.gnu.org/software/octave/>>url:https://www.gnu.org/software/octave/||shape="rect"]] | ||
| 159 | * Julia, [[high-level, high-performance dynamic programming language for numerical computing>>url:https://julialang.org/||shape="rect"]] | ||
| 160 | * Matlab | ||
| 161 | * IDL [[Interactive Data Language>>url:https://www.harrisgeospatial.com/SoftwareTechnology/IDL.aspx||shape="rect"]] | ||
| 162 | * SPSS | ||
| 163 | * Qgis Open Source Geographic Information System | ||
| 164 | * NoMachine Enterprise client | ||
| 165 | |||
| 166 | 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: | ||
| 167 | |||
| 168 | * FreeSurfer open source software suite for processing and analyzing (human) brain MRI images. [[https:~~/~~/surfer.nmr.mgh.harvard.edu/>>url:https://surfer.nmr.mgh.harvard.edu/||shape="rect"]] | ||
| 169 | * Mathematica | ||
| 170 | * SPSS | ||
| 171 | * VMD Visual Molecular Dynamics: [[http:~~/~~/www.ks.uiuc.edu/Research/vmd/>>url:http://www.ks.uiuc.edu/Research/vmd/||shape="rect"]] | ||
| 172 | |||
| 173 | |||
| 174 | == Common problems and suggestions for admins == | ||
| 175 | |||
| 176 | [[https:~~/~~/version.helsinki.fi/it4scifi/cubbli-help/-/issues>>https://version.helsinki.fi/it4scifi/cubbli-help/-/issues]] here you can find known problems, possibly solutions and let us know how we can improve Cubbli (requesting software for example) by creating and commenting on issues. | ||
| 177 | |||
| 178 | |||
| 179 | Cubbli Linux is maintained by IT Center's IT for Science group. | ||
| 180 | |||
| 181 | |||
| 182 | |||
| 183 | |||
| 184 | {{id name="news"/}} |