Fedora 20 issues

The disadvantage of the free Fedora Linux distribution is its short lifecycle. When we adopted this version, we knew we might have to upgrade all computers approximately once a year, which is actually a small price to pay for a free and up-to-date operating system. The advantage of this disadvantage is of course, that our software collection is always very up-to-date.

And now it is about time to start upgrading again. Actually, we have already started on student pcs and a few others, and over the next month or so we will upgrade as many of the systems as possible. We have spent quite some time to streamline the upgrade process, so on most reasonably fast pcs an upgrade will take approximately 2 hours. Therefore we think it is most efficient that we just execute the upgrades whenever a computer seems to be unused for part of the day, without wasting too much time on planning. Experience has shown that most plans fall apart due to changes in schedule anyway. However, if you know you desperately need your computer due to an upcoming deadline or so, please let us know. Otherwise, just log out whenever you don't need your computer for a while, and chances are, we will at some point detect this and perform the upgrade.

• Fedora 20 release notes [html version, pdf and versions in various other languages available from the menu]http://docs.fedoraproject.org/en-US/Fedora/20/html/Release_Notes/

• Common Bugs and Known Issues https://fedoraproject.org/wiki/Common_F20_bugs

Local links:

• Linux desktop environments
• Fedora compatibility settings
• Fedora tips

• Gnome 3.10 (see below for details)
• After many years, the Enlightenment desktop environment is updated, and back as a choice from the login screen.
• TeX has been upgraded to the TeX Live 2012 distribution, with many new styles and possibilities. Many additional TeX packages are available on demand.
• New aplications (new in Fedora 20 or newly added in our standard installation):
  • X2GO, a free Nomachine-like VNC interface. Also includes X2GOdesktopsharing, to take over your default desktop from another system. X2GO clients for Windows, MacOS X and Linux can be downloaded at http://x2go.org/. As an added bonus, it offers disk sharing, client side printing, and audio forwarding.
  • Gnome Boxes, a simplified virtualization tool, lets you easily set up and use virtual environments. But it also offers an interface to VNC and Windows Remote Desktop. Now mostly functional on all desktop environments, not just on Gnome 3.
  • Mendely desktop, scientific paper/document management package
• First time login wizard: The first time you log in on the new Fedora system, you will be presented with a wizard that will help you set up language, keyboard and some online connections.
• Python local user directories: It is now possible, to have your own set of python modules, and uses tools like pip to maintain them. If .local/lib/python2.7 exists, it will be added to your $PYTHONPATH automatically, and then you will be able to use pip install –user packagename to install a package in that location, for your own use.
• Significant updates:
  • Cinnamon desktop updated to version 2.0
  • Skype is now installed by default (and upgraded to 4.1). Audio hardware is not; bring your own headset (or have one ordered from your budget)!
  • Many other packages available on demand.

• Gnome 3 (existing issue). Gnome 3 is a completely different desktop design, which makes the desktop look like a Tablet PC. Some people may like it, but if you don't, “Mate” is available as an alternative, to give you the experience of good old Gnome 2, or “Cinnamon”, for a more desktop-like version of the new Gnome. Also, there is a “new” Gnome Classic session (was called “Gnome fallback” in the previous releases).
  More on Gnome 3
• Gnome: missing mouse cursor: On some systems (or for some users) the mouse cursor becomes invisible, either after login, or at other times during the session. This bug seems to be caused by the cursor plugin of gnome-settings-daemon. To deactivate that plugin, execute this command (should only be needed once since it will be saved in your settings): gsettings set org.gnome.settings-daemon.plugins.cursor active false

To execute this, if you don't have any terminals open after logging in, press Alt-F2 to get the run dialog.

• Cinnamon desktop tweaks: In general, Cinnamon looks like ordinary desktops, but it is Gnome 3 at the core. But starting with version 2.0, there are now separate tools for Cinnamon, eg, if you want to modify the programs that start in each session, use cinnamon-session-properties for that (also available from the settings overview).
  More on Cinnamon
• Programs that start with each session: A lot of programs are started by default in each desktop session. many of them are unnecessary; some of them are annoying or can cause problems. users can disable everything they don't need.
  More on session tweaking
• The gnome-mount utility was dropped after Gnome 2. As replacement, pmount can be used to mount removable media (cdrom,dvd,usb-disks) from the commandline. E.g.: pmount /dev/cdrom mounts the cd/dvd as /media/cdrom.
• VNC issues: Desktop environments that require hardware accelleration (3D desktop effects) are too heavy to be used inside a virtual desktop (VNC, NX, X2GO). See VNC desktop issues for details and workarounds.
• Various programs work fine, but print a line like:

  Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9:  reading  configurations from ~/.fonts.conf is deprecated.

  To get rid of these warnings, move the configuration files to their new locations:

  mkdir ~/.config/fontconfig
  mv ~/.fonts.conf.d ~/.config/fontconfig/conf.d
  mv ~/.fonts.conf   ~/.config/fontconfig/fonts.conf

  Unfortunately, once you do that, older versions of Fontconfig will not see your personal preferences (eg on RedHat machines like the computation nodes and servers).
  PS: when you do change these locations, you may want to cleanup the even older files and directories .fontconfig and .fonts.cache-* if they exist, to free some space.

• Emacs 24. The new emacs version contains quite a number of changes. For the most part: it tries to work nicer with current desktop systems, since the way people expect an X application to behave, have changed a lot over the years. Best to enable the KDE or Gnome clipboard manager, and enjoy the new feature of emacs and of your desktop the way they were programmed to be.
  But emacs being emacs, all of this behaviour can be configured and fine-tuned. Read the news, available from the help menu (C-h n).
  If you realy, realy, realy want the old selection, cut and paste behaviour back, add this in your .emacs:

              (setq select-active-regions nil)
              (setq mouse-drag-copy-region t)
              (setq x-select-enable-primary t)
              (setq x-select-enable-clipboard nil)
              (global-set-key [mouse-2] 'mouse-yank-at-click)          

• evince: Evince has a known bug with postscript files that contain a rotation matrix (all or part of the image is rotated). The bug will be fixed eventually, but here are some workarounds:
  • Rotate the image: ctrl-left or ctrl-right
  • Convert the image to pdf (eg using ps2pdf)
  • Use another viewer, such as gv or okular
• Intel compilers: The Intel compilers (ifort,icc) are not enabled by default. The latest freely available version is 10.1, which can be loaded using module load intel. However, for most code, the GNU compilers are better than these slightly older Intel compiler versions. (if you read that the Intel compiler has speed benefits, this probably refers to the very expensive current version, which we cannot install on a system-wide basis)
• OOolatex: we used to have the OOolatex add-on for OpenOffice / LibreOffice, which allowed to use LaTeX syntax for formula input in Writer and Impress. Unfortunately, this package is still not updated for version 4.x of the office suite.
  After some searching, we found a workaround, to install TexMaths as a replacement. Unfortunately, there is no package available to install it systemwide, but installation on a per-user basis is rather straightforward:
  Go to http://sourceforge.net/projects/texmaths/files/ and download the latest version (currently 0.38). This will download TexMaths-0.38.oxt and offer to open this in LibreOffice. When you do that, it will install itself as an extension, ready to be used. Added benefit: this version works in all parts of LibreOffice, so including a formula in a drawing is now also possible.
• Python's matplotlib may need some tweaking. If you run into fornt problems when using TeX fonts, create a file ~/.config/matplotlib/matplotlibrc including:

  mathtext.fontset : stix

  And while you're at it, it often makes sense to add these settings as well:

  backend : TkAgg
  ps.papersize : A4