Changes impacting scientific staff in RHEL6->RHEL7 migration


RHEL6 is reaching end of life, and is no longer going to be supported by NRAO CIS. See for more information on Red Hat support, dates, etc., for the various versions. Because of this, migrating to RHEL7 is necessary for all employees using computers with the Linux OS. As scientific staff, we have particular things that we do with our desktop machines that others in the observatory who are making this migration may not. We need to understand how the migration will impact these things that we do, in order to be prepared for the day when it happens, and to then work around them as efficiently as possible.

There are a handful of us in Socorro who have already made the switch, some that are making it now, and the rest of us are on a schedule that CIS is using to plan these migrations. Many have already migrated in Charlottesville as well (I don't have an accurate count of those - could be 2, could be 20). Given that, it would seem prudent to start keeping track of the things that those who have already migrated, or have at least used RHEL7 machines (half of our public machines in Socorro have been migrated already), have run into. This wiki page is an attempt to do that. It is meant as a living document, so anybody that is making this transition is welcome to edit the page with differences they have found, alternatives or workarounds to RHEL6 solutions, etc.

The List

  1. In the standard RHEL7 release, there is no acroread. That software has not been maintained for several years, apparently. The replacements are okular and evince; okular tends to get higher ratings (if you google them). But there is no ability to digitally sign documents in either of these. For that, in Socorro, you have to log in to the machine aoctsa (a windows box), and do it there. There is a report that acroread was installed for a scientific staff member in Charlottesville. If so, a more clear and consistent treatment of this should be considered by CIS.
  2. For logging in to aoctsa in Socorro, you no longer use rdesktop, but rather xfreerdp.
  3. There are some remote connection (VNC) oddities. x11vnc (which is needed, or something similar, if you want to connect to your actual desktop, i.e., the :0 X display) does not come installed by default, but has been installed on request on machines in Socorro. But experience for different people seems to vary. For me in my tests, it seems to work just fine. Urvashi reports that she needs to start it up with -shared -forever command line switches in order to get proper mouse control and to make it persistent across sessions. Josh reports that he had some difficulties but it got ironed out eventually (not sure exactly what was done). CIS initially recommended NoMachine to me, but I tried it and it didn't work.
  4. There are a number of window manager/desktop differences. gnome is apparently quite resource intensive, at least for VNC. It also has configuration differences that will likely cause you to scrap your old configuration file, install the default, and work from scratch. At least this is what CIS is currently recommending. There are issues with gnome applets as well. All of this caused Urvashi and Josh to just switch to KDE (I was on KDE already). But Josh reports an issue with KDE and CASA GUIs not rendering properly - he had to use an older window theme to get it to work. Talk to Josh for details. It appears that neither gnome nor KDE has a graphical system monitor that fits on the desktop toolbar. Desktop preferences (focus policy, etc., including turning off the "maximize when touching top of screen" feature) may have to be reset. Note that Red Hat has announced that it is deprecating use of KDE, and while it won't go away immediately, it will eventually (
  5. If you use pine as your email client (what? in 2018? yes, we still have pine users), that is gone. The replacement is alpine, but apparently you need to tweak the configuration to make it work properly. [LS, info from Schlake:] That is, for the inbox-path set the server to [username] and the folder to inbox . Note however that this requires you to type in your password each time you start alpine which particularly annoying if you rely on short email sessions and/or are typing on limited keyboards (such as on phones/tablets).
  6. There is a report that the mounting of external disks is done differently, which may require modification of existing scripts or programs that you have that do this.
  7. ispell may or may not be installed by default (in Socorro, it seems to be in some installations, not in others). If it is, it doesn't work out-of-the-box, and needs updates applied.
  8. Anna reports that sound and microphone don't work for her. CIS has found no solution in many months.
  9. Source-Navigator is not installed by default. This may not be of interest to very many of us, but some have used it and miss it.
  10. Image viewing has differences. gthumb is not installed by default, and when installed on one machine hung X. gwenview is the replacement. It's not as capable as gthumb in some ways, but more capable in others. The venerable xv is still around, though is maintained by a different opensource consortium now so may have slight differences. The gimp is also still around.
  11. There is an updated version of the OpenOffice suite, and version incompatibilities with the version on RHEL6 (especially with equations) have been reported.
  12. All firefox bookmarks may be lost - they can be restored from a .snapshot directory.
  13. In Charlottesville, gv, xv, and pdftk were not installed by default, and had to be requested. This is not true for gv and xv in Socorro, but is true for pdftk.
  14. timetrax is not installed by default. hamster-time-tracker was installed for Todd in Charlottesville, and works, after learning the differences.
  15. After upgrading from 7.5 to 7.6, Todd reports that he had to add /usr/lib64 to LD_LIBRARY_PATH, or even things like emacs wouldn't run. Also, his preferred desktop (Cinnamon) is not installed.
  16. The default python is in /usr/bin/python. In Socorro, installs seem to also have the various flavors in /opt/local/bin/python*, but in Charlottesville that may not be the case. If they are not there, you may need to edit python scripts. I heard a rumor that matplotlib has changed significantly, or had problems, or somesuch, but have not confirmed that.
  17. python3 is missing all of the useful libraries like: numpy, scipy, pylab, matplotlib, etc. and you need to request them to be installed
  18. There are many perl libraries which are not installed by default. The installed version of perl has gone from 5.10.1 to 5.16.3. I haven't found anything that has broken between the two (other than the missing libraries).
  19. Programs compiled under RHEL6 will not work under RHEL7 unless they were compiled with static libraries. You will have to recompile them under RHEL7 to have them work. Whether you want to compile them with static libraries or not is up to you.
  20. Related to item 17, the standard installed compilers (in /usr/bin) for C (gcc) and FORTRAN (gfortran) are old - both 4.8.5 (2015). By default newer versions are installed at /opt/local/compilers/gcc-7.3.0/bin (you can guess that they are version 7.3.0), at least in Socorro. But you'll need to add that not-so-obvious path to your default $PATH to find them. There are reports of some instabilities with the 7.3.0 compilers - it at least does not work for AIPS (Eric just tried it). CIS is installing the 6.3 compilers now (afternoon of 12/12/2018) to see if that fixes the problem.
  21. svn in RH7 is now 1.7.14 which is apparently not compatible with the RH6 version (1.6.11). Running svn update on an existing checkout will not work. It looks like you have to run "svn upgrade" while in the main directory of the checked out code. This worked for me (Todd) for my svn repository in Socorro where I keep my bandpasstool and API web interface code. I haven't tried it yet on the pipeline trunk checkout in CV since we still have RH6 on our CV Lustre nodes. [BJB note: I found that the easiest way to convert is to just blow away your old 1.6 checkout and fully check out a new one using 1.7. Note that svn 1.9 (which is even more recent) won't even check out the projects in our svn repository!]
  22. perl modules that use libraries installed under RHEL6 may not work. It depends on the library. For instance, if you installed IO::Socket::Multicast under RHEL6, and try to execute a script which uses that library, it will fail, with something like: "/usr/bin/perl: symbol lookup error: /users/bbutler/perl/new/lib/x86_64-linux-thread-multi/auto/IO/Socket/Multicast/ undefined symbol: Perl_Gthr_key_ptr". The libraries will likely have to be re-installed with RHEL7 (I haven't done it myself yet).
  23. Drew Medlin reports that ssh-keygen works differently.
  24. Todd reported to Tracy Halstead via helpdesk 112613 that aplpy does not import into python2.7, like it used to on RH6. It fails with: "cannot import name ccompiler" (from distutils import ccompiler). She is going to try to install python 2.7.3 (to match the old RHEL6 system)
  25. Todd filed a HD ticket for the problem that the emacs toolbar icons do not appear -- they are just a blank gray band at the top of the emacs window.
  26. Todd filed a HD ticket for the poor behavior of gnome-terminal when run from tshell: new tabs no longer inherit the working directory of the existing tab (
  27. Todd filed a HD ticket to fix the policy.xml file of ImageMagick to allow users to add labels to pngs via the "convert" command. This capability was initially available in RedHat6, was removed during an update of the package, and was subsequently restored when HD ticket 89555 was then filed.

-- BryanButler - 2018-12-20
Topic revision: r11 - 2019-06-13, ToddHunter
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