Hoffman2 maintenance and Issues

Issues and Solutions

Update date: 2021.10.19

FSL 6.0.3 has been re-installed and the FSLeyes in this version is working in x2go and noMachine.

Update date: 2021.10.15

Here's a list of the known issues after Hoffman2 maintenance

Known issue 1

x2go and noMachine interface looks froze or in full screen mode, user cannot find menu bar.

Solution:

If you are using GNOME as the desktop interface, please change to MATE. KDE works as well but you might have to delete the ~/.x2go and ~/.x2goclient in your local machine (with MacOS).

Known issue 2

FSLeyes in FSL 6.0.4 and 6.0.3 does not load GUI on x2go and noMachine (Other versions work, as well as fslview)

Solution (for both x2go and noMachine):

For FSLeyes in FSL 6.0.4, type in the following command line after you start interactive session, and before you run fsleyes

unset LIBGL_ALWAYS_INDIRECT

For FSLeyes in FSL 6.0.3, fsleyes will be upgraded shortly to fix the current issue.

Known issue 3

FreeView GUI opens but cannot load images successfully

Solution:

In noMachine, use "unset LIBGL_ALWAYS_INDIRECT" command should fix the issue

In x2go, "unset LIBGL_ALWAYS_INDIRECT" does not seem to work all the time. We are still looking into it.

Known issue 4

Jupyter Notebook does not open properly with IDRE's script h2jupynb

Reason: The previous version of this script which was used before the maintenance tries to load Python/3.7.1 which does not exit in CentOS 7 after the upgrade.

Solution:

Download the newest h2jupynb script from IDRE's gitlab

https://gitlab.idre.ucla.edu/dauria/jupyter-notebook