Hoffman2 maintenance and Issues

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Issues and Solutions

Update date: 2023.04.06

Trying to launch freeview results in a segmentation fault error on gpu nodes


run on the gpu node: export __GLX_VENDOR_LIBRARY_NAME=mesa

Now launch freeview

Update date: 2023.01.13

After launching freesurfer or RStudio one cannot launch the application and encounters:

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.


Comment out any matlab modules in the bashrc or module unload bashrc and launch the application again.

Update date: 2022.07.05

After login noMachine client, one cannot start a new session because of error message "No available session on this server"


On Hoffman

rm -r  ~/.nx

On your local machine

rm -r ~/.nx

Reconnect and this doesn't solver your problem, repeat these steps and uninstall noMachine then install it again with the most recent version.

Update date: 2021.12.02

Some functions in FSL/6.0.4 gets "Illegal instruction" error message and fail on AMD nodes


Request a Intel node by adding "arch=intel*" in the option, for example

qrsh -l arch=intel*,h_rt=4:00:00,h_data=8G

Update date: 2021.11.10

IDRE team's gitlab is not responding.

For users who need to download the newer version of h2jupynb, please find it in Hoffman at


Update date: 2021.11.05

I am able to login to NX1 currently. So both NX1 and NX2 are working at this point.

Update date: 2021.11.02

NX2 is accepting new connections currently after IDRE team made some changes on the server. User can login nx1 but not able to create new sessions or connect to the old session. Requesting investigation from IDRE team.

Update date: 2021.11.01

Unable to connect to nx1 and nx2 with noMachine. Waiting for IDRE team's reply.

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.


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


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


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.


Download the newest h2jupynb script from IDRE's gitlab


Known issue 5

Matlab GUI gives out warning messages as following

[1029/151141.170798:ERROR:gles2_cmd_decoder.cc(9632)] [.Offscreen-MainThread-0x2ac244e220f0]RENDER WARNING: texture bound to texture unit 0 is not renderable. It maybe non-power-of-2 and have incompatible texture filtering.
[1029/151204.562839:ERROR:gles2_cmd_decoder.cc(17399)] [.Offscreen-MainThread-0x2ac244e220f0]GL ERROR :GL_INVALID_OPERATION : glCreateAndConsumeTextureCHROMIUM: invalid mailbox name


Run "unset LIBGL_ALWAYS_INDIRECT" command in the terminal after you start interactive mode and before you launch Matlab GUI.