Matlab window problem

Hi, I’m having some problems with Matlab interactive app. Matlab does launch normally but window is very small and cannot be resized. I’m using xfce, have tried also Mate with same result. Desktop app works fine (fit to screen) but haven’t tried any other GUI apps yet. Any help would be appreciated.

My output.log file:

Setting VNC password...
Starting VNC server...

WARNING: pxsw1:1 is taken because of /tmp/.X1-lock
Remove this file if there is no X server pxsw1:1
Killing Xvnc process ID 7686
Xvnc process ID 7686 already killed
Xvnc did not appear to shut down cleanly. Removing /tmp/.X11-unix/X1
Xvnc did not appear to shut down cleanly. Removing /tmp/.X1-lock

Desktop 'TurboVNC: pxsw1:1 (username)' started on display pxsw1:1

Log file is vnc.log
Successfully started VNC server on pxsw1:5901...
Script starting...
Starting websocket server...
ERROR: Collection default cannot be found
++ xfwm4 --compositor=off --daemon --sm-client-disable
ERROR: Unable to locate a modulefile for 'xalt/latest'
ERROR: Unable to locate a modulefile for 'matlab/r2022b'
xfwm4: Unknown option --daemon.
Type "xfwm4 --help" for usage.
++ xsetroot -solid '#D3D3D3'
++ xfsettingsd --sm-client-disable
No Modulefiles Currently Loaded.
++ matlab -desktop

(xfsettingsd:8543): xfsettingsd-WARNING **: 16:51:07.994: Unknown mode '2560x1297 @ 60.0' for output VNC-0, aborting.
WebSocket server settings:
  - Listen on :40507
  - Flash security policy server
  - No SSL/TLS support (no cert file)
  - Backgrounding (daemon)
Scanning VNC log file for user authentications...
Generating connection YAML file...
MATLAB is selecting SOFTWARE OPENGL rendering.
xfsettingsd: No window manager registered on screen 0.

(xfsettingsd:8543): xfsettingsd-WARNING **: 16:51:13.252: Failed to get the _NET_NUMBER_OF_DESKTOPS property.
Setting VNC password...
Generating connection YAML file...
xfsettingsd: Another instance took over. Leaving...
++ xfce4-panel --sm-client-disable

(xfce4-panel:8777): xfce4-panel-WARNING **: 16:51:16.813: Failed to connect to the D-BUS session bus: Could not connect: No such file or directory

(xfce4-panel:8777): xfce4-panel-CRITICAL **: 16:51:16.824: Name org.xfce.Panel lost on the message dbus, exiting.
xfce4-panel: There is already a running instance

Hey sorry for the troubles.

So I understand correctly, are you using a modified version of this app for your location:

If so, would it be possible to see the scritp.sh.erb you are using for the app?

What version of OOD are you using?

This would give me the best view of what is missing when the environment is setup and it sounds like the window manager is missing so knowing how the app is getting setup will help.

Yes, I’m using this version of the app. For script.sh.erb I am using a little modified template for XFCE use case
provided in your documentation. This is how it looks:

  #
  # Launch Xfce Window Manager and Panel
  #

  (
    export SEND_256_COLORS_TO_REMOTE=1
    # session.staged_root.join("config") refers to /.../bc_my_center_matlab/template/config
    # which is copied at job start time to a session specifc directory.
    # It will override without replacing any XFCE settings that the user
    # already has.
    export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
    export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
    export XDG_CACHE_HOME="$(mktemp -d)"
    module restore
    set -x
    xfwm4 --compositor=off --daemon --sm-client-disable
    xsetroot -solid "#D3D3D3"
    xfsettingsd --sm-client-disable
    xfce4-panel --sm-client-disable
  ) &

  cd "$HOME"

  #
  # Start MATLAB
  #
  # Launch MATLAB
  set -x
  matlab -desktop  # Launch MATLAB

One thing to do is make sure to include the module purge to ensure you are working in a clean environment for LMOD as the app builds. It looks like that is missing at the start.

The ERROR messages in the logs all suggest that there is nothing being loaded for those modules and so I guess I’d be curious if those modules are on the system. Can you put a module list at the end of the script.sh.erb to capture what modules are loaded in the output.log.

Is there a reason for removing the some of those LMOD commands overall?

Did you have the following line in mind?
module load xalt/latest <%= context.version %>

I am currently testing OOD on a testing system which has no modules available, but I have installed required packages on worker node and set up environment locally on that node for my user.

My logs on worker after starting Matlab if it is to any help:

Sep 28 10:21:17 pxsw1 su[44626]: (to slorencic) root on none
Sep 28 10:21:17 pxsw1 systemd[1]: Created slice User Slice of UID 1977550619.
Sep 28 10:21:17 pxsw1 systemd[1]: Starting User runtime directory /run/user/1977550619...
Sep 28 10:21:17 pxsw1 systemd[1]: Started User runtime directory /run/user/1977550619.
Sep 28 10:21:17 pxsw1 systemd[1]: Starting User Manager for UID 1977550619...
Sep 28 10:21:17 pxsw1 systemd[44632]: Listening on Multimedia System.
Sep 28 10:21:17 pxsw1 systemd[44632]: Reached target Paths.
Sep 28 10:21:17 pxsw1 systemd[44632]: Starting D-Bus User Message Bus Socket.
Sep 28 10:21:17 pxsw1 systemd[44632]: Started Mark boot as successful after the user session has run 2 minutes.
Sep 28 10:21:17 pxsw1 systemd[44632]: Reached target Timers.
Sep 28 10:21:17 pxsw1 systemd[44632]: Listening on Sound System.
Sep 28 10:21:17 pxsw1 systemd[44632]: Listening on D-Bus User Message Bus Socket.
Sep 28 10:21:17 pxsw1 systemd[44632]: Reached target Sockets.
Sep 28 10:21:17 pxsw1 systemd[44632]: Reached target Basic System.
Sep 28 10:21:17 pxsw1 systemd[1]: Started User Manager for UID 1977550619.
Sep 28 10:21:17 pxsw1 systemd[44632]: Starting Sound Service...
Sep 28 10:21:17 pxsw1 systemd[1]: Started Session c18 of user slorencic.
Sep 28 10:21:17 pxsw1 slurmd[1382]: slurmd: Launching batch job 2862 for UID 1977550619
Sep 28 10:21:17 pxsw1 systemd[1]: session-c18.scope: Succeeded.
Sep 28 10:21:18 pxsw1 systemd[44632]: Started D-Bus User Message Bus.
Sep 28 10:21:18 pxsw1 systemd[44632]: Started Sound Service.
Sep 28 10:21:18 pxsw1 systemd[44632]: Reached target Default.
Sep 28 10:21:18 pxsw1 systemd[44632]: Startup finished in 576ms.
Sep 28 10:21:18 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Activating via systemd: service name='org.a11y.Bus' unit='at-spi-dbus-bus.service' requested by ':1.2' (uid=1977550619 pid=44899 comm="xfsettingsd --sm-client-disable ")
Sep 28 10:21:18 pxsw1 systemd[44632]: Starting Accessibility services bus...
Sep 28 10:21:18 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Successfully activated service 'org.a11y.Bus'
Sep 28 10:21:18 pxsw1 systemd[44632]: Started Accessibility services bus.
Sep 28 10:21:18 pxsw1 at-spi-bus-launcher[44944]: dbus-daemon[44944]: Activating service name='org.a11y.atspi.Registry' requested by ':1.0' (uid=1977550619 pid=44899 comm="xfsettingsd --sm-client-disable ")
Sep 28 10:21:18 pxsw1 at-spi-bus-launcher[44944]: dbus-daemon[44944]: Successfully activated service 'org.a11y.atspi.Registry'
Sep 28 10:21:18 pxsw1 at-spi-bus-launcher[44952]: SpiRegistry daemon is running with well-known name - org.a11y.atspi.Registry
Sep 28 10:21:19 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Activating service name='org.xfce.Xfconf' requested by ':1.6' (uid=1977550619 pid=44899 comm="xfsettingsd --sm-client-disable ")
Sep 28 10:21:19 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Successfully activated service 'org.xfce.Xfconf'
Sep 28 10:21:19 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Activating via systemd: service name='org.gtk.vfs.Daemon' unit='gvfs-daemon.service' requested by ':1.6' (uid=1977550619 pid=44899 comm="xfsettingsd --sm-client-disable ")
Sep 28 10:21:19 pxsw1 systemd[44632]: Starting Virtual filesystem service...
Sep 28 10:21:19 pxsw1 dbus-daemon[44852]: [session uid=1977550619 pid=44852] Successfully activated service 'org.gtk.vfs.Daemon'
Sep 28 10:21:19 pxsw1 systemd[44632]: Started Virtual filesystem service.
Sep 28 10:21:27 pxsw1 systemd[1]: Started Session 23 of user samo.
Sep 28 10:21:27 pxsw1 systemd-logind[1125]: New session 23 of user samo.
Sep 28 10:21:27 pxsw1 dbus-daemon[45197]: [session uid=1000 pid=45195] Activating service name='org.gtk.vfs.Daemon' requested by ':1.0' (uid=1000 pid=45205 comm="gio monitor -f /run/systemd/sessions/23 /tmp/dbus-")
Sep 28 10:21:27 pxsw1 dbus-daemon[45197]: [session uid=1000 pid=45195] Successfully activated service 'org.gtk.vfs.Daemon'
Sep 28 10:21:27 pxsw1 org.gtk.vfs.Daemon[45223]: fusermount: failed to access mountpoint /run/user/1000/gvfs: Permission denied
Sep 28 10:21:27 pxsw1 systemd[1]: Stopping User Manager for UID 1977550619...
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopping D-Bus User Message Bus...
Sep 28 10:21:27 pxsw1 gvfsd[44971]: A connection to the bus can't be made
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopping Accessibility services bus...
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped target Default.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopping Sound Service...
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopping Virtual filesystem service...
Sep 28 10:21:27 pxsw1 journal[44960]: Name org.xfce.Xfconf lost on the message dbus, exiting.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped D-Bus User Message Bus.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped Accessibility services bus.
Sep 28 10:21:27 pxsw1 systemd[1]: run-user-1977550619-gvfs.mount: Succeeded.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped Sound Service.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped Virtual filesystem service.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped target Basic System.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped target Sockets.
Sep 28 10:21:27 pxsw1 systemd[44632]: Closed Sound System.
Sep 28 10:21:27 pxsw1 systemd[44632]: Closed Multimedia System.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped target Paths.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped target Timers.
Sep 28 10:21:27 pxsw1 systemd[44632]: Stopped Mark boot as successful after the user session has run 2 minutes.
Sep 28 10:21:27 pxsw1 systemd[44632]: Closed D-Bus User Message Bus Socket.
Sep 28 10:21:27 pxsw1 systemd[44632]: Reached target Shutdown.
Sep 28 10:21:27 pxsw1 systemd[44632]: Started Exit the Session.
Sep 28 10:21:27 pxsw1 systemd[44632]: Reached target Exit the Session.
Sep 28 10:21:27 pxsw1 systemd[1]: user@1977550619.service: Succeeded.
Sep 28 10:21:27 pxsw1 systemd[1]: Stopped User Manager for UID 1977550619.
Sep 28 10:21:27 pxsw1 systemd[1]: Stopping User runtime directory /run/user/1977550619...
Sep 28 10:21:27 pxsw1 systemd[1]: run-user-1977550619.mount: Succeeded.
Sep 28 10:21:27 pxsw1 systemd[1]: user-runtime-dir@1977550619.service: Succeeded.
Sep 28 10:21:27 pxsw1 systemd[1]: Stopped User runtime directory /run/user/1977550619.
Sep 28 10:21:27 pxsw1 systemd[1]: Removed slice User Slice of UID 1977550619.
Sep 28 10:21:29 pxsw1 su[45358]: (to root) samo on pts/1

Thanks for that information. Knowing there’s packages there and looking at the script I can’t see anything there that looks wrong.

Ok, so looking at the script things look fine knowing there’s packages there to use (also, you can remove all the module lines to get rid of those missing module errors in the logs).

Looking at the logs, this looks to be a problem of which display is being used. Notice this message in the first logs you posted:

So this is using display :1.

But then subsequent errors for xfsettingsd it is trying to use :0 and this is not where the window manager is running.

Now, why that is happening I’m trying to debug currently still, but that looks to be the problem.

This is the other error I’m looking at as it may be the main culprit and not the display:

Sep 28 10:21:27 pxsw1 dbus-daemon[45197]: [session uid=1000 pid=45195] Activating service name='org.gtk.vfs.Daemon' requested by ':1.0' (uid=1000 pid=45205 comm="gio monitor -f /run/systemd/sessions/23 /tmp/dbus-")