Issues running vmd on ood on cluster

We have a cluster built on RHEL 8 and using slurm for scheduling. We are getting an error with the bc_osd_vmd. We meet the minimum specs for prereqs. The xfce desktop environment, turbovnc, and websockify are yum installed. The virtualgl and vmd programs are loaded as modules. We have not used xfce before.

bc_osc_vmd fails with the following output in the log:

Show Dotfiles Show Owner/Mode
/home/wew/ondemand/data/sys/dashboard/batch_connect/dev/bc_osc_vmd/output/8265f977-28b7-4ca0-9c4d-7891438b8fd6/
Setting VNC password…
Starting VNC server…

Desktop ‘TurboVNC: cn4:2 (wew)’ started on display cn4:2

Log file is vnc.log
Successfully started VNC server on cn4:5902…
Script starting…
Starting websocket server…
Starting /bin/xfwm4
The system default contains no modules
(env var: LMOD_SYSTEM_DEFAULT_MODULES is empty)
No changes in loaded modules

  • xfwm4 --compositor=off --sm-client-disable
    WARNING: no ‘numpy’ module, HyBi protocol will be slower
    WebSocket server settings:
    • Listen on :6213
    • Flash security policy server
    • No SSL/TLS support (no cert file)
    • Backgrounding (daemon)
      Scanning VNC log file for user authentications…
      Generating connection YAML file…

(xfwm4:366366): xfwm4-CRITICAL **: 14:25:21.750: Xfconf could not be initialized

(xfwm4:366366): xfwm4-WARNING **: 14:25:21.750: Missing data from default files

  • xsetroot -solid ‘#D3D3D3
  • xfsettingsd --sm-client-disable
  • xfce4-panel --sm-client-disable
    xfsettingsd: Could not connect: No such file or directory.

(xfsettingsd:366409): xfsettingsd-ERROR **: 14:25:21.779: Failed to connect to the dbus session bus.

(xfce4-panel:366410): xfce4-panel-WARNING **: 14:25:21.782: Failed to connect to the D-BUS session bus: Could not connect: No such file or directory
xfce4-panel: There is already a running instance

Currently Loaded Modules:

  1. anaconda3/2020.11 2) virtualgl/2.6.6 3) vmd/1.9.4
  • xfce4-terminal -e ‘vglrun vmd’ -T ‘VMD Terminal’ --disable-server
    Failed to connect to session manager: Failed to connect to the session manager: SESSION_MANAGER environment variable not defined
    Cleaning up…
    Killing Xvnc process ID 366303

Any idea where we should start looking?

Check for missing packages on the system where xfce is supposed to run. xfce4-terminal, for example is its own package, as is xfwm4, etc. If those packages are installed, make sure the PATH available to the script includes /usr/bin, which is where most, if not all, of the executables are installed.

Also, did you do

yum groupinstall Xfce

If not, you’re likely to be finding and adding packages for quite a while.

Cheers,

Ric

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xfce was group installed. I see xfce4-terminal on the path and /usr/bin is on the path.

I think this is the error message you want to hone in on. I would check system logs like /var/log/messages or journalctl for errors. But also maybe start a job and run through those scripts manually. I mean step to that log directory and you’ll see shell scripts you can run and/or just run the commands directly and try to see what other output you may see interactively. That’d be my suggestion to triage - replicate all these commands interactively and check system logs.

We’re still having no luck getting past the xfconf error. I started from scratch and reinstalled all of the pre-requisites. We do not have experience with using turbovnc or xfce.

I notice that you have an anaconda3 module loaded. Does its bin directory contain any
dbus-* commands? If so, they are over-riding the system versions are likely to cause problems.
Try deleting them (or disabling them) and see it that works.

Yes, definitely! The Anaconda dbus-* is a problem for OnDemand desktop applications.

We’ve had much grief because of that.

So I installed a new anaconda3 module just for vmd and made sure no dbus-* files. I get the following. So still having xfconf issues.

Setting VNC password…
Starting VNC server…

Desktop ‘TurboVNC: cn10:1 (wew)’ started on display cn10:1

Log file is vnc.log
Successfully started VNC server on cn10:5901…
Script starting…
Starting websocket server…
Is dbus on path?
/bin/dbus-launch
Starting /bin/xfwm4
The system default contains no modules
(env var: LMOD_SYSTEM_DEFAULT_MODULES is empty)
No changes in loaded modules

  • xfwm4 --compositor=off --sm-client-disable
    WARNING: no ‘numpy’ module, HyBi protocol will be slower
    WebSocket server settings:
    • Listen on :14593
    • Flash security policy server
    • No SSL/TLS support (no cert file)
    • Backgrounding (daemon)
      Scanning VNC log file for user authentications…
      Generating connection YAML file…

(xfwm4:3816896): xfwm4-CRITICAL **: 15:05:08.250: Xfconf could not be initialized

(xfwm4:3816896): xfwm4-WARNING **: 15:05:08.250: Missing data from default files

  • xsetroot -solid ‘#D3D3D3
  • xfsettingsd --sm-client-disable
  • xfce4-panel --sm-client-disable
    xfsettingsd: Could not connect: No such file or directory.

(xfsettingsd:3816939): xfsettingsd-ERROR **: 15:05:08.284: Failed to connect to the dbus session bus.

(xfce4-panel:3816940): xfce4-panel-WARNING **: 15:05:08.304: Failed to connect to the D-BUS session bus: Could not connect: No such file or directory
xfce4-panel: There is already a running instance

Currently Loaded Modules:

  1. anaconda3/2021.05-vmd 2) virtualgl/2.6.6 3) vmd/1.9.4
  • xfce4-terminal -e ‘vglrun vmd’ -T ‘VMD Terminal’ --disable-server
    Failed to connect to session manager: Failed to connect to the session manager: SESSION_MANAGER environment variable not defined
    Cleaning up…
    Killing Xvnc process ID 3816833