Xfce4 Desktop app using container_vnc

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1

Hi all, I’m using OOD 3.0.1 and I’m currently trying to use the vnc_container in the tutorial (Batch Connect VNC Container Options — Open OnDemand 3.1.0 documentation) to have a Desktop app. I took the .def file to build and all the commands seem to exist inside the container. The image also has all xfce binaries, but when I put xfce4-session in the script.sh.erb file this is run outside of the container and therefore it doesn’t find it. How can I make sure that I run the commands inside the container? I couldn’t find any options…

Thank you so much,
Bernardo

My submit.yml.erb is

---
batch_connect:
    template: "vnc_container"
    websockify_cmd: "/usr/bin/websockify"
    container_path: "/share/apps-x86/containers/singularity/rockylinux_8.sif"
    container_command: "singularity"
    container_module: ""
    container_bindpath: ""

The output file reads:

Loading ...
 Starting instance...
 INFO:    Instance stats will not be available - requires cgroups v2 with systemd as manager.
 INFO:    Converting SIF file to temporary sandbox...
 INFO:    instance started successfully
 Setting VNC password...
 Starting VNC server...
 59548
 
 Desktop 'TurboVNC: cnx035:1 (malaca)' started on display cnx035:1
 
 Log file is vnc.log
 Successfully started VNC server on cnx035:5901...
 Script starting...
 Before starting up
 Starting websocket server...
 /usr/lib/python3.6/site-packages/websockify/websocket.py:31: UserWarning: no 'numpy' module, HyBi protocol will be slower
   warnings.warn("no 'numpy' module, HyBi protocol will be slower")
 WebSocket server settings:
   - Listen on :53570
   - No SSL/TLS support (no cert file)
   - Backgrounding (daemon)
 Scanning VNC log file for user authentications...
 Generating connection YAML file...
 Cleaning up...
 Killing Xvnc process ID 54
 /var/spool/slurm/d/job06085/slurm_script: line 25: vncserver: command not found
 INFO:    Stopping bd8b3cb3-e1db-4917-8b8d-910b48ec35fc instance of /tmp/rootfs-254472145/root (PID=59392)
 ~
2

I was able to solve this.
The system runs the container just to run vnc and you can’t easily make it also run xfce. So to open xfce/gnome/etc. you need to add a line in your script.sh.erb:

singularity exec /path/to/image/rockylinux_8.sif /path/to/script/xfce.sh

xfce.sh is the script file you get from the original app inside “templates”.
Essentially you run two parallel singularity containers, each with its own app.

2 Likes
3

Hi @BMalaca . I’m trying to do this same thing right now. I modified my script.sh.erb like you mentioned:

apptainer exec xfce.sif "desktops/xfce.sh"

My job starts successfully but when I try to connect I get the “Failed to connect to server” error.

Did you have to make any other changes? Here’s some of the relevant lines from the logs:

Log file is vnc.log
Successfully started VNC server on node:5901...
Script starting...
Launching desktop 'xfce'...
Starting websocket server...
Failed to init libxfconf: Error spawning command line ?dbus-launch --autolaunch= --binary-syntax --close-stderr?: Child process exited with code 1.
Failed to init libxfconf: Error spawning command line ?dbus-launch --autolaunch= --binary-syntax --close-stderr?: Child process exited with code 1.
D-Bus library appears to be incorrectly set up: see the manual page for dbus-uuidgen to correct this issue. (UUID file '/var/lib/dbus/machine-id' should contain a hex string of length 32, not length 0, with no other text; UUID file '/etc/machine-id' should contain a hex string of length 32, not length 0, with no other text)
/usr/lib/python3.6/site-packages/websockify/websocket.py:31: UserWarning: no 'numpy' module, HyBi protocol will be slower
  warnings.warn("no 'numpy' module, HyBi protocol will be slower")
WebSocket server settings:
  - Listen on :34688
  - No SSL/TLS support (no cert file)
  - Backgrounding (daemon)
Scanning VNC log file for user authentications...
Generating connection YAML file...
4

Hi and welcome @BMalaca! Sorry we didn’t get to this earlier.

Shouldn’t it use the existing container instance? We populate the INSTANCE_NAME environment variable and export it for use in script.sh.erb.

apptainer exec "instance://$INSTANCE_NAME" "desktops/xfce.sh"
5

That was my initial thought too Jeff. I bind mounted /var/lib/dbus/machine-id and am getting the following in my output.log:


Desktop 'TurboVNC: node137:1 (user)' started on display node137:1

Log file is vnc.log
Successfully started VNC server on node137:5901...
Script starting...
Launching desktop 'xfce'...
Starting websocket server...
_IceTransmkdir: Owner of /tmp/.ICE-unix should be set to root
/usr/lib/python3.6/site-packages/websockify/websocket.py:31: UserWarning: no 'numpy' module, HyBi protocol will be slower
  warnings.warn("no 'numpy' module, HyBi protocol will be slower")
WebSocket server settings:
  - Listen on :47677
  - No SSL/TLS support (no cert file)
  - Backgrounding (daemon)
Scanning VNC log file for user authentications...
Generating connection YAML file...

The job is running, but still getting the “Can’t connect to server” VNC error.

6

After alot of finagling I got this to work on my system to boot up the application visit inside the container.

I know for sure it boots inside the container because all sorts of dynamic library issues I had where I couldn’t mount /lib64 directly, had to mount each .so file individually.

#!/usr/bin/env bash

# Clean the environment
module purge

# Set working directory to home directory
cd "${HOME}"

export APPTAINERENV_DISPLAY=$DISPLAY

#
# Launch Xfce Window Manager and Panel
#
export SEND_256_COLORS_TO_REMOTE=1
export APPTAINERENV_SEND_256_COLORS_TO_REMOTE="$SEND_256_COLORS_TO_REMOTE"

export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
export APPTAINERENV_XDG_CONFIG_HOME="$XDG_CONFIG_HOME"

export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
export APPTAINERENV_XDG_DATA_HOME="$XDG_DATA_HOME"

export XDG_CACHE_HOME="/tmp/xdg"
export APPTAINERENV_XDG_CACHE_HOME="$XDG_CACHE_HOME"

export $(apptainer exec instance://$INSTANCE_NAME dbus-launch 2>/dev/null)
export APPTAINERENV_DBUS_SESSION_BUS_ADDRESS=$DBUS_SESSION_BUS_ADDRESS
export APPTAINERENV_DBUS_SESSION_BUS_PID=$DBUS_SESSION_BUS_PID

module restore
set -x
apptainer exec instance://$INSTANCE_NAME xfwm4 --compositor=off --sm-client-disable &
apptainer exec instance://$INSTANCE_NAME xsetroot -solid "#D3D3D3"
apptainer exec instance://$INSTANCE_NAME xfsettingsd --sm-client-disable --daemon
apptainer exec instance://$INSTANCE_NAME xfce4-panel --sm-client-disable &

set +x
#
# Start Visit
#

# Load the required environment
module load xalt/latest <%= context.auto_modules_visit %>

export APPTAINERENV_PATH=$PATH
export APPTAINERENV_LD_LIBRARY_PATH=$LD_LIBRARY_PATH

sleep 5

apptainer exec "instance://$INSTANCE_NAME" visit -small