Fiji ImageJ App Deployment

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1

I am working to get Fiji imageJ deployed as an app through OnDemand. I have the app configured as a VNC app. When I launch the app, it gives me a noVNC session that shows only a black screen. I can run the app just fine through an interactive desktop session. My submission script is located below. The VNC and XFCE options were pulled from an example Matlab script.

#!/usr/bin/env bash

# Benchmark info
echo "TIMING - Starting main script at: $(date)"

# Add Caffe Unet Libraries to LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/share/apps/fiji/caffe_unet/lib:/share/apps/fiji/caffe_unet/extlib:$LD_LIBRARY_PATH

# Add VirtualGL to PATH
export PATH=/opt/VirtualGL/bin:$PATH

# Configure VNC and XFCE
export SEND_256_COLORS_TO_REMOTE=1
xfwm4 --compositor=off --sm-client-disable
xsetroot -solid "#D3D3D3"
xfsettingsd --sm-client-disable
xfce4-panel --sm-client-disable

# Purge the module environment to avoid conflicts
module purge

# Load the require modules
module load shared cuda10.2/toolkit cudnn7.6-cuda10.2

# List loaded modules
module list

# Benchmark info
echo "TIMING - Starting Fiji at: $(date)"

# Launch the Fiji desktop app
set -x
/share/apps/fiji/Fiji.app/ImageJ-linux64 --heap 1G --no-splash --dont-patch-ij1 --ij2
2

My guess is you’re missing the --deamonize arguement for `xfwm4.

My guess is, with a set -x you’d see it hang on that command.

3

Jeff,

I had --daemon and --daemonize in the initial versions of my script (never together, either one or the other). Both of those flags came back as “unrecognized options” on the xfwm4 command.

4

OK - do you know if you’re proceeding after that statement or is the script hanging somewhere?

What’s the OS of the compute node and the output logs of one of these jobs?

5

It’s getting past that line. It looks like it’s hanging on the xfsettingsd command. OS is RHEL 8.3. output.log is below:

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

WARNING: talon35:1 is taken because of /tmp/.X1-lock
Remove this file if there is no X server talon35:1
Killing Xvnc process ID 2292940
Xvnc process ID 2292940 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: talon35:1 (brad.traver)' started on display talon35:1

Log file is vnc.log
Successfully started VNC server on talon35.ib.cluster:5901...
Starting before.sh...
Script starting...
Starting websocket server...
TIMING - Starting main script at: Tue Jun  7 11:45:08 CDT 2022
xfwm4: Unknown option --daemon.
Type "xfwm4 --help" for usage.
XFWM4 configured

xsetroot done

WebSocket server settings:
  - Listen on :23584
  - No SSL/TLS support (no cert file)
  - Backgrounding (daemon)
Scanning VNC log file for user authentications...
Generating connection YAML file...
xfsettingsd: No window manager registered on screen 0.

(xfsettingsd:2294433): xfsettingsd-WARNING **: 11:45:13.704: Failed to get the _NET_NUMBER_OF_DESKTOPS property.
Setting VNC password...
Generating connection YAML file...
6

What’s the log from a job when xfwm4 actually starts correctly?

7

It looks like it never starts correctly. It seems to hang on the xfwm4 command. This is the only error I see:
(xfwm4:2326764): GLib-CRITICAL **: 14:40:43.777: g_str_has_prefix: assertion 'prefix != NULL' failed

8

hang, meaning it doesn’t background itself. Maybe try an & to do so. Again - we haven’t upgraded yet so I’m sure there’s something on the internet about them removing that option and what to do instead. Maybe a simple --replace?

xfwm4 --compositor=off --sm-client-disable 2>&1 &
9

I’m getting a few more errors but it still hangs at the same command. The addition of --replace didn’t seem to do anything. Errors are below. The last error was printed three times. I only put it once here.

(xfwm4:2330423): GLib-CRITICAL **: 14:59:09.157: g_str_has_prefix: assertion 'prefix != NULL' failed
(xfsettingsd:2330425): GLib-CRITICAL **: 14:59:12.079: g_str_has_prefix: assertion 'prefix != NULL' failed
(xfsettingsd:2330425): GLib-GObject-CRITICAL **: 14:59:12.081: g_value_get_string: assertion 'G_VALUE_HOLDS_STRING (value)' failed
10

Yea I’m not sure what, if any, of those errors are meaningful. Seems to me you need to background the process with a & or similar.

11

I’ve added 2>&1 & to the end of the command. It hasn’t done anything.

12

I removed the 2>&1 and just left the &. No dice.

13

It turns out that the --daemon option needs to be moved to the xfsettingsd command. I’m now getting hung up on the xfce4-panel command.

14

Adding the & to background xfce4-panel seems to fix it.

15

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