Unable to load IGV app with VNC template


I am trying to bring up this app.

But the job is stuck at starting.
When i check the logs in scheduler . I see this:

<< output from stdout >>
Setting VNC password…
Starting VNC server…

Desktop ‘TurboVNC: je17:1 (vallerul)’ started on display je17:1

Log file is vnc.log
Successfully started VNC server on je17:5901…
Script starting…
Starting websocket server…

  • singularity exec -B /var:/var /opt/common/ondemand/igv/xfce-ood-desktop_latest.sif xfwm4 --compositor=off --daemon --sm-client-disable
    Currently Loaded Modulefiles:
    1. singularity/3.6.0 2) igv/2.12.1
  • igv
    echo Using bundled JDK.
    WebSocket server settings:
    • Listen on :5018
    • Flash security policy server
    • No SSL/TLS support (no cert file)
    • Backgrounding (daemon)
      Scanning VNC log file for user authentications…
      /scratch/lsftmp/1644535625.14952649.shell: line 198: syntax error near unexpected token (' /scratch/lsftmp/1644535625.14952649.shell: line 198: done << (tail -f --pid=${SCRIPT_PID} “vnc.log”) &’
      WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
      WARNING: package sun.awt.windows not in java.desktop
      openjdk version “11.0.13” 2021-10-19
      OpenJDK Runtime Environment Temurin-11.0.13+8 (build 11.0.13+8)
      OpenJDK 64-Bit Server VM Temurin-11.0.13+8 (build 11.0.13+8, mixed mode)
      INFO [Feb 10,2022 18:27] [Globals] Development mode is enabled
      INFO [Feb 10,2022 18:27] [Main] Startup IGV Version 2.12.1 02/09/2022 05:27 PM
      INFO [Feb 10,2022 18:27] [Main] Java 11.0.13 (build 11.0.13+8) 2021-10-19
      INFO [Feb 10,2022 18:27] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
      INFO [Feb 10,2022 18:27] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-11.0.13+8
      INFO [Feb 10,2022 18:27] [Main] OS: Linux 3.10.0-1160.45.1.el7.x86_64 amd64
      INFO [Feb 10,2022 18:27] [Main] IGV Directory: /sysadmin/home/vallerul/igv
      INFO [Feb 10,2022 18:27] [GenomeManager] Loading genome: https://s3.amazonaws.com/igv.org.genomes/hg19/hg19.json
      INFO [Feb 10,2022 18:27] [TrackLoader] Loading resource: https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz

(xfwm4:76768): GLib-CRITICAL **: 18:27:41.604: g_str_has_prefix: assertion ‘prefix != NULL’ failed

(xfwm4:76768): xfwm4-WARNING **: 18:27:43.846: The property ‘/general/double_click_distance’ of type int is not supported

I see syntax errors for vnc.log, and i am not sure why the app is not working.

May i know if i could get help to fix this?


It happens to be a bash substitution issue. I see that it was mentioned under sun grid engine issues. I added the respective commands as below, and it now works as expected.
script_wrapper: |
set +o posix

Looks like you’re running LSF? This is a known issue with SGE, maybe it applies to LSF too?


Yes Jeff,

I had realized later that , it was indeed the issue.

Thank you


Thanks. So are you on LSF? If so, I can add the same docs to that page so other LSF folks know they may run into the same issue.

Yes Jeff,
We use LSF.
I did find it surprising that no one else found this as an issue when running on LSF.
May be they did, and used the above solution.
But yes - it would be good to add this under LSF known issues.
Thank you.

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