I have the VMD app in the dashboard and get the Launch VMD button show up as expected. However, when I clicked the button to open the web browser, the desktop session does not load (only the 3 flashing dots). I checked the websockify.log file and it seems that it stuck without establishing a WebSocket connection
WebSocket server settings:
- Listen on :11684
- No SSL/TLS support (no cert file)
- proxying from :11684 to localhost:5901
vnc.log looks normal:
TurboVNC Server (Xvnc) 64-bit v3.1.1 (build 20240127)
Copyright (C) 1999-2024 The VirtualGL Project and many others (see README.md)
Visit http://www.TurboVNC.org for more information on TurboVNC
18/04/2025 16:03:17 Using security configuration file /etc/turbovncserver-security.conf
18/04/2025 16:03:17 Enabled security type 'tlsvnc'
18/04/2025 16:03:17 Enabled security type 'tlsotp'
18/04/2025 16:03:17 Enabled security type 'tlsplain'
18/04/2025 16:03:17 Enabled security type 'x509vnc'
18/04/2025 16:03:17 Enabled security type 'x509otp'
18/04/2025 16:03:17 Enabled security type 'x509plain'
18/04/2025 16:03:17 Enabled security type 'vnc'
18/04/2025 16:03:17 Enabled security type 'otp'
18/04/2025 16:03:17 Enabled security type 'unixlogin'
18/04/2025 16:03:17 Enabled security type 'plain'
_XSERVTransmkdir: Owner of /tmp/.X11-unix should be set to root
18/04/2025 16:03:17 Desktop name 'TurboVNC: midway3-0200.rcc.local:1 (ndtrung)' (midway3-0200.rcc.local:1)
18/04/2025 16:03:17 Protocol versions supported: 3.3, 3.7, 3.8, 3.7t, 3.8t
18/04/2025 16:03:17 Listening for VNC connections on TCP port 5901
18/04/2025 16:03:17 Interface 0.0.0.0
18/04/2025 16:03:17 Framebuffer: BGRX 8/8/8/8
18/04/2025 16:03:17 New desktop size: 1920 x 1080
18/04/2025 16:03:17 New screen layout:
18/04/2025 16:03:17 0x00000040 (output 0x00000040): 1920x1080+0+0
18/04/2025 16:03:17 Maximum clipboard transfer size: 1048576 bytes
18/04/2025 16:03:17 VNC extension running
Could you please give me some suggestions to troubleshoot this issue?
FWIW, the app worked fine earlier in the week, and this issue started on Wednesday without any changes to the OOD configuration and settings that I can recall.
The issue also persists with other VNC apps (such as MATLAB, COMSOL), which worked successfully earlier.
Setting VNC password...
Starting VNC server...
WARNING: midway3-0200.rcc.local:1 is taken because of /tmp/.X1-lock
Remove this file if there is no X server midway3-0200.rcc.local:1
WARNING: midway3-0200.rcc.local:3 is taken because of /tmp/.X3-lock
Remove this file if there is no X server midway3-0200.rcc.local:3
Killing Xvnc process ID 2441047
Xvnc process ID 2441047 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
Killing Xvnc process ID 2441786
Xvnc process ID 2441786 already killed
Xvnc did not appear to shut down cleanly. Removing /tmp/.X11-unix/X3
Xvnc did not appear to shut down cleanly. Removing /tmp/.X3-lock
Desktop 'TurboVNC: midway3-0200.rcc.local:1 (ndtrung)' started on display midway3-0200.rcc.local:1
Log file is vnc.log
Successfully started VNC server on midway3-0200.rcc.local:5901...
Script starting...
Starting websocket server...
[websockify]: pid: 2676063 (proxying 62996 ==> localhost:5901)
[websockify]: log file: ./websockify.log
[websockify]: waiting ...
dbus[2676072]: Unable to set up transient service directory: XDG_RUNTIME_DIR "/run/user/366719390" not available: No such file or directory
ERROR: Collection default cannot be found
++ dbus-launch
dbus[2676080]: Unable to set up transient service directory: XDG_RUNTIME_DIR "/run/user/366719390" not available: No such file or directory
+ export DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-Mx4NSzLxAF,guid=05c95147c3b3232fb67b6ff268064e5c DBUS_SESSION_BUS_PID=2676082 DBUS_SESSION_BUS_WINDOWID=2097153
+ DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-Mx4NSzLxAF,guid=05c95147c3b3232fb67b6ff268064e5c
+ DBUS_SESSION_BUS_PID=2676082
+ DBUS_SESSION_BUS_WINDOWID=2097153
+ source /etc/os-release
++ NAME='CentOS Linux'
++ VERSION=8
++ ID=centos
++ ID_LIKE='rhel fedora'
++ VERSION_ID=8
++ PLATFORM_ID=platform:el8
++ PRETTY_NAME='CentOS Linux 8'
++ ANSI_COLOR='0;31'
++ CPE_NAME=cpe:/o:centos:centos:8
++ HOME_URL=https://centos.org/
++ BUG_REPORT_URL=https://bugs.centos.org/
++ CENTOS_MANTISBT_PROJECT=CentOS-8
++ CENTOS_MANTISBT_PROJECT_VERSION=8
+ export XDG_RUNTIME_DIR=/scratch/local/jobs/30561076/xdg_runtime
+ XDG_RUNTIME_DIR=/scratch/local/jobs/30561076/xdg_runtime
+ WRAPPER=/home/ndtrung/rcc_ondemand_devlopment/data/sys/dashboard/batch_connect/sys/bc_vmd/output/6175f41d-e18d-4f33-8264-4724538ee7c2/vmd_wrapper.sh
+ echo 'prepare to lauch vmd'
prepare to lauch vmd
+ module load vmd
+ unset _mlshdbg
+ '[' 0 = 1 ']'
+ unset _mlre _mlIFS
+ '[' -n x ']'
+ _mlIFS='
'
+ IFS=' '
+ '[' -n '' ']'
+ xfwm4 --replace
++ /usr/bin/tclsh /software/modules/libexec/modulecmd.tcl bash load vmd
+ eval 'LD_LIBRARY_PATH=/software/vmd-1.9.4-el8-x86_64/lib:/software/slurm-current-el8-x86_64/lib:/software/spack/lib;' export 'LD_LIBRARY_PATH;
LIBRARY_PATH=/software/vmd-1.9.4-el8-x86_64/lib;' export 'LIBRARY_PATH;
LOADEDMODULES=slurm/current:rcc/default:vmd/1.9.4;' export 'LOADEDMODULES;
_LMFILES_=/software/modulefiles/slurm/current:/software/modulefiles/rcc/default:/software/modulefiles/vmd/1.9.4;' export '_LMFILES_;
MODULES_LMALTNAME=vmd/1.9.4\&vmd/default\&vmd;' export 'MODULES_LMALTNAME;
LIBRARY_PATH_modshare=/software/vmd-1.9.4-el8-x86_64/lib:1;' export 'LIBRARY_PATH_modshare;
MODULES_LMCONFLICT=vmd/1.9.4\&vmd;' export 'MODULES_LMCONFLICT;
MODULES_LMALTNAME_modshare=vmd/1.9.4\&vmd/default\&vmd:1;' export 'MODULES_LMALTNAME_modshare;
MODULES_LMCONFLICT_modshare=vmd/1.9.4\&vmd:1;' export 'MODULES_LMCONFLICT_modshare;
LD_LIBRARY_PATH_modshare=/software/slurm-current-el8-x86_64/lib:1:/software/spack/lib:1:/software/vmd-1.9.4-el8-x86_64/lib:1;' export 'LD_LIBRARY_PATH_modshare;
LOADEDMODULES_modshare=vmd/1.9.4:1:rcc/default:1:slurm/current:1;' export 'LOADEDMODULES_modshare;
_LMFILES__modshare=/software/modulefiles/vmd/1.9.4:1:/software/modulefiles/rcc/default:1:/software/modulefiles/slurm/current:1;' export '_LMFILES__modshare;
PATH=/software/vmd-1.9.4-el8-x86_64/bin:/software/bin:/software/slurm-current-el8-x86_64/bin:/opt/TurboVNC/bin:/software/intel/oneapi_hpc_2022.1/vtune/2022.0.0/bin64:/software/intel/oneapi_hpc_2023.1/debugger/2023.1.0/gdb/intel64/bin:/software/intel/oneapi_hpc_2023.1/inspector/2023.1.0/bin64:/home/ndtrung/.local/bin:/home/ndtrung/bin:/software/modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/project/rcc/trung/scalasca-2.6/install/bin:/project/rcc/trung/scorep-7.1/install/bin:/project/rcc/trung/cubelib-4.7/install/bin:/project/rcc/trung/cubegui-4.6/install/bin:/project/rcc/trung/apptainer/install/bin:/project/rcc/trung/mmseqs/bin:/project/rcc/trung/sources/VSCode-linux-x64/bin:/project/rcc/trung/meld-3.20.4/bin:/project/rcc/trung/SimNIBS/bin;' export 'PATH;
PATH_modshare=/project/rcc/trung/SimNIBS/bin:1:/home/ndtrung/.local/bin:1:/home/ndtrung/bin:1:/usr/bin:1:/software/bin:1:/software/intel/oneapi_hpc_2022.1/vtune/2022.0.0/bin64:1:/usr/local/bin:1:/project/rcc/trung/apptainer/install/bin:1:/project/rcc/trung/sources/VSCode-linux-x64/bin:1:/software/slurm-current-el8-x86_64/bin:1:/project/rcc/trung/meld-3.20.4/bin:1:/software/intel/oneapi_hpc_2023.1/debugger/2023.1.0/gdb/intel64/bin:1:/project/rcc/trung/scorep-7.1/install/bin:1:/software/vmd-1.9.4-el8-x86_64/bin:1:/project/rcc/trung/mmseqs/bin:1:/software/modules/bin:1:/software/intel/oneapi_hpc_2023.1/inspector/2023.1.0/bin64:1:/project/rcc/trung/cubegui-4.6/install/bin:1:/opt/TurboVNC/bin:1:/usr/sbin:1:/project/rcc/trung/cubelib-4.7/install/bin:1:/usr/local/sbin:1:/project/rcc/trung/scalasca-2.6/install/bin:1;' export 'PATH_modshare;
test' '0;'
++ LD_LIBRARY_PATH=/software/vmd-1.9.4-el8-x86_64/lib:/software/slurm-current-el8-x86_64/lib:/software/spack/lib
++ export LD_LIBRARY_PATH
++ LIBRARY_PATH=/software/vmd-1.9.4-el8-x86_64/lib
++ export LIBRARY_PATH
++ LOADEDMODULES=slurm/current:rcc/default:vmd/1.9.4
++ export LOADEDMODULES
++ _LMFILES_=/software/modulefiles/slurm/current:/software/modulefiles/rcc/default:/software/modulefiles/vmd/1.9.4
++ export _LMFILES_
++ MODULES_LMALTNAME='vmd/1.9.4&vmd/default&vmd'
++ export MODULES_LMALTNAME
++ LIBRARY_PATH_modshare=/software/vmd-1.9.4-el8-x86_64/lib:1
++ export LIBRARY_PATH_modshare
++ MODULES_LMCONFLICT='vmd/1.9.4&vmd'
++ export MODULES_LMCONFLICT
++ MODULES_LMALTNAME_modshare='vmd/1.9.4&vmd/default&vmd:1'
++ export MODULES_LMALTNAME_modshare
++ MODULES_LMCONFLICT_modshare='vmd/1.9.4&vmd:1'
++ export MODULES_LMCONFLICT_modshare
++ LD_LIBRARY_PATH_modshare=/software/slurm-current-el8-x86_64/lib:1:/software/spack/lib:1:/software/vmd-1.9.4-el8-x86_64/lib:1
++ export LD_LIBRARY_PATH_modshare
++ LOADEDMODULES_modshare=vmd/1.9.4:1:rcc/default:1:slurm/current:1
++ export LOADEDMODULES_modshare
++ _LMFILES__modshare=/software/modulefiles/vmd/1.9.4:1:/software/modulefiles/rcc/default:1:/software/modulefiles/slurm/current:1
++ export _LMFILES__modshare
++ PATH=/software/vmd-1.9.4-el8-x86_64/bin:/software/bin:/software/slurm-current-el8-x86_64/bin:/opt/TurboVNC/bin:/software/intel/oneapi_hpc_2022.1/vtune/2022.0.0/bin64:/software/intel/oneapi_hpc_2023.1/debugger/2023.1.0/gdb/intel64/bin:/software/intel/oneapi_hpc_2023.1/inspector/2023.1.0/bin64:/home/ndtrung/.local/bin:/home/ndtrung/bin:/software/modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/project/rcc/trung/scalasca-2.6/install/bin:/project/rcc/trung/scorep-7.1/install/bin:/project/rcc/trung/cubelib-4.7/install/bin:/project/rcc/trung/cubegui-4.6/install/bin:/project/rcc/trung/apptainer/install/bin:/project/rcc/trung/mmseqs/bin:/project/rcc/trung/sources/VSCode-linux-x64/bin:/project/rcc/trung/meld-3.20.4/bin:/project/rcc/trung/SimNIBS/bin
++ export PATH
++ PATH_modshare=/project/rcc/trung/SimNIBS/bin:1:/home/ndtrung/.local/bin:1:/home/ndtrung/bin:1:/usr/bin:1:/software/bin:1:/software/intel/oneapi_hpc_2022.1/vtune/2022.0.0/bin64:1:/usr/local/bin:1:/project/rcc/trung/apptainer/install/bin:1:/project/rcc/trung/sources/VSCode-linux-x64/bin:1:/software/slurm-current-el8-x86_64/bin:1:/project/rcc/trung/meld-3.20.4/bin:1:/software/intel/oneapi_hpc_2023.1/debugger/2023.1.0/gdb/intel64/bin:1:/project/rcc/trung/scorep-7.1/install/bin:1:/software/vmd-1.9.4-el8-x86_64/bin:1:/project/rcc/trung/mmseqs/bin:1:/software/modules/bin:1:/software/intel/oneapi_hpc_2023.1/inspector/2023.1.0/bin64:1:/project/rcc/trung/cubegui-4.6/install/bin:1:/opt/TurboVNC/bin:1:/usr/sbin:1:/project/rcc/trung/cubelib-4.7/install/bin:1:/usr/local/sbin:1:/project/rcc/trung/scalasca-2.6/install/bin:1
++ export PATH_modshare
++ test 0
+ _mlstatus=0
+ '[' -n x ']'
+ IFS='
'
+ unset _mlre _mlv _mlrv _mlIFS
+ '[' -n '' ']'
+ unset _mlshdbg
+ return 0
+ which vmd
/software/vmd-1.9.4-el8-x86_64/bin/vmd
+ sleep 2
(xfwm4:2676083): GLib-CRITICAL **: 08:55:41.158: g_str_has_prefix: assertion 'prefix != NULL' failed
[websockify]: started successfully (proxying 62996 ==> localhost:5901)
Scanning VNC log file for user authentications...
Generating connection YAML file...
(xfwm4:2676083): xfwm4-WARNING **: 08:55:41.713: Another compositing manager is running on screen 0
(xfwm4:2676083): xfwm4-WARNING **: 08:55:41.714: Failed to connect to session manager: Failed to connect to the session manager: SESSION_MANAGER environment variable not defined
+ set -x
+ export VGL_DISPLAY=:1
+ VGL_DISPLAY=:1
+ xfce4-terminal -e 'vglrun /software/vmd-1.9.4-el8-x86_64/bin/vmd' -T 'VMD Terminal'
Failed to connect to session manager: Failed to connect to the session manager: SESSION_MANAGER environment variable not defined
This is OOD 4.0.1.
FWIW, the issue only arose after April 17 on my site, the same app folder had functioned normally earlier. Is there any possiblity that some changes made outside the app folder that lead to this issue?
Sure - if the OS is updated/reconfigured or anything like that.
This may be your underlying issue. Here’s what we do for desktops that run MATE to avoid the issue. Note we do this for desktops, but you can set it globally in the cluster.d file for all your VNC applications.
My colleague and I have tracked down the issue to the missing common.js under dashboard/public/noVNC-1.3.0/vendor/pako/lib/utils. We found the error message
ActionController::RoutingError (No route matches [GET] \"/noVNC-1.3.0/vendor/pako/lib/utils/common.js\"):
in /var/log/ondemand-nginx/ood/error.log
All the VNC apps are back to working now with that file put in place.