Mounting Large Volume #82

etmaddox-creator · 2025-12-19T18:21:26Z

etmaddox-creator
Dec 19, 2025

Hello! Has anyone found success mounting a large drive (~50TB) inside Neurodesktop? I have been trying to mount an nfs drive around that size but Jupyterlab consistently times out before successful startup. I can start an instance with a smaller folder on the nfs drive, but that doesn't contain all of the data that I'm hoping to access. When I try to mount the whole drive, the container is created but does not start, and while it's possible to start this container from the command line, it's quite slow and doesn't provide access to the GUI. I am running Neurodesk with Docker on Linux. Any suggestions you all may have for this issue would be greatly appreciated!

stebo85 · 2025-12-19T18:53:44Z

stebo85
Dec 19, 2025
Maintainer

Dear @etmaddox-creator - can you share more details on how you are mounting that drive exactly? Did you try it via the mount options of docker? Have you tried mounting it after the hub started? Is this nfs drive mapped on your Linux machine and you are trying to pass it through to docker?

4 replies

etmaddox-creator Dec 19, 2025
Author

Yes, the drive is mapped on the Linux machine and I am trying to make it accessible to the Neurodesktop container. To do so, I've added it as an additional data directory in the Neurodesktop settings prior to actually creating the Desktop environment. I've given Docker access to the drive and once the container is created it shows up under the "bind mount" section of the container settings within Docker Desktop. Once I try to start the desktop environment, it hangs on the "creating new session" screen before timing out after 40 minutes (I think that's what the logs show, I've attached them below). I'm not 100% what you mean by trying to mount it after the hub started. Does this answer that question? If not, how can I do that? Thanks for the response!

[2025-12-12 09:55:59.441] [info] In production mode
[2025-12-12 09:55:59.479] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'debug' level
[2025-12-12 09:55:59.572] [info] startupMode welcome-page
[2025-12-12 09:55:59.573] [info] sessionConfig undefined
[2025-12-12 09:56:02.017] [debug] serverOptions {
workingDirectory: '/nfs/tpolk/mind/',
environment: {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
}
}
[2025-12-12 09:56:02.018] [info] ~ createServer {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
}
[2025-12-12 09:56:02.019] [debug] Starting Jupyter server....
[2025-12-12 09:56:02.020] [debug] isWin: false
[2025-12-12 09:56:02.023] [debug] ~ createServer ~ {
factoryId: 1,
server: {
_stopServer: null,
_startServer: {},
_info: {
type: 'local',
engine: 'docker',
url: null,
port: null,
token: null,
workingDirectory: '/nfs/tpolk/mind/',
environment: {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
},
serverArgs: '/nfs/tpolk/mind/',
overrideDefaultServerArgs: false,
serverEnvVars: {},
version: null,
cvmfsMode: 'false'
},
_stopping: false,
_restartCount: 0,
_options: {
workingDirectory: '/nfs/tpolk/mind/',
environment: {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
}
},
_progressView: {
_view: { _isDarkTheme: true, _view: {} },
_pageBody: '\n' +
' <style>\n' +
' .container {\n' +
' display: flex;\n' +
' height: 100%;\n' +
' flex-direction: column;\n' +
' font-size: 16px;\n' +
' }\n' +
' .row {\n' +
' display: flex;\n' +
' flex-direction: row;\n' +
' line-height: 18px;\n' +
' }\n' +
' .progress-logo-row {\n' +
' flex-direction: column;\n' +
' align-items: center;\n' +
' flex-grow: 1;\n' +
' padding-top: 100px;\n' +
' }\n' +
' .progress-logo {\n' +
' height: 100%;\n' +
' display: flex;\n' +
' flex-direction: row;\n' +
' align-items: center;\n' +
' }\n' +
' .progress-logo svg {\n' +
' width: 200px;\n' +
' height: 200px;\n' +
' }\n' +
' .progress-message-row {\n' +
' width: 100%;\n' +
' height: 50%;\n' +
' flex-direction: column;\n' +
' align-items: center;\n' +
' }\n' +
' #progress-title, #progress-detail, #child-process-log {\n' +
' width: 80%;\n' +
' text-align: center;\n' +
' }\n' +
' #progress-title {\n' +
' margin-bottom: 15px;\n' +
' font-weight: bold;\n' +
' }\n' +
' #progress-detail {\n' +
' font-size: 14px;\n' +
' }\n' +
' #child-process-log {\n' +
' border-top: 1px solid #e7e7e7;\n' +
' padding-top: 20px;\n' +
' font-size: 12px;\n' +
' overflow-y: scroll;\n' +
' max-height: 150px;\n' +
' }\n' +
' .message-row {\n' +
' padding-bottom: 10px;\n' +
' }\n' +
' </style>\n' +
' \n' +
'

\n' +
'

\n' +
'\n' +
' \n' +
' \n' +
' <style>\n' +
' .st0 {\n' +
' fill: none;\n' +
' stroke-width: 5px;\n' +
' }\n' +
'\n' +
' .st0, .st1 {\n' +
' stroke: #fff;\n' +
' stroke-miterlimit: 10;\n' +
' }\n' +
'\n' +
' .st2 {\n' +
' fill: #6aa329;\n' +
' }\n' +
'\n' +
' .st3, .st1 {\n' +
' fill: #fff;\n' +
' }\n' +
'\n' +
' .st4 {\n' +
' fill: #101806;\n' +
' }\n' +
' </style>\n' +
' \n' +
' \n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' \n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' />\n' +
' \n' +
' <animateMotion\n' +
' path="M0,0 0 90 0 0"\n' +
' begin="0s" dur="4s" repeatCount="indefinite"\n' +
' /><'... 4912 more characters,
_viewReady: {}
}
},
closing: null,
used: true
}
[2025-12-12 09:56:02.029] [info] token jlab:srvr:0f9776631a3b6f24c3c3cbe7bdd2f689ee8dd1
[2025-12-12 09:56:02.031] [debug] Loading config from /opt/NeurodeskApp/resources/app.asar/build/out/neurodesktop.toml...
[2025-12-12 09:56:02.055] [info] isDev false
[2025-12-12 09:56:02.136] [debug] !!!..... 40415 engineType docker
[2025-12-12 09:56:02.141] [debug] Server launch script:

    if [[ "$(docker image inspect vnmd/neurodesktop:2025-06-10 --format='exists' 2> /dev/null)" == "exists" ]]; then 
      docker rm -f neurodeskapp-40415 &> /dev/null 
      
      docker run -d --rm --shm-size=1gb -it --privileged --user=root --name neurodeskapp-40415 -p 40415:40415 -e NEURODESKTOP_VERSION=2025-06-10 -e CVMFS_DISABLE=false -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6   --volume "/nfs/tpolk/mind/":/data vnmd/neurodesktop:2025-06-10  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:0f9776631a3b6f24c3c3cbe7bdd2f689ee8dd1' --ServerApp.port=40415 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember 
    else
      docker rm -f neurodeskapp-40415 &> /dev/null
      
      docker pull docker.io/vnmd/neurodesktop:2025-06-10
      docker run -d --rm --shm-size=1gb -it --privileged --user=root --name neurodeskapp-40415 -p 40415:40415 -e NEURODESKTOP_VERSION=2025-06-10 -e CVMFS_DISABLE=false -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6   --volume "/nfs/tpolk/mind/":/data vnmd/neurodesktop:2025-06-10  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:0f9776631a3b6f24c3c3cbe7bdd2f689ee8dd1' --ServerApp.port=40415 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember 
    fi

[2025-12-12 09:56:04.644] [debug] setChildProcessLog a94376bbd404ef797268e2eeddb1c1b2333258f1c4bee61384345558e3e1d081

[2025-12-12 10:36:02.153] [debug] Server didn't start in time
[2025-12-12 10:36:02.155] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 40415a94376bbd404ef797268e2eeddb1c1b2333258f1c4bee61384345558e3e1d081

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:355:28

[2025-12-12 10:36:02.161] [error] (node:1385470) UnhandledPromiseRejectionWarning: TypeError: Cannot read properties of undefined (reading 'protocol')
at new LabView (/opt/NeurodeskApp/resources/app.asar/build/out/main/labview/labview.js:45:50)
at SessionWindow._loadLabView (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:267:25)
at SessionWindow._updateContentView (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:677:18)
at IpcMainImpl. (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:421:18)
(Use neurodeskapp --trace-warnings ... to show where the warning was created)
[2025-12-12 10:36:02.162] [error] (node:1385470) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag --unhandled-rejections=strict (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 1)

stebo85 Dec 19, 2025
Maintainer

Dear @etmaddox-creator,

Let's try to find out where the problem comes from. It sounds like something is trying to change ownership of files on this mount which times out.

Can you try to start the container manually without the neurodesk-app?

docker volume create neurodesk-home &&
sudo docker run \
  --shm-size=1gb -it --security-opt apparmor=neurodeskapp --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  --mount source=neurodesk-home,target=/home/jovyan \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2025-12-03 vnmd/neurodesktop:2025-12-03

if that works, add your mount:

docker volume create neurodesk-home &&
sudo docker run \
  --shm-size=1gb -it --security-opt apparmor=neurodeskapp --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  --mount source=neurodesk-home,target=/home/jovyan \
  -v /nfs/tpolk/mind/:/data \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2025-12-03 vnmd/neurodesktop:2025-12-03

etmaddox-creator Dec 19, 2025
Author

That works, thank you so much!! I can access the web UI with the NFS drive mounted and it appears to be responsive.

I had to change apparmor=unconfined because I kept getting an error when trying to run those commands with apparmor=neurodesktop. Could this be causing the issues? I'm running Ubuntu 22.04.5 LTS. I've tried to run the container without any apparmor changes and by adding the profile shown here.

stebo85 Dec 19, 2025
Maintainer

Dear @etmaddox-creator - that's very helpful! The problem is that the Neurodesk-app appears to be performing chown operations on the additional data mount (@iishiishii - can you verify?). Ubuntu 22.04.5 shouldn't need the apparmor setting at all, so that's why it failed, but apparmor=uncfonfined will not cause any problems.

We will update the neurodeskapp once we found out what the cause is and then it would be wonderful if you could test again. For now, I hope the workaround is ok.

etmaddox-creator · 2025-12-19T20:27:46Z

etmaddox-creator
Dec 19, 2025
Author

That workaround is perfect for now, thank you so much for your help. I'm happy to test it again in the future.

8 replies

stebo85 Apr 10, 2026
Maintainer

@iishiishii - are you looking into this for the next release?

iishiishii Apr 24, 2026
Maintainer

@jsneal1 @ethanmaddox @etmaddox-creator apologies for the delayed fix, this latest version will allow you to mount the storage without us touching on its permissions. The files inside /data have the same ownership as the host filesystem, so non-root process inside the container will be subject to host dir's permission. You can test the pre-release here

etmaddox-creator Apr 24, 2026
Author

@stebo85 @iishiishii Thank you for this update. Unfortunately, the pre-release version is still giving me an error when starting up the container.

[2026-04-24 15:44:21.704] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-04-24 15:44:21.788] [info] startupMode welcome-page
[2026-04-24 15:44:21.788] [info] sessionConfig undefined
[2026-04-24 15:44:24.279] [info] ~ createServer { workingDirectory: '/nfs/tpolk/mind' }
[2026-04-24 15:44:24.284] [info] token jlab:srvr:b6008bb4f498335d443e5c13299f76833d6f11
[2026-04-24 15:44:24.284] [info] ServerApp.port=36015
[2026-04-24 15:44:24.292] [info] isDev false
[2026-04-24 16:12:54.949] [info] child process exited with code 0 and signal null
[2026-04-24 16:12:54.950] [info] token jlab:srvr:b6008bb4f498335d443e5c13299f76833d6f11
[2026-04-24 16:12:54.951] [info] ServerApp.port=36015
[2026-04-24 16:12:54.958] [info] isDev false
[2026-04-24 16:24:24.409] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 36015a0f664bfc08ab1462c8e1f9cd3c6ea0545063e308939ff740e6104cb4913c282

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:412:28

[2026-04-24 16:24:24.415] [error] (node:2600228) UnhandledPromiseRejectionWarning: TypeError: Cannot read properties of undefined (reading 'protocol')
at new LabView (/opt/NeurodeskApp/resources/app.asar/build/out/main/labview/labview.js:45:50)
at SessionWindow._loadLabView (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:240:25)
at SessionWindow._updateContentView (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:585:18)
at IpcMainImpl. (/opt/NeurodeskApp/resources/app.asar/build/out/main/sessionwindow/sessionwindow.js:387:18)
(Use neurodeskapp --trace-warnings ... to show where the warning was created)
[2026-04-24 16:24:24.416] [error] (node:2600228) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag --unhandled-rejections=strict (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 1)

stebo85 Apr 24, 2026
Maintainer

thank you for testing this - we try to replicate this and get back to you with a new version to try

iishiishii Apr 27, 2026
Maintainer

and make sure to uninstall previous version and remove cache https://github.com/neurodesk/neurodesk-app/blob/master/user-guide.md#uninstalling-neurodesk-app, the latest log above doesn't seem to print out the launch script before failing so it might have old state that won't work in the latest version.

jsneal1 · 2026-04-24T20:45:26Z

jsneal1
Apr 24, 2026

Does it matter that we are using nfs version 3 to mount the shared drive? It’s handled by /etc/fstab to mount at startup. If there’s any info we can gather for you let us know we are happy to help. Best Regards, Jeffrey Neal ***@***.*** LSA EHTS Desktop Support Specialist Senior University of Michigan

…

On Apr 24, 2026, at 4:41 PM, Steffen Bollmann ***@***.***> wrote: a

3 replies

stebo85 Apr 24, 2026
Maintainer

yes, most likely it is related to this because we cannot replicate the exact problem you get. we now added a few mitigations against known nfs issues and the new version is currently building. I think we will just have to test a few iterations until we get to the core of this.

stebo85 Apr 24, 2026
Maintainer

@ethanmaddox @etmaddox-creator @jsneal1 : https://github.com/neurodesk/neurodesk-app/actions/runs/24911409436 - can you test this and report back with error logs?

etmaddox-creator Apr 27, 2026
Author

@stebo85 It looks like this patch made some progress but the end result was still the same (timed out at 40 minutes on loading screen). Thank you for the reminder about fully uninstalling the previous version, I believe that I was doing that before but have double checked it this time.

[2026-04-27 13:27:27.116] [info] In production mode
[2026-04-27 13:27:27.118] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-04-27 13:27:27.231] [info] startupMode welcome-page
[2026-04-27 13:27:27.232] [info] sessionConfig undefined
[2026-04-27 13:27:46.431] [info] In production mode
[2026-04-27 13:27:46.433] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-04-27 13:27:46.536] [info] startupMode welcome-page
[2026-04-27 13:27:46.537] [info] sessionConfig undefined
[2026-04-27 13:27:51.243] [info] ~ createServer {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
}
[2026-04-27 13:27:51.247] [info] token jlab:srvr:70e1f1325ef139cb7da7aa55b9fac59c125415
[2026-04-27 13:27:51.265] [info] isDev false
[2026-04-27 13:27:51.366] [info] Skipping chmod for network/remote directory: /nfs/tpolk/mind
[2026-04-27 13:27:51.366] [info] Detected nfs working directory; mounting /nfs/tpolk/mind at its native path
[2026-04-27 14:07:51.375] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 46447d6f9f671ecdd89c0061779a456c4aaacabb4d8b29f0f4edc79b5f42036740c57

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:398:28

jsneal1 · 2026-04-28T13:05:21Z

jsneal1
Apr 28, 2026

Are there any specific cached files / locations we need to delete? I would assume it writes cached data to a users profile? Best Regards, Jeffrey Neal ***@***.*** LSA EHTS Desktop Support Specialist Senior University of Michigan

…

On Apr 27, 2026, at 2:20 PM, etmaddox-creator ***@***.***> wrote: @stebo85 <https://github.com/stebo85> It looks like this patch made some progress but the end result was still the same (timed out at 40 minutes on loading screen). Thank you for the reminder about fully uninstalling the previous version, I believe that I was doing that before but have double checked it this time. [2026-04-27 13:27:27.116] [info] In production mode [2026-04-27 13:27:27.118] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level [2026-04-27 13:27:27.231] [info] startupMode welcome-page [2026-04-27 13:27:27.232] [info] sessionConfig undefined [2026-04-27 13:27:46.431] [info] In production mode [2026-04-27 13:27:46.433] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level [2026-04-27 13:27:46.536] [info] startupMode welcome-page [2026-04-27 13:27:46.537] [info] sessionConfig undefined [2026-04-27 13:27:51.243] [info] ~ createServer { name: 'python', path: 'C:\', type: 'path', versions: {}, defaultKernel: 'python3' } [2026-04-27 13:27:51.247] [info] token jlab:srvr:70e1f1325ef139cb7da7aa55b9fac59c125415 [2026-04-27 13:27:51.265] [info] isDev false [2026-04-27 13:27:51.366] [info] Skipping chmod for network/remote directory: /nfs/tpolk/mind [2026-04-27 13:27:51.366] [info] Detected nfs working directory; mounting /nfs/tpolk/mind at its native path [2026-04-27 14:07:51.375] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 46447d6f9f671ecdd89c0061779a456c4aaacabb4d8b29f0f4edc79b5f42036740c57 at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:398:28 — Reply to this email directly, view it on GitHub <https://github.com/orgs/neurodesk/discussions/661#discussioncomment-16732863>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALYJWG7SMNHE4JY66GTYQOL4X6QGJAVCNFSM6AAAAACPSEXOLSVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMNZTGI4DMMY>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.

7 replies

iishiishii Apr 29, 2026
Maintainer

appreciate sending the log @etmaddox-creator, could you also please send me the docker logs when running the app with nfs mounted? I'll look into both of the errors.

etmaddox-creator Apr 29, 2026
Author

Surprisingly, I was able to open the desktop environment with the nfs drive mounted! I've attached the docker and neurodesk logs below. It was very glitchy. I tried to close the container and reopen it but have gotten a new set of errors. I'm not sure why it is saying second instance, the container was deleted. There are no docker logs for this as it doesn't appear to be creating a container.

New errors when trying to reopen it:

[2026-04-29 13:27:00.842] [warn] [SECOND-INSTANCE] No files found in cliArgs
[2026-04-29 13:27:00.843] [error] undefined
[2026-04-29 13:27:08.149] [info] In production mode
[2026-04-29 13:27:08.151] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level

Neurodesktop:
In production mode
[2026-04-29 10:26:52.931] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-04-29 10:26:53.063] [info] startupMode welcome-page
[2026-04-29 10:26:53.063] [info] sessionConfig undefined
[2026-04-29 10:27:10.139] [info] ~ createServer {
name: 'python',
path: 'C:\',
type: 'path',
versions: {},
defaultKernel: 'python3'
}
[2026-04-29 10:27:10.144] [info] token jlab:srvr:5b7c8c97811e71a06c74f839b945398d496637
[2026-04-29 10:27:10.157] [info] isDev false
[2026-04-29 10:27:10.249] [info] Skipping chmod for network/remote directory: /nfs/tpolk/mind
[2026-04-29 10:27:10.250] [info] Detected nfs working directory; mounting /nfs/tpolk/mind at its native path
[2026-04-29 10:55:04.950] [info] child process exited with code 0 and signal null
[2026-04-29 10:59:49.998] [info] delete launchScriptPath /tmp/neurodesk_appXa6UeE/launch.sh
[2026-04-29 10:59:51.178] [warn] Unsatisfied version 4.6.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/apputils (required ^4.7.0-alpha.4)
[2026-04-29 10:59:51.178] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/launcher (required ^4.6.0-alpha.4)
[2026-04-29 10:59:51.178] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/ui-components (required ^4.6.0-alpha.4)
[2026-04-29 10:59:51.179] [warn] Unsatisfied version 7.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/services (required ^7.6.0-alpha.4)
[2026-04-29 10:59:51.179] [warn] Unsatisfied version 6.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/coreutils (required ^6.6.0-alpha.4)
[2026-04-29 10:59:51.187] [warn] Unsatisfied version 4.1.7 from @jupyter-widgets/jupyterlab-manager of shared singleton module @jupyter-widgets/base (required ^6)
[2026-04-29 10:59:51.214] [warn] Unsatisfied version 2.2.2 from @jupyterlab/application-top of shared singleton module @lumino/coreutils (required ^1.11.0)
[2026-04-29 10:59:51.234] [warn] Unsatisfied version 2.0.4 from @jupyterlab/application-top of shared singleton module @lumino/messaging (required ^1.10.0)
[2026-04-29 10:59:51.237] [warn] Unsatisfied version 2.7.5 from @jupyterlab/application-top of shared singleton module @lumino/widgets (required ^1.37.2)
[2026-04-29 10:59:51.252] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/rendermime (required ^3.2.8)
[2026-04-29 10:59:51.293] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/application (required ^4.6.0-alpha.4)
[2026-04-29 10:59:51.293] [warn] Unsatisfied version 4.6.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/apputils (required ^4.7.0-alpha.4)
[2026-04-29 10:59:51.294] [warn] Unsatisfied version 6.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/coreutils (required ^6.6.0-alpha.4)
[2026-04-29 10:59:51.294] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/filebrowser (required ^4.6.0-alpha.4)
[2026-04-29 10:59:51.294] [warn] Unsatisfied version 4.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/launcher (required ^4.6.0-alpha.4)
[2026-04-29 10:59:51.295] [warn] Unsatisfied version 7.5.6 from @jupyterlab/application-top of shared singleton module @jupyterlab/services (required ^7.6.0-alpha.4)
[2026-04-29 10:59:53.086] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 10:59:53.344] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 10:59:53.463] [warn] Deprecated shortcut selectors: ".jp-Notebook:focus" was replaced with ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus" in JupyterLab 4.1 (present in ".lm-Widget.reveal .jp-Notebook:focus")
".jp-Notebook:focus" was replaced with ".jp-Notebook.jp-mod-commandMode:not(.jp-mod-readWrite) :focus" in JupyterLab 4.1 (present in ".jp-Notebook:focus")

The selectors will be substituted transparently this time, but need to be updated at source before next major release.
[2026-04-29 10:59:53.573] [info] JupyterLab extension jupyterlab-myst is activated!
[2026-04-29 10:59:53.629] [verbose] Starting application in workspace: "default"
[2026-04-29 10:59:53.719] [info] JupyterLab extension jupyterlab-niivue is activated!
[2026-04-29 10:59:53.743] [info] Using jupyterlab-myst:mime-renderer
[2026-04-29 10:59:53.764] [info] JupyterLab extension @notebook-intelligence/notebook-intelligence is activated!
[2026-04-29 10:59:53.783] [info] JupyterLab extension jupyterlab-slurm is activated!
[2026-04-29 10:59:53.784] [info] After restore:
[2026-04-29 10:59:53.804] [info] [object Object]
[2026-04-29 10:59:53.804] [info] Loaded UserSettings: [object Object]
[2026-04-29 10:59:53.817] [info] Using jupyterlab-myst:executor
[2026-04-29 10:59:53.818] [info] JupyterLab extension jupyterlab-rise is activated!
[2026-04-29 10:59:53.927] [verbose] SyntaxError: Unexpected token 'i', "file or dir"... is not valid JSON
[2026-04-29 10:59:53.997] [info] get_example [object Object]
[2026-04-29 10:59:53.997] [info] user jovyan
[2026-04-29 10:59:54.032] [info] JupyterFrontEnd extension lmod/tmod is activated!
[2026-04-29 10:59:54.052] [info] Module system found: lmod
[2026-04-29 10:59:54.053] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 10:59:55.170] [warn] Skipping [object Object] default shortcut because it collides with another enabled default shortcut: [object Object]
[2026-04-29 10:59:55.171] [warn] Skipping [object Object] default shortcut because it collides with another enabled default shortcut: [object Object]
[2026-04-29 11:00:55.103] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:01:56.119] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:02:57.165] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:03:58.211] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:04:59.257] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:06:00.303] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:07:01.353] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:08:02.396] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:09:03.415] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:10:04.461] [warn] Default kernel not found, using 'conda-base-py'
[2026-04-29 11:11:05.508] [warn] Default kernel not found, using 'conda-base-py'

Docker:

Entered start.sh with args: start.sh jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:5b7c8c97811e71a06c74f839b945398d496637 --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
Running hooks in: /usr/local/bin/start-notebook.d as uid: 0 gid: 0
Sourcing shell script: /usr/local/bin/start-notebook.d/start_notebook.sh
Done running hooks in: /usr/local/bin/start-notebook.d
Update jovyan's UID:GID to 114461999:513
userdel: group jovyan not removed because it is not the primary group of user jovyan.
useradd warning: jovyan's uid 114461999 outside of the UID_MIN 1000 and UID_MAX 60000 range.
Granting jovyan passwordless sudo rights!
Running hooks in: /usr/local/bin/before-notebook.d as uid: 0 gid: 0
Sourcing shell script: /usr/local/bin/before-notebook.d/10activate-conda-env.sh
Sourcing shell script: /usr/local/bin/before-notebook.d/before_notebook.sh
[TIMING] critical-startup started
binfmt_misc directory exists but is not mounted. Mounting now...
[INFO] NEURODESKTOP_CVMFS_STARTUP_MODE=lazy: deferring CVMFS mount to background worker.
Detecting container resource limits from cgroups...
Memory limit: unlimited
CPU limit: unlimited
[INFO] NEURODESKTOP_SLURM_STARTUP_MODE=lazy: deferring Slurm startup to background worker.
[TIMING] critical-startup completed in 426ms
[INFO] Launching deferred startup worker (CVMFS=lazy, Slurm=lazy)...
[restore_home_defaults] Processing: .local/bin/claude
[restore_home_defaults] Processing: .local/share/code-server/User/settings.json
[restore_home_defaults] Processing: .vnc/xstartup
[restore_home_defaults] Processing: .vnc/passwd
[restore_home_defaults] Processing: .jupyter/nbi/rules/neurodesk.md
[restore_home_defaults] Processing: .jupyter/nbi/config.json
[restore_home_defaults] Processing: .jupyter/labconfig/page_config.json
[restore_home_defaults] Processing: .ssh/sshd_config
[restore_home_defaults] Processing: .codex/config.toml
[restore_home_defaults] Processing: .config/opencode/opencode.json
[restore_home_defaults] Processing: .config/libfm/libfm.conf
[restore_home_defaults] Processing: .config/lxpanel/LXDE/panels/panel
[restore_home_defaults] Processing: .config/mimeapps.list
[restore_home_defaults] Processing: .claude/mcp_config.json
[restore_home_defaults] Processing: .claude/settings.local.json
[restore_home_defaults] Processing: conda-readme.md
[restore_home_defaults] Processing: .itksnap.org/ITK-SNAP/UserPreferences.xml
[restore_home_defaults] Configuring git credential helper for github.com via gh
[restore_home_defaults] Home directory defaults restoration complete
[INFO] Checking for ARM CPU and adding a CPU Mhz entry in /proc/cpuinfo to work around a bug in Matlab that expects this value to be present.
[INFO] Setting up VNC...
Done running hooks in: /usr/local/bin/before-notebook.d
Running as jovyan: start.sh jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:5b7c8c97811e71a06c74f839b945398d496637 --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
Entered start.sh with args: jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:5b7c8c97811e71a06c74f839b945398d496637 --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
WARNING: start.sh is the default ENTRYPOINT, do not include it in CMD
Executing the command: jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:5b7c8c97811e71a06c74f839b945398d496637 --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
[W 2026-04-29 14:59:44.188 ServerApp] ServerApp.token config is deprecated in 2.0. Use IdentityProvider.token.
2026-04-29 14:59:48,392 - traitlets - utils.py - INFO - Extension package notebook_intelligence took 3.8321s to import
[I 2026-04-29 14:59:48.393 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2026-04-29 14:59:48.394 ServerApp] jupyter_resource_usage | extension was successfully linked.
[I 2026-04-29 14:59:48.398 ServerApp] jupyter_scheduler | extension was successfully linked.
[I 2026-04-29 14:59:48.398 ServerApp] jupyter_server_proxy | extension was successfully linked.
[I 2026-04-29 14:59:48.401 ServerApp] jupyter_server_terminals | extension was successfully linked.
[W 2026-04-29 14:59:48.403 LabApp] 'quit_button' is not found in LabApp, but it was found in both NotebookApp and ServerApp. This is likely a recent change. This config will only be set in ServerApp. Please check if you should also config these traits in NotebookApp for your purpose.
[W 2026-04-29 14:59:48.403 LabApp] 'quit_button' is not found in LabApp, but it was found in both NotebookApp and ServerApp. This is likely a recent change. This config will only be set in ServerApp. Please check if you should also config these traits in NotebookApp for your purpose.
[I 2026-04-29 14:59:48.406 ServerApp] jupyterlab | extension was successfully linked.
[I 2026-04-29 14:59:48.406 ServerApp] jupyterlab_git | extension was successfully linked.
[I 2026-04-29 14:59:48.406 ServerApp] jupyterlab_myst | extension was successfully linked.
[I 2026-04-29 14:59:48.410 ServerApp] jupyterlab_rise | extension was successfully linked.
[I 2026-04-29 14:59:48.410 ServerApp] jupyterlab_slurm | extension was successfully linked.
[I 2026-04-29 14:59:48.410 ServerApp] jupyterlmod | extension was successfully linked.
[I 2026-04-29 14:59:48.414 ServerApp] nbclassic | extension was successfully linked.
[I 2026-04-29 14:59:48.414 ServerApp] nbdime | extension was successfully linked.
[I 2026-04-29 14:59:48.414 ServerApp] nbgitpuller | extension was successfully linked.
[I 2026-04-29 14:59:48.418 ServerApp] notebook | extension was successfully linked.
[W 2026-04-29 14:59:48.420 NotebookIntelligence] Config option github_access_token not recognized by NotebookIntelligence.
[W 2026-04-29 14:59:48.422 NotebookIntelligence] Config option github_access_token not recognized by NotebookIntelligence.
[I 2026-04-29 14:59:48.423 ServerApp] notebook_intelligence | extension was successfully linked.
[I 2026-04-29 14:59:48.608 ServerApp] notebook_shim | extension was successfully linked.
[I 2026-04-29 14:59:49.560 ServerApp] nb_conda_kernels | enabled, 1 kernels found.
[W 2026-04-29 14:59:49.573 ServerApp] WARNING: The Jupyter server is listening on all IP addresses and not using encryption. This is not recommended.
[I 2026-04-29 14:59:49.574 ServerApp] notebook_shim | extension was successfully loaded.
[I 2026-04-29 14:59:49.576 ServerApp] jupyter_lsp | extension was successfully loaded.
[I 2026-04-29 14:59:49.577 ServerApp] jupyter_resource_usage | extension was successfully loaded.
[I 2026-04-29 14:59:49.718 ServerApp] jupyter_scheduler | extension was successfully loaded.
[I 2026-04-29 14:59:49.751 ServerApp] jupyter_server_proxy | extension was successfully loaded.
[I 2026-04-29 14:59:49.752 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2026-04-29 14:59:49.757 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.13/site-packages/jupyterlab
[I 2026-04-29 14:59:49.758 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 2026-04-29 14:59:49.758 LabApp] Extension Manager is 'pypi'.
[I 2026-04-29 14:59:49.769 ServerApp] jupyterlab | extension was successfully loaded.
[I 2026-04-29 14:59:49.773 ServerApp] jupyterlab_git | extension was successfully loaded.
[I 2026-04-29 14:59:49.775 ServerApp] jupyterlab_myst | extension was successfully loaded.
[I 2026-04-29 14:59:49.780 ServerApp] jupyterlab_rise | extension was successfully loaded.
[I 2026-04-29 14:59:49.780 ServerApp] Registered jupyterlab_slurm server extension
[I 2026-04-29 14:59:49.780 ServerApp] {'squeue_path': 'squeue', 'scancel_path': 'scancel', 'scontrol_path': 'scontrol', 'sbatch_path': 'sbatch'}
[I 2026-04-29 14:59:49.780 ServerApp] Slurm command paths:
squeue: squeue
scancel: scancel
scontrol: scontrol
sbatch: sbatch

[I 2026-04-29 14:59:49.780 ServerApp] Starting up handlers....

[I 2026-04-29 14:59:49.780 ServerApp] Handler: ExampleHandler URI: /jupyterlab_slurm/get_example dict: {'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.780 ServerApp] Handler: UserFetchHandler URI: /jupyterlab_slurm/user dict: {'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.780 ServerApp] Handler: SqueueHandler URI: /jupyterlab_slurm/squeue dict: {'squeue': 'squeue', 'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.780 ServerApp] Handler: ScancelHandler URI: /jupyterlab_slurm/scancel dict: {'scancel': 'scancel', 'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.780 ServerApp] Handler: ScontrolHandler URI: /jupyterlab_slurm/scontrol/(?P.*) dict: {'scontrol': 'scontrol', 'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.780 ServerApp] Handler: SbatchHandler URI: /jupyterlab_slurm/sbatch dict: {'sbatch': 'sbatch', 'temporary_directory': None, 'log': <Logger ServerApp (DEBUG)>}

[I 2026-04-29 14:59:49.781 ServerApp] jupyterlab_slurm | extension was successfully loaded.
[I 2026-04-29 14:59:49.781 ServerApp] Loading lmod/tmod extension
[I 2026-04-29 14:59:49.782 ServerApp] jupyterlmod | extension was successfully loaded.

| | | |_ __ | | | | ___
| || | ' / / _ | / -)
_/| ./_,_,|____|
|_|

Read the migration plan to Notebook 7 to learn about the new features and the actions to take if you are using extensions.

https://jupyter-notebook.readthedocs.io/en/latest/migrate_to_notebook7.html

Please note that updating to Notebook 7 might break some of your extensions.

[I 2026-04-29 14:59:49.786 ServerApp] nbclassic | extension was successfully loaded.
[I 2026-04-29 14:59:49.823 ServerApp] nbdime | extension was successfully loaded.
[I 2026-04-29 14:59:49.825 ServerApp] nbgitpuller | extension was successfully loaded.
[I 2026-04-29 14:59:49.830 ServerApp] notebook | extension was successfully loaded.
2026-04-29 14:59:49,832 - notebook_intelligence.llm_providers.ollama_llm_provider - ollama_llm_provider.py - WARNING - Failed to update supported Ollama models: Failed to connect to Ollama. Please check that Ollama is downloaded, running and accessible. https://ollama.com/download
[I 2026-04-29 14:59:49.835 ServerApp] Registered notebook_intelligence server extension
[I 2026-04-29 14:59:49.835 ServerApp] notebook_intelligence | extension was successfully loaded.
[I 2026-04-29 14:59:49.837 ServerApp] Serving notebooks from local directory: /home/jovyan
[I 2026-04-29 14:59:49.837 ServerApp] Jupyter Server 2.17.0 is running at:
[I 2026-04-29 14:59:49.837 ServerApp] http://localhost:8888/lab?token=...
[I 2026-04-29 14:59:49.837 ServerApp] http://127.0.0.1:8888/lab?token=...
[I 2026-04-29 14:59:49.837 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
2026-04-29 14:59:49,851 - claude_agent_sdk._internal.transport.subprocess_cli - subprocess_cli.py - INFO - Using bundled Claude Code CLI: /opt/conda/lib/python3.13/site-packages/claude_agent_sdk/_bundled/claude
[I 2026-04-29 14:59:50.007 ServerApp] Skipped non-installed server(s): basedpyright, bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-langserver, jedi-language-server, julia-language-server, pyrefly, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, yaml-language-server
[W 2026-04-29 14:59:53.148 ServerApp] The websocket_ping_timeout (60) cannot be longer than the websocket_ping_interval (30).
Setting websocket_ping_timeout=30
[W 2026-04-29 14:59:53.787 ServerApp] 404 GET /api/contents/.config/neurodesk_supporter?content=0&hash=0&1777474793781 (638accb84f094d9ab9b23b1710a6161a@172.17.0.1) 2.29ms referer=http://127.0.0.1:34479/lab
[W 2026-04-29 14:59:53.788 ServerApp] 404 GET /api/contents/.config/neurodesk_supporter?content=0&hash=0&1777474793781 (172.17.0.1): No such file or directory: .config/neurodesk_supporter
[I 2026-04-29 14:59:53.805 ServerApp] ExampleHandler.initialize()
[I 2026-04-29 14:59:53.806 ServerApp] ExampleHandler.get()
[I 2026-04-29 14:59:53.807 ServerApp] UserFetchHandler.initialize()
[I 2026-04-29 14:59:53.808 ServerApp] UserFetchHandler.get() jovyan
[I 2026-04-29 14:59:54.151 LabApp] Build is up to date
[TIMING] guacamole-startup started

Starting Remote Desktop Protocol server xrdp-sesman[24270]: [INFO ] starting xrdp-sesman with pid 24270

                                                                  [ OK ]

[DEBUG] VNC setup - checking prerequisites...
[DEBUG] HOME=/home/jovyan
[DEBUG] Contents of /home/jovyan/.vnc:
total 64
drwxrwsr-x 2 jovyan jovyan 4096 Apr 29 17:17 .
drwsr-sr-x 25 jovyan jovyan 4096 Apr 29 14:59 ..
-rw------- 1 jovyan jovyan 42471 Apr 28 16:46 c09dae0a279e:1.log
-rw------- 1 jovyan jovyan 5 Apr 28 16:45 c09dae0a279e:1.pid
-rw------- 1 jovyan jovyan 8 Apr 29 17:17 passwd
-rwxr-xr-x 1 jovyan jovyan 124 Apr 21 03:24 xstartup
[DEBUG] Attempting to start VNC on display :1...
[DEBUG] vncserver exit code: 0
[DEBUG] vncserver output:
New Xtigervnc server 'VNC' on port 5901 for display :1.
Use xtigervncviewer -SecurityTypes VncAuth -passwd /tmp/tigervnc.Vi5Cpk/passwd :1 to connect to the VNC server.
VNC server started on display :1
Using CATALINA_BASE: /home/jovyan/.neurodesk/tomcat
Using CATALINA_HOME: /usr/local/tomcat
Using CATALINA_TMPDIR: /home/jovyan/.neurodesk/tomcat/temp
Using JRE_HOME: /usr
Using CLASSPATH: /usr/local/tomcat/bin/bootstrap.jar:/usr/local/tomcat/bin/tomcat-juli.jar
Using CATALINA_OPTS:
Tomcat started.
guacd[24560]: INFO: Guacamole proxy daemon (guacd) version 1.6.0 started
Running guacamole
[INFO] Neurodesktop session ports (docker):
[INFO] Tomcat/Guacamole HTTP : 60121
[INFO] guacd : 127.0.0.1:4822
[INFO] VNC display / port : :1 / 5901 (localhost-only, random password)
[INFO] RDP port : 3389
[INFO] SFTP port : 2222
[INFO] Guacamole web login : jovyan (password rotated, see /home/jovyan/.neurodesk/secrets/guacamole_web_password)
[TIMING] guacamole-startup completed in 8632ms
[I 2026-04-29 17:17:34.330 ServerApp] Trying to establish websocket connection to ws://localhost:60121/websocket-tunnel?token=75919E8F7069900563912A8C71F0596B5B8C93BB85CDC94C5EF2C116199FDE4D&GUAC_DATA_SOURCE=default&GUAC_ID=Desktop%20RDP%20-%20changes%20resolution%20by%20setting%20zoom%20level%20or%20resizing%20window%20and%20reloading%20site&GUAC_TYPE=c&GUAC_WIDTH=800&GUAC_HEIGHT=575&GUAC_DPI=96&GUAC_TIMEZONE=America%2FDetroit&GUAC_AUDIO=audio%2FL8&GUAC_AUDIO=audio%2FL16&GUAC_IMAGE=image%2Fjpeg&GUAC_IMAGE=image%2Fpng&GUAC_IMAGE=image%2Fwebp
[I 2026-04-29 17:17:34.374 ServerApp] Websocket connection established to ws://localhost:60121/websocket-tunnel?token=75919E8F7069900563912A8C71F0596B5B8C93BB85CDC94C5EF2C116199FDE4D&GUAC_DATA_SOURCE=default&GUAC_ID=Desktop%20RDP%20-%20changes%20resolution%20by%20setting%20zoom%20level%20or%20resizing%20window%20and%20reloading%20site&GUAC_TYPE=c&GUAC_WIDTH=800&GUAC_HEIGHT=575&GUAC_DPI=96&GUAC_TIMEZONE=America%2FDetroit&GUAC_AUDIO=audio%2FL8&GUAC_AUDIO=audio%2FL16&GUAC_IMAGE=image%2Fjpeg&GUAC_IMAGE=image%2Fpng&GUAC_IMAGE=image%2Fwebp
[W 2026-04-29 17:17:36.086 ServerApp] 404 GET /neurodesktop/api/session/tunnels/2c19a8a6-57b7-4d36-9821-726d3a5e7ee2/activeConnection/connection/sharingProfiles (638accb84f094d9ab9b23b1710a6161a@172.17.0.1) 47.76ms referer=http://127.0.0.1:34479/neurodesktop/
xrdp-sesman[24270]: [INFO ] Socket 11: AF_INET6 connection received from ::1 port 42984

xrdp-sesman[24270]: [INFO ] Terminal Server Users group is disabled, allowing authentication

xrdp-sesman[24270]: [INFO ] ++ created session (access granted): username jovyan, ip ::ffff:127.0.0.1:52026 - socket: 11

xrdp-sesman[24270]: [INFO ] starting Xorg session...

xrdp-sesman[24270]: [INFO ] Starting session: session_pid 24668, display :10.0, width 800, height 575, bpp 24, client ip ::ffff:127.0.0.1:52026 - socket: 11, user name jovyan

xrdp-sesman[24668]: [INFO ] [session start] (display 10): calling auth_start_session from pid 24668

xrdp-sesman[24270]: [ERROR] sesman_data_in: scp_process_msg failed

xrdp-sesman[24668]: pam_unix(xrdp-sesman:session): session opened for user jovyan(uid=114461999) by (uid=0)
xrdp-sesman[24270]: [ERROR] sesman_main_loop: trans_check_wait_objs failed, removing trans

xrdp-sesman[24668]: pam_systemd(xrdp-sesman:session): Failed to connect to system bus: No such file or directory
xrdp-sesman[24671]: [INFO ] Found X server running at /tmp/.X11-unix/X10

xrdp-sesman[24668]: [INFO ] Found X server running at /tmp/.X11-unix/X10

xrdp-sesman[24668]: [INFO ] Session started successfully for user jovyan on display 10

xrdp-sesman[24675]: [INFO ] Starting the xrdp channel server for display 10

xrdp-sesman[24668]: [INFO ] Session in progress on display 10, waiting until the window manager (pid 24671) exits to end the session

xrdp-sesman[24270]: [INFO ] Socket 11: AF_INET6 connection received from ::1 port 40994

xrdp-sesman[24270]: [INFO ] ++ reconnected session: username jovyan, display :10.0, session_pid 24668, ip ::ffff:127.0.0.1:39016 - socket: 11

xrdp-sesman[24270]: [ERROR] sesman_data_in: scp_process_msg failed

xrdp-sesman[24270]: [ERROR] sesman_main_loop: trans_check_wait_objs failed, removing trans

xrdp-sesman[24270]: [INFO ] Process 24845 has exited

xrdp-sesman[24270]: [INFO ] Socket 11: AF_INET6 connection received from ::1 port 33004

xrdp-sesman[24270]: [INFO ] ++ reconnected session: username jovyan, display :10.0, session_pid 24668, ip ::ffff:127.0.0.1:55146 - socket: 11

xrdp-sesman[24270]: [ERROR] sesman_data_in: scp_process_msg failed

xrdp-sesman[24270]: [ERROR] sesman_main_loop: trans_check_wait_objs failed, removing trans

xrdp-sesman[24270]: [INFO ] Process 25075 has exited

xrdp-sesman[24270]: [INFO ] Socket 11: AF_INET6 connection received from ::1 port 49316

xrdp-sesman[24270]: [INFO ] ++ reconnected session: username jovyan, display :10.0, session_pid 24668, ip ::ffff:127.0.0.1:35880 - socket: 11

xrdp-sesman[24270]: [ERROR] sesman_data_in: scp_process_msg failed

xrdp-sesman[24270]: [ERROR] sesman_main_loop: trans_check_wait_objs failed, removing trans

xrdp-sesman[24270]: [INFO ] Process 25157 has exited

xrdp-sesman[24270]: [INFO ] Socket 11: AF_INET6 connection received from ::1 port 48484

xrdp-sesman[24270]: [INFO ] ++ reconnected session: username jovyan, display :10.0, session_pid 24668, ip ::ffff:127.0.0.1:51382 - socket: 11

xrdp-sesman[24270]: [ERROR] sesman_data_in: scp_process_msg failed

xrdp-sesman[24270]: [ERROR] sesman_main_loop: trans_check_wait_objs failed, removing trans

xrdp-sesman[24270]: [INFO ] Process 25258 has exited

iishiishii May 4, 2026
Maintainer

Thanks @etmaddox-creator for sharing the log. This inconsistent behaviour is not ideal, but really appreciate your testing. We added more logging in this version https://github.com/neurodesk/neurodesk-app/releases/download/v1.15.0/NeurodeskApp-Setup-Debian-x64.deb. We want to see if the NFS drive is ready or stale (I assume it is as it's mounted at startup as you said).

etmaddox-creator May 4, 2026
Author

Yea, I'm not sure what's causing that behavior. I tried running this version twice with the nfs drive (after confirming that it worked normally without the drive bound). It gave an error both times, but for the first attempt docker didn't show any logs because I think the container was created but not started. The second time, the container started and I copied the logs from it. Please let me know if I can provide any additional information and thanks again for all of your help with this!

FIRST NEURODESK LOGS:
[2026-05-04 09:31:36.874] [info] Application disposed successfully
[2026-05-04 09:32:27.340] [info] In production mode
[2026-05-04 09:32:27.341] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-05-04 09:32:27.471] [info] startupMode welcome-page
[2026-05-04 09:32:27.471] [info] sessionConfig undefined
[2026-05-04 09:32:39.590] [info] Application disposed successfully
[2026-05-04 09:32:40.118] [info] In production mode
[2026-05-04 09:32:40.119] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-05-04 09:32:40.178] [info] startupMode welcome-page
[2026-05-04 09:32:40.178] [info] sessionConfig undefined
[2026-05-04 09:33:03.203] [info] ~ createServer { workingDirectory: '/nfs/tpolk/mind' }
[2026-05-04 09:33:03.205] [info] Starting Jupyter server....
[2026-05-04 09:33:03.208] [info] ServerApp.port=35657
[2026-05-04 09:33:03.348] [info] Server launch: port=35657 engine=docker container=neurodeskapp
[2026-05-04 09:33:03.348] [info] Working directory diagnostics: raw="/nfs/tpolk/mind" resolved="/nfs/tpolk/mind" fsType="nfs" isNfs=true
[2026-05-04 09:33:03.349] [info] Working directory access: exists=true isDir=true uid=6711 gid=2496038 mode=40777
[2026-05-04 09:33:03.349] [info] Detected NFS working directory; mounting /nfs/tpolk/mind at its native path
[2026-05-04 09:33:03.350] [info] Server launch script:

    echo "[neurodesk-app] Launch script started at $(date -Iseconds)"
    echo "[neurodesk-app] Engine: docker"
    echo "[neurodesk-app] Working directory: /nfs/tpolk/mind"
    echo "[neurodesk-app] NFS working directory: true"
    echo "[neurodesk-app] Container name: neurodeskapp"
    echo "[neurodesk-app] Port: 35657"
    echo "[neurodesk-app] Working dir mount info: $(mount | grep '/nfs/tpolk' 2>/dev/null || echo 'no mount found')"
    echo "[neurodesk-app] Working dir accessible: $(ls -ld '/nfs/tpolk/mind' 2>&1)"
    
    if ! timeout 5 ls -ld '/nfs/tpolk/mind' &>/dev/null; then
      echo "[neurodesk-app] ERROR: Working directory not accessible (NFS mount may be stale)" >&2
      exit 1
    fi
    echo "[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind"
    
    if [[ "$(docker image inspect vnmd/neurodesktop:2026-04-28 --format='exists' 2> /dev/null)" == "exists" ]]; then
      docker rm -f neurodeskapp &> /dev/null
      
      CONTAINER_ID=$(docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:35657:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=no -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data  --volume "/nfs/tpolk/mind":"/nfs/tpolk/mind" vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:86919f7c84b469df7897da0193ac1329ccf8a4' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    else
      docker rm -f neurodeskapp &> /dev/null
      
      docker pull docker.io/vnmd/neurodesktop:2026-04-28
      CONTAINER_ID=$(docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:35657:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=no -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data  --volume "/nfs/tpolk/mind":"/nfs/tpolk/mind" vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:86919f7c84b469df7897da0193ac1329ccf8a4' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    fi

    if [ $LAUNCH_EXIT -ne 0 ]; then
      echo "[neurodesk-app] ERROR: docker run exited with code $LAUNCH_EXIT" >&2
      echo "[neurodesk-app] ERROR: Checking container status:" >&2
      docker ps -a --filter name=neurodeskapp --format '{{.ID}} {{.Status}} {{.Names}}' 2>&1 >&2
      docker logs neurodeskapp 2>&1 || true
      exit $LAUNCH_EXIT
    else
      echo "[neurodesk-app] Container started: $CONTAINER_ID"
      docker logs -f neurodeskapp 2>&1
    fi

^[[2026-05-04 10:13:03.357] [error] Server didn't start in time
[2026-05-04 10:13:03.384] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 35657[neurodesk-app] Launch script started at 2026-05-04T09:33:03-04:00
[neurodesk-app] Engine: docker
[neurodesk-app] Working directory: /nfs/tpolk/mind
[neurodesk-app] NFS working directory: true
[neurodesk-app] Container name: neurodeskapp
[neurodesk-app] Port: 35657
,[neurodesk-app] Working dir mount info: lsa-tpolk.turbo.storage.umich.edu:/lsa-tpolk/tpolk-mistorage on /nfs/tpolk type nfs (rw,relatime,vers=3,rsize=131072,wsize=524288,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=10.242.100.229,mountvers=3,mountport=300,mountproto=udp,local_lock=none,addr=10.242.100.229)
,[neurodesk-app] Working dir accessible: drwxrwxrwx 81 tpolk lsa-tpolk-mistorage 2743 Apr 21 14:52 /nfs/tpolk/mind
,[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:517:28

SECOND NEURODESK LOGS:
[2026-05-04 10:36:22.336] [info] Application disposed successfully
[2026-05-04 10:36:35.414] [info] In production mode
[2026-05-04 10:36:35.416] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-05-04 10:36:35.517] [info] startupMode welcome-page
[2026-05-04 10:36:35.518] [info] sessionConfig undefined
[2026-05-04 10:36:45.816] [info] ~ createServer { workingDirectory: '/nfs/tpolk/mind' }
[2026-05-04 10:36:45.819] [info] Starting Jupyter server....
[2026-05-04 10:36:45.824] [info] ServerApp.port=40295
[2026-05-04 10:36:46.022] [info] Server launch: port=40295 engine=docker container=neurodeskapp
[2026-05-04 10:36:46.023] [info] Working directory diagnostics: raw="/nfs/tpolk/mind" resolved="/nfs/tpolk/mind" fsType="nfs" isNfs=true
[2026-05-04 10:36:46.024] [info] Working directory access: exists=true isDir=true uid=6711 gid=2496038 mode=40777
[2026-05-04 10:36:46.024] [info] Detected NFS working directory; mounting /nfs/tpolk/mind at its native path
[2026-05-04 10:36:46.025] [info] Server launch script:

    echo "[neurodesk-app] Launch script started at $(date -Iseconds)"
    echo "[neurodesk-app] Engine: docker"
    echo "[neurodesk-app] Working directory: /nfs/tpolk/mind"
    echo "[neurodesk-app] NFS working directory: true"
    echo "[neurodesk-app] Container name: neurodeskapp"
    echo "[neurodesk-app] Port: 40295"
    echo "[neurodesk-app] Working dir mount info: $(mount | grep '/nfs/tpolk' 2>/dev/null || echo 'no mount found')"
    echo "[neurodesk-app] Working dir accessible: $(ls -ld '/nfs/tpolk/mind' 2>&1)"
    
    if ! timeout 5 ls -ld '/nfs/tpolk/mind' &>/dev/null; then
      echo "[neurodesk-app] ERROR: Working directory not accessible (NFS mount may be stale)" >&2
      exit 1
    fi
    echo "[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind"
    
    if [[ "$(docker image inspect vnmd/neurodesktop:2026-04-28 --format='exists' 2> /dev/null)" == "exists" ]]; then
      docker rm -f neurodeskapp &> /dev/null
      
      CONTAINER_ID=$(docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:40295:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=no -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data  --volume "/nfs/tpolk/mind":"/nfs/tpolk/mind" vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    else
      docker rm -f neurodeskapp &> /dev/null
      
      docker pull docker.io/vnmd/neurodesktop:2026-04-28
      CONTAINER_ID=$(docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:40295:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=no -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data  --volume "/nfs/tpolk/mind":"/nfs/tpolk/mind" vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    fi

    if [ $LAUNCH_EXIT -ne 0 ]; then
      echo "[neurodesk-app] ERROR: docker run exited with code $LAUNCH_EXIT" >&2
      echo "[neurodesk-app] ERROR: Checking container status:" >&2
      docker ps -a --filter name=neurodeskapp --format '{{.ID}} {{.Status}} {{.Names}}' 2>&1 >&2
      docker logs neurodeskapp 2>&1 || true
      exit $LAUNCH_EXIT
    else
      echo "[neurodesk-app] Container started: $CONTAINER_ID"
      docker logs -f neurodeskapp 2>&1
    fi

[2026-05-04 11:16:46.033] [error] Server didn't start in time
[2026-05-04 11:16:46.093] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 40295[neurodesk-app] Launch script started at 2026-05-04T10:36:46-04:00
[neurodesk-app] Engine: docker
[neurodesk-app] Working directory: /nfs/tpolk/mind
[neurodesk-app] NFS working directory: true
[neurodesk-app] Container name: neurodeskapp
[neurodesk-app] Port: 40295
,[neurodesk-app] Working dir mount info: lsa-tpolk.turbo.storage.umich.edu:/lsa-tpolk/tpolk-mistorage on /nfs/tpolk type nfs (rw,relatime,vers=3,rsize=131072,wsize=524288,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=10.242.100.229,mountvers=3,mountport=300,mountproto=udp,local_lock=none,addr=10.242.100.229)
,[neurodesk-app] Working dir accessible: drwxrwxrwx 81 tpolk lsa-tpolk-mistorage 2743 Apr 21 14:52 /nfs/tpolk/mind
,[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind
,[neurodesk-app] Container started: 83f7bf7b5c4ed5eb58f5c0716eb8bba9dd4854800275b44014406d5f72c80769
,Entered start.sh with args: start.sh jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
Running hooks in: /usr/local/bin/start-notebook.d as uid: 0 gid: 0
Sourcing shell script: /usr/local/bin/start-notebook.d/start_notebook.sh
Done running hooks in: /usr/local/bin/start-notebook.d
Update jovyan's UID:GID to 114461999:513
,userdel: group jovyan not removed because it is not the primary group of user jovyan.
,useradd warning: jovyan's uid 114461999 outside of the UID_MIN 1000 and UID_MAX 60000 range.
,Running hooks in: /usr/local/bin/before-notebook.d as uid: 0 gid: 0
,Sourcing shell script: /usr/local/bin/before-notebook.d/10activate-conda-env.sh
,Sourcing shell script: /usr/local/bin/before-notebook.d/before_notebook.sh
,[TIMING] critical-startup started
,binfmt_misc directory exists but is not mounted. Mounting now...
,[INFO] NEURODESKTOP_CVMFS_STARTUP_MODE=lazy: deferring CVMFS mount to background worker.
,Detecting container resource limits from cgroups...
,Memory limit: unlimited
,CPU limit: unlimited
,[INFO] NEURODESKTOP_SLURM_STARTUP_MODE=lazy: deferring Slurm startup to background worker.
,[TIMING] critical-startup completed in 246ms
[INFO] Launching deferred startup worker (CVMFS=lazy, Slurm=lazy)...

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:517:28

DOCKER LOGS:
2026-05-04 11:15:20.301 | Entered start.sh with args: start.sh jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
2026-05-04 11:15:20.304 | Running hooks in: /usr/local/bin/start-notebook.d as uid: 0 gid: 0
2026-05-04 11:15:20.304 | Sourcing shell script: /usr/local/bin/start-notebook.d/start_notebook.sh
2026-05-04 11:15:20.309 | Done running hooks in: /usr/local/bin/start-notebook.d
2026-05-04 11:15:20.314 | Update jovyan's UID:GID to 114461999:513
2026-05-04 11:15:23.273 | userdel: group jovyan not removed because it is not the primary group of user jovyan.
2026-05-04 11:15:25.151 | useradd warning: jovyan's uid 114461999 outside of the UID_MIN 1000 and UID_MAX 60000 range.
2026-05-04 11:15:26.345 | Running hooks in: /usr/local/bin/before-notebook.d as uid: 0 gid: 0
2026-05-04 11:15:26.345 | Sourcing shell script: /usr/local/bin/before-notebook.d/10activate-conda-env.sh
2026-05-04 11:15:27.114 | Sourcing shell script: /usr/local/bin/before-notebook.d/before_notebook.sh
2026-05-04 11:15:27.115 | [TIMING] critical-startup started
2026-05-04 11:15:27.281 | binfmt_misc directory exists but is not mounted. Mounting now...
2026-05-04 11:15:27.307 | [INFO] NEURODESKTOP_CVMFS_STARTUP_MODE=lazy: deferring CVMFS mount to background worker.
2026-05-04 11:15:27.322 | Detecting container resource limits from cgroups...
2026-05-04 11:15:27.329 | Memory limit: unlimited
2026-05-04 11:15:27.348 | CPU limit: unlimited
2026-05-04 11:15:27.353 | [INFO] NEURODESKTOP_SLURM_STARTUP_MODE=lazy: deferring Slurm startup to background worker.
2026-05-04 11:15:27.361 | [TIMING] critical-startup completed in 246ms
2026-05-04 11:15:27.361 | [INFO] Launching deferred startup worker (CVMFS=lazy, Slurm=lazy)...
2026-05-04 11:20:12.774 | [restore_home_defaults] Processing: .local/bin/claude
2026-05-04 11:20:12.780 | [restore_home_defaults] Processing: .local/share/code-server/User/settings.json
2026-05-04 11:20:12.786 | [restore_home_defaults] Processing: .claude/mcp_config.json
2026-05-04 11:20:12.791 | [restore_home_defaults] Processing: .claude/settings.local.json
2026-05-04 11:20:12.795 | [restore_home_defaults] Processing: .codex/config.toml
2026-05-04 11:20:12.798 | [restore_home_defaults] Processing: .config/opencode/opencode.json
2026-05-04 11:20:12.801 | [restore_home_defaults] Processing: .config/libfm/libfm.conf
2026-05-04 11:20:12.803 | [restore_home_defaults] Processing: .config/lxpanel/LXDE/panels/panel
2026-05-04 11:20:12.806 | [restore_home_defaults] Processing: .config/mimeapps.list
2026-05-04 11:20:12.808 | [restore_home_defaults] Processing: .vnc/xstartup
2026-05-04 11:20:12.810 | [restore_home_defaults] Processing: .vnc/passwd
2026-05-04 11:20:12.812 | [restore_home_defaults] Processing: .itksnap.org/ITK-SNAP/UserPreferences.xml
2026-05-04 11:20:12.814 | [restore_home_defaults] Processing: .ssh/sshd_config
2026-05-04 11:20:12.816 | [restore_home_defaults] Processing: conda-readme.md
2026-05-04 11:20:12.818 | [restore_home_defaults] Processing: .jupyter/nbi/rules/neurodesk.md
2026-05-04 11:20:12.819 | [restore_home_defaults] Processing: .jupyter/nbi/mcp.json
2026-05-04 11:20:12.821 | [restore_home_defaults] Processing: .jupyter/nbi/config.json
2026-05-04 11:20:12.823 | [restore_home_defaults] Processing: .jupyter/labconfig/page_config.json
2026-05-04 11:20:12.832 | [restore_home_defaults] Configuring git credential helper for github.com via gh
2026-05-04 11:20:12.834 | [restore_home_defaults] Home directory defaults restoration complete
2026-05-04 11:20:12.953 | [INFO] Checking for ARM CPU and adding a CPU Mhz entry in /proc/cpuinfo to work around a bug in Matlab that expects this value to be present.
2026-05-04 11:20:13.025 | [INFO] Setting up VNC...
2026-05-04 11:20:13.311 | Done running hooks in: /usr/local/bin/before-notebook.d
2026-05-04 11:20:13.312 | Running as jovyan: start.sh jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
2026-05-04 11:20:13.338 | Entered start.sh with args: jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
2026-05-04 11:20:13.338 | WARNING: start.sh is the default ENTRYPOINT, do not include it in CMD
2026-05-04 11:20:13.338 | Executing the command: jupyter lab --ServerApp.password= --no-browser --expose-app-in-browser --ServerApp.token=jlab:srvr:92bd13a5a6f1249cb3c4b0eec72a09fd29c81d --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember
2026-05-04 11:20:15.053 | [W 2026-05-04 15:20:15.053 ServerApp] ServerApp.token config is deprecated in 2.0. Use IdentityProvider.token.
2026-05-04 11:20:18.728 | 2026-05-04 15:20:18,728 - traitlets - utils.py - INFO - Extension package notebook_intelligence took 3.3033s to import
2026-05-04 11:20:18.729 | [I 2026-05-04 15:20:18.729 ServerApp] jupyter_lsp | extension was successfully linked.
2026-05-04 11:20:18.729 | [I 2026-05-04 15:20:18.729 ServerApp] jupyter_resource_usage | extension was successfully linked.
2026-05-04 11:20:18.735 | [I 2026-05-04 15:20:18.735 ServerApp] jupyter_scheduler | extension was successfully linked.
2026-05-04 11:20:18.735 | [I 2026-05-04 15:20:18.735 ServerApp] jupyter_server_proxy | extension was successfully linked.
2026-05-04 11:20:18.739 | [I 2026-05-04 15:20:18.738 ServerApp] jupyter_server_terminals | extension was successfully linked.
2026-05-04 11:20:18.741 | [W 2026-05-04 15:20:18.741 LabApp] 'quit_button' is not found in LabApp, but it was found in both NotebookApp and ServerApp. This is likely a recent change. This config will only be set in ServerApp. Please check if you should also config these traits in NotebookApp for your purpose.
2026-05-04 11:20:18.741 | [W 2026-05-04 15:20:18.741 LabApp] 'quit_button' is not found in LabApp, but it was found in both NotebookApp and ServerApp. This is likely a recent change. This config will only be set in ServerApp. Please check if you should also config these traits in NotebookApp for your purpose.
2026-05-04 11:20:18.744 | [I 2026-05-04 15:20:18.744 ServerApp] jupyterlab | extension was successfully linked.
2026-05-04 11:20:18.744 | [I 2026-05-04 15:20:18.744 ServerApp] jupyterlab_git | extension was successfully linked.
2026-05-04 11:20:18.744 | [I 2026-05-04 15:20:18.744 ServerApp] jupyterlab_myst | extension was successfully linked.
2026-05-04 11:20:18.749 | [I 2026-05-04 15:20:18.749 ServerApp] jupyterlab_rise | extension was successfully linked.
2026-05-04 11:20:18.749 | [I 2026-05-04 15:20:18.749 ServerApp] jupyterlab_slurm | extension was successfully linked.
2026-05-04 11:20:18.749 | [I 2026-05-04 15:20:18.749 ServerApp] jupyterlmod | extension was successfully linked.
2026-05-04 11:20:18.756 | [I 2026-05-04 15:20:18.756 ServerApp] nbclassic | extension was successfully linked.
2026-05-04 11:20:18.756 | [I 2026-05-04 15:20:18.756 ServerApp] nbdime | extension was successfully linked.
2026-05-04 11:20:18.756 | [I 2026-05-04 15:20:18.756 ServerApp] nbgitpuller | extension was successfully linked.
2026-05-04 11:20:18.762 | [I 2026-05-04 15:20:18.762 ServerApp] notebook | extension was successfully linked.
2026-05-04 11:20:18.764 | [W 2026-05-04 15:20:18.764 NotebookIntelligence] Config option github_access_token not recognized by NotebookIntelligence.
2026-05-04 11:20:18.766 | [W 2026-05-04 15:20:18.766 NotebookIntelligence] Config option github_access_token not recognized by NotebookIntelligence.
2026-05-04 11:20:18.767 | [I 2026-05-04 15:20:18.767 ServerApp] notebook_intelligence | extension was successfully linked.
2026-05-04 11:20:18.987 | [I 2026-05-04 15:20:18.987 ServerApp] notebook_shim | extension was successfully linked.
2026-05-04 11:20:20.020 | [I 2026-05-04 15:20:20.020 ServerApp] nb_conda_kernels | enabled, 1 kernels found.
2026-05-04 11:20:20.033 | [W 2026-05-04 15:20:20.032 ServerApp] WARNING: The Jupyter server is listening on all IP addresses and not using encryption. This is not recommended.
2026-05-04 11:20:20.033 | [I 2026-05-04 15:20:20.033 ServerApp] notebook_shim | extension was successfully loaded.
2026-05-04 11:20:20.035 | [I 2026-05-04 15:20:20.035 ServerApp] jupyter_lsp | extension was successfully loaded.
2026-05-04 11:20:20.036 | [I 2026-05-04 15:20:20.035 ServerApp] jupyter_resource_usage | extension was successfully loaded.
2026-05-04 11:20:20.175 | [I 2026-05-04 15:20:20.175 ServerApp] jupyter_scheduler | extension was successfully loaded.
2026-05-04 11:20:20.205 | [I 2026-05-04 15:20:20.205 ServerApp] jupyter_server_proxy | extension was successfully loaded.
2026-05-04 11:20:20.206 | [I 2026-05-04 15:20:20.206 ServerApp] jupyter_server_terminals | extension was successfully loaded.
2026-05-04 11:20:20.212 | [I 2026-05-04 15:20:20.212 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.13/site-packages/jupyterlab
2026-05-04 11:20:20.212 | [I 2026-05-04 15:20:20.212 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
2026-05-04 11:20:20.213 | [I 2026-05-04 15:20:20.213 LabApp] Extension Manager is 'pypi'.
2026-05-04 11:20:20.231 | [I 2026-05-04 15:20:20.231 ServerApp] jupyterlab | extension was successfully loaded.
2026-05-04 11:20:20.238 | [I 2026-05-04 15:20:20.238 ServerApp] jupyterlab_git | extension was successfully loaded.
2026-05-04 11:20:20.239 | [I 2026-05-04 15:20:20.239 ServerApp] jupyterlab_myst | extension was successfully loaded.
2026-05-04 11:20:20.245 | [I 2026-05-04 15:20:20.245 ServerApp] jupyterlab_rise | extension was successfully loaded.
2026-05-04 11:20:20.245 | [I 2026-05-04 15:20:20.245 ServerApp] Registered jupyterlab_slurm server extension
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.245 ServerApp] {'squeue_path': 'squeue', 'scancel_path': 'scancel', 'scontrol_path': 'scontrol', 'sbatch_path': 'sbatch'}
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Slurm command paths:
2026-05-04 11:20:20.246 | squeue: squeue
2026-05-04 11:20:20.246 | scancel: scancel
2026-05-04 11:20:20.246 | scontrol: scontrol
2026-05-04 11:20:20.246 | sbatch: sbatch
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Starting up handlers....
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: ExampleHandler URI: /jupyterlab_slurm/get_example dict: {'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: UserFetchHandler URI: /jupyterlab_slurm/user dict: {'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: SqueueHandler URI: /jupyterlab_slurm/squeue dict: {'squeue': 'squeue', 'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: ScancelHandler URI: /jupyterlab_slurm/scancel dict: {'scancel': 'scancel', 'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: ScontrolHandler URI: /jupyterlab_slurm/scontrol/(?P.*) dict: {'scontrol': 'scontrol', 'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.246 | [I 2026-05-04 15:20:20.246 ServerApp] Handler: SbatchHandler URI: /jupyterlab_slurm/sbatch dict: {'sbatch': 'sbatch', 'temporary_directory': None, 'log': <Logger ServerApp (DEBUG)>}
2026-05-04 11:20:20.246 |
2026-05-04 11:20:20.247 | [I 2026-05-04 15:20:20.247 ServerApp] jupyterlab_slurm | extension was successfully loaded.
2026-05-04 11:20:20.247 | [I 2026-05-04 15:20:20.247 ServerApp] Loading lmod/tmod extension
2026-05-04 11:20:20.248 | [I 2026-05-04 15:20:20.248 ServerApp] jupyterlmod | extension was successfully loaded.
2026-05-04 11:20:20.252 | [I 2026-05-04 15:20:20.251 ServerApp] nbclassic | extension was successfully loaded.
2026-05-04 11:20:20.291 | [I 2026-05-04 15:20:20.291 ServerApp] nbdime | extension was successfully loaded.
2026-05-04 11:20:20.292 | [I 2026-05-04 15:20:20.292 ServerApp] nbgitpuller | extension was successfully loaded.
2026-05-04 11:20:20.298 | [I 2026-05-04 15:20:20.298 ServerApp] notebook | extension was successfully loaded.
2026-05-04 11:20:20.300 | 2026-05-04 15:20:20,300 - notebook_intelligence.llm_providers.ollama_llm_provider - ollama_llm_provider.py - WARNING - Failed to update supported Ollama models: Failed to connect to Ollama. Please check that Ollama is downloaded, running and accessible. https://ollama.com/download
2026-05-04 11:20:20.304 | [I 2026-05-04 15:20:20.304 ServerApp] Registered notebook_intelligence server extension
2026-05-04 11:20:20.304 | [I 2026-05-04 15:20:20.304 ServerApp] notebook_intelligence | extension was successfully loaded.
2026-05-04 11:20:20.306 | [I 2026-05-04 15:20:20.306 ServerApp] Serving notebooks from local directory: /home/jovyan
2026-05-04 11:20:20.307 | [I 2026-05-04 15:20:20.306 ServerApp] Jupyter Server 2.17.0 is running at:
2026-05-04 11:20:20.307 | [I 2026-05-04 15:20:20.306 ServerApp] http://localhost:8888/lab?token=...
2026-05-04 11:20:20.307 | [I 2026-05-04 15:20:20.307 ServerApp] http://127.0.0.1:8888/lab?token=...
2026-05-04 11:20:20.307 | [I 2026-05-04 15:20:20.307 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
2026-05-04 11:20:20.320 | 2026-05-04 15:20:20,320 - claude_agent_sdk._internal.transport.subprocess_cli - subprocess_cli.py - INFO - Using bundled Claude Code CLI: /opt/conda/lib/python3.13/site-packages/claude_agent_sdk/_bundled/claude
2026-05-04 11:20:20.470 | [I 2026-05-04 15:20:20.470 ServerApp] Skipped non-installed server(s): basedpyright, bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-langserver, jedi-language-server, julia-language-server, pyrefly, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, yaml-language-server

iishiishii May 6, 2026
Maintainer

Thanks for sharing @etmaddox-creator

Looking more closely at the most recent logs, the issue is tied to the container's startup latency.
The system is getting stuck for nearly 40 minutes while Docker attempts to create bind mounts, which eventually triggers a timeout in the app.

Did you notice a significant speed improvement when using the Docker CLI workaround that Steffen suggested previously?

While we look into ways to prevent these failures, is it possible to update your /etc/fstab settings on the host? Reducing the timeout to timeo=150 and increasing the rsize could help the kernel recover faster and handle data more efficiently.

jsneal1 · 2026-05-06T13:15:27Z

jsneal1
May 6, 2026

We can certainly try that. While I don’t want to post the full path from fstab I can post mount options if that helps. I can update their timeout to start and see if that helps at all. Best Regards, Jeffrey Neal ***@***.*** LSA EHTS Desktop Support Specialist Senior University of Michigan

…

On May 6, 2026, at 9:07 AM, Thuy Dao ***@***.***> wrote: Thanks for sharing @etmaddox-creator <https://github.com/etmaddox-creator> Looking more closely at the most recent logs, the issue is tied to the container's startup latency. The system is getting stuck for nearly 40 minutes while Docker attempts to create bind mounts, which eventually triggers a timeout in the app. Did you notice a significant speed improvement when using the Docker CLI workaround that Steffen suggested previously? While we look into ways to prevent these failures, is it possible to update your /etc/fstab settings on the host? Reducing the timeout to timeo=150 and increasing the rsize could help the kernel recover faster and handle data more efficiently. — Reply to this email directly, view it on GitHub <https://github.com/orgs/neurodesk/discussions/661#discussioncomment-16827494>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALYJWG5LNPFD67RJADX27RD4ZM2HXAVCNFSM6AAAAACPSEXOLSVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMOBSG42DSNA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.

0 replies

jsneal1 · 2026-05-06T13:35:39Z

jsneal1
May 6, 2026

I increased the timeo to 150, here is the default rsize=131072 Best Regards, Jeffrey Neal ***@***.*** LSA EHTS Desktop Support Specialist Senior University of Michigan

…

On May 6, 2026, at 9:07 AM, Thuy Dao ***@***.***> wrote: Thanks for sharing @etmaddox-creator <https://github.com/etmaddox-creator> Looking more closely at the most recent logs, the issue is tied to the container's startup latency. The system is getting stuck for nearly 40 minutes while Docker attempts to create bind mounts, which eventually triggers a timeout in the app. Did you notice a significant speed improvement when using the Docker CLI workaround that Steffen suggested previously? While we look into ways to prevent these failures, is it possible to update your /etc/fstab settings on the host? Reducing the timeout to timeo=150 and increasing the rsize could help the kernel recover faster and handle data more efficiently. — Reply to this email directly, view it on GitHub <https://github.com/orgs/neurodesk/discussions/661#discussioncomment-16827494>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALYJWG5LNPFD67RJADX27RD4ZM2HXAVCNFSM6AAAAACPSEXOLSVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMOBSG42DSNA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.

4 replies

etmaddox-creator May 6, 2026
Author

@iishiishii I think the CLI was faster than the GUI. Thank you Jeffery for updating the fstab settings. I tried running it again after that but didn't notice any changes.

iishiishii May 7, 2026
Maintainer

Appreciate that @jsneal1 and @etmaddox-creator
Good news is I finally replicated the issue with a mockup NFS drive nfsvers=3,rw,hard,nolock,timeo=600,retrans=2, deeper nested dir and a bit of injected latency.

iishiishii May 7, 2026
Maintainer

I found that with the mount, some processes freeze without retrying, so we now strictly set a timeout on docker run command to error out rather than hanging indefinitely. I also noticed it didn't wait enough for the endpoint so we extended the wait time for that. Here's the latest build.
https://github.com/neurodesk/neurodesk-app/releases/download/v1.15.0/NeurodeskApp-Setup-Debian-x64.deb

etmaddox-creator May 7, 2026
Author

I'm glad that you were able to replicate the issue on your end. With this version, I was able to open the jupiter hub environment but not the guacamole desktop environment without the nfs drive mounted. With it mounted, it again created the container but didn't start it. Logs are below. I also restarted docker per the logs suggestion.

Also, the container is now being deleted after neurodesk fails to start or when I close the neurodesktop app. Unsure if this behavior is intended, I think it started in one of the recent builds.

[2026-05-07 10:43:36.623] [info] In production mode
[2026-05-07 10:43:36.625] [info] Logging to file (/home/etmaddox/.config/neurodeskapp/logs/main.log) at 'verbose' level
[2026-05-07 10:43:36.787] [info] startupMode welcome-page
[2026-05-07 10:43:36.787] [info] sessionConfig undefined
[2026-05-07 10:43:45.018] [info] ~ createServer { workingDirectory: '/nfs/tpolk/mind' }
[2026-05-07 10:43:45.022] [info] Starting Jupyter server....
[2026-05-07 10:43:45.027] [info] ServerApp.port=46509
[2026-05-07 10:43:59.007] [info] Server launch: port=46509 engine=docker container=neurodeskapp
[2026-05-07 10:43:59.009] [info] Working directory diagnostics: raw="/nfs/tpolk/mind" resolved="/nfs/tpolk/mind" fsType="nfs" isNfs=true
[2026-05-07 10:43:59.011] [info] Skipping statSync for NFS working directory /nfs/tpolk/mind (may hang on stale mounts)
[2026-05-07 10:43:59.013] [info] Server launch script:

    echo "[neurodesk-app] Launch script started at $(date -Iseconds)"
    echo "[neurodesk-app] Engine: docker"
    echo "[neurodesk-app] Working directory: /nfs/tpolk/mind"
    echo "[neurodesk-app] NFS working directory: true"
    echo "[neurodesk-app] Container name: neurodeskapp"
    echo "[neurodesk-app] Port: 46509"
    echo "[neurodesk-app] Working dir mount info: $(mount | grep '/nfs/tpolk' 2>/dev/null || echo 'no mount found')"
    echo "[neurodesk-app] Working dir accessible: $(ls -ld '/nfs/tpolk/mind' 2>&1)"
    
    if ! timeout 5 ls -ld '/nfs/tpolk/mind' &>/dev/null; then
      echo "[neurodesk-app] ERROR: Working directory not accessible (NFS mount may be stale)" >&2
      exit 1
    fi
    echo "[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind"
    
    if [[ "$(docker image inspect vnmd/neurodesktop:2026-04-28 --format='exists' 2> /dev/null)" == "exists" ]]; then
      timeout 30 docker rm -f neurodeskapp &> /dev/null
      
      CONTAINER_ID=$(timeout 300 docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:46509:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=yes -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:fc8dcd6b72743003797ac24a6eb6e6f14f3cf4' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    else
      timeout 30 docker rm -f neurodeskapp &> /dev/null
      
      timeout 300 docker pull docker.io/vnmd/neurodesktop:2026-04-28
      CONTAINER_ID=$(timeout 300 docker run -d --rm --shm-size=1gb --privileged --user=root --name neurodeskapp -p 127.0.0.1:46509:8888 -e NEURODESKTOP_VERSION=2026-04-28 -e CVMFS_DISABLE=false -e GRANT_SUDO=yes -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" -v ~/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan --mac-address=88:75:56:ef:3e:d6 --add-host=host.docker.internal:host-gateway -e OLLAMA_HOST="http://host.docker.internal:11434"   --volume "/nfs/tpolk/mind":/data vnmd/neurodesktop:2026-04-28  start.sh jupyter lab --ServerApp.password='' --no-browser --expose-app-in-browser --ServerApp.token='jlab:srvr:fc8dcd6b72743003797ac24a6eb6e6f14f3cf4' --ServerApp.port=8888 --LabApp.quit_button=False --NotebookIntelligence.github_access_token=remember)
      LAUNCH_EXIT=$?
    fi
    
    if [ $LAUNCH_EXIT -eq 124 ]; then
      echo "[neurodesk-app] ERROR: docker run timed out after 300s — Docker daemon may be stuck on NFS mount operations" >&2
      echo "[neurodesk-app] ERROR: If this persists, try: sudo systemctl restart docker" >&2
      exit 124
    fi

    if [ $LAUNCH_EXIT -ne 0 ]; then
      echo "[neurodesk-app] ERROR: docker run exited with code $LAUNCH_EXIT" >&2
      echo "[neurodesk-app] ERROR: Checking container status:" >&2
      docker ps -a --filter name=neurodeskapp --format '{{.ID}} {{.Status}} {{.Names}}' 2>&1 >&2
      docker logs neurodeskapp 2>&1 || true
      exit $LAUNCH_EXIT
    else
      echo "[neurodesk-app] Container started: $CONTAINER_ID"
      docker logs -f neurodeskapp 2>&1
    fi

[2026-05-07 11:23:59.442] [error] Server didn't start in time
[2026-05-07 11:23:59.464] [error] ~ Failed to start server Error: Failed to launch Neurodesk from Promise 46509[neurodesk-app] Launch script started at 2026-05-07T10:43:59-04:00
[neurodesk-app] Engine: docker
[neurodesk-app] Working directory: /nfs/tpolk/mind
[neurodesk-app] NFS working directory: true
[neurodesk-app] Container name: neurodeskapp
[neurodesk-app] Port: 46509
[neurodesk-app] Working dir mount info: lsa-tpolk.turbo.storage.umich.edu:/lsa-tpolk/tpolk-mistorage on /nfs/tpolk type nfs (rw,relatime,vers=3,rsize=131072,wsize=524288,namlen=255,hard,proto=tcp,timeo=150,retrans=2,sec=sys,mountaddr=10.242.100.125,mountvers=3,mountport=300,mountproto=udp,local_lock=none,addr=10.242.100.125)
,[neurodesk-app] Working dir accessible: drwxrwxrwx 81 tpolk lsa-tpolk-mistorage 2743 Apr 21 14:52 /nfs/tpolk/mind
,[neurodesk-app] NFS mount check passed for /nfs/tpolk/mind

at /opt/NeurodeskApp/resources/app.asar/build/out/main/server.js:551:28

Neurodesk Organisation

Mounting Large Volume #82

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