Kernel dying out repeatedly

[tashrifbillah]

Followed your video, copied command to clipboard and installed on a Terminal that I launched from Notebook:

Installation went fine.

Error snapshot:

It's dying every three seconds or so.

@pieper might be able to reproduce this error.

Since our data are on the ERIS cluster, we won't be able to use public binder to run SlicerJupyter on. On the other hand, we won't have docker. So, we are left with making use of Parters Jupyter server to run SlicerJupyter on.

[lassoan]

Can you check if you can launch Slicer successfully on that system (without Jupyter) and maybe get a stack trace?

[tashrifbillah]

Okay, it looks like it isn't even starting properly ... dying right after connecting.

[lassoan]

Most common issue in a server environment is wrong X or OpenGL configuration. See all the questions on the Slicer forum about running Slicer on a headless system.

[tashrifbillah]

Can you check if you can launch Slicer successfully on that system

It does.

running Slicer on a headless system.

I know about compatibility mode we discussed on Slicer forum. Even if that is the issue, which is not supported by the above log, how may that help me solving this issue?

[lassoan]

@pieper I guess your experience is needed here.

[pieper]

@pieper I guess your experience is needed here.

Sorry, I've never used a Partners Jupyter server, but I probably have access if you need help debugging. @tashrifbillah can you describe exactly what system you are using?

[tashrifbillah]

• grx04.research.partners.org-- a CentOS 7 node through NoMachine
• module load libGLU/9.0.0-foss-2018b
• https://jupyterhub.partners.org

[tashrifbillah]

@pieper if you please hold, I am looking at ~/.local/share/jupyter/kernels/slicer-4.11/kernel.json and might have found the problem.

[tashrifbillah]

Never mind.

If I try the following on a Linux terminal:

[tb571@grx04 slicer-4.11]$ cat kernel.json
{
    "display_name": "Slicer 4.11",
    "language" : "python",
    "argv": [
        "/data/pnl/soft/pnlpipe3/Slicer-4.11.0-linux-amd64/bin/../SlicerWithExtensions.sh",
        "--no-splash",
        "--python-code",
        "connection_file=r'{connection_file}'; print('Jupyter connection file: ['+connection_file+']'); slicer.modules.jupyterkernel.startKernel(connection_file);slicer.util.mainWindow().showMinimized()"
    ]
}

I get this:

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-tb571'
Switch to module:  "Welcome"
Jupyter connection file: [{connection_file}]
startKernel connectionFile does not exist "{connection_file}"

Is this expected?

[lassoan]

Jupyter replaces {connection_file} in kernel.json with the actual connection file. You need to do the same if you want to test it by running the command yourself.

[tashrifbillah]

Hi @pieper , did you get a chance to look at it?
In the meantime, I found Partners VPN connection instruction which was easy to follow on my Windows laptop. After connecting through VPN, you can log into https://jupyterhub.partners.org/ from your laptop browser. Once you are in https://jupyterhub.partners.org/, you can open a terminal on the Notebook and follow SlicerJupyter installation instructions.

This is a way around NoMachine in case you don't have that setup. Happy to work with you over a call as well.

[tashrifbillah]

Hi @lassoan , is there a log where I may find the events during kernel initiation and failure that I described in the above?

[pieper]

Hi @tashrifbillah - I don't really use partner's jupyterhub or slicerjupyter much myself, so not sure I can do anything other than you will be able to do. Let's see what @lassoan suggests for debugging techniques and I can jump in if needed.

[lassoan]

Slicer logs everything into the Slicer log files.