Problem running with podman on HPC #5
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Most likely due to |
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jupyterlab-r-docker-stack/base/scripts/usr/local/bin/start.sh Lines 13 to 15 in bfcd656 This might not be required when run as @bernt-matthias I will look into this and provide a patched image so you can test it on the HPC. |
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Excellent. Thanks a lot |
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@bernt-matthias Try with podman run --rm \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpcThanks for your feedback. |
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Seems that it gets closer, but there is still some error: |
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That is due to jupyterlab-r-docker-stack/base/scripts/usr/local/bin/start.sh Lines 240 to 244 in bfcd656
Let me see what I can do... |
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@bernt-matthias I patched the image once more. Please pull |
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There seem to be two files with unexpected permissions: |
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@bernt-matthias Try with podman run --rm \
-p 8888:8888 \
-u root \
-e NB_UMASK=0077 \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpc |
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Or (better) podman run --rm \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_ALLOW_INSECURE_WRITES=true \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpc |
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Or (alternatively) podman run --rm \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_RUNTIME_DIR=/directory/not/in/mounted/filesystem \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpcshould Cross reference: |
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You have quite an edge case here... (Openshift?) Because on a regular Linux machine, the mentioned files have permission |
This worked :) |
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Could you explain to me the connection between jupyter and rocker/rstudio? |
There is none. These are separate projects. |
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The Jupyter Docker Stacks do not include RStudio. |
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What makes this project different:
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Does everything work as expected when you access in a browser? What about the permissions? Could you please open the JupyterLab Terminal, execute mkdir test-folder
touch test-file
ls -aland post the output here? Alternative: podman run -it --rm \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_ALLOW_INSECURE_WRITES=true \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpc bash(For direct Zsh access you should install the recommended font on the host) |
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@bernt-matthias I will do some further tests. If nothing unexpected occurs, all JupyterLab docker stacks will be patched tomorrow. |
Everything as expected: |
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But I did not notice the following in the terminal running the container |
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There will be one or the other error message. The question is whether code-server and RStudio work smoothly. |
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Code server worked. RStudio failed. |
What does it output/log? |
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After the link + token is reported the output is: |
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RStudio should work once v2024.10 is out and
is merged. |
4 tasks
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My fault: Seems that I have forgotten the podman run --rm \
--entrypoint /bin/bash \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_ALLOW_INSECURE_WRITES=true \
-e NOTEBOOK_ARGS="--allow-root" \
-ti glcr.b-data.ch/jupyterlab/r/base |
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This worked (i.e. failed as expected): |
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@bernt-matthias Please check the permissions on I.e. what does |
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@bernt-matthias What does Cross references: |
This could be caused by Btw. thanks a lot for all the time you invest here. |
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@bernt-matthias Maybe. If sed -i '82,93d' /usr/local/bin/start.sh
start.shworks from within the container, I might be able to fix this. Because there is no need to call |
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Then I have: Just to be sure, here is the diff introduced by the 83,94d82
< # Refit the jovyan user to the desired the user (NB_USER)
< if id jovyan &> /dev/null; then
< if ! usermod --home "/home/${NB_USER}${DOMAIN:+@$DOMAIN}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
< _log "Updated the jovyan user:"
< _log "- username: jovyan -> ${NB_USER}"
< _log "- home dir: /home/jovyan -> /home/${NB_USER}${DOMAIN:+@$DOMAIN}"
< fi
< elif ! id -u "${NB_USER}" &> /dev/null; then
< _log "ERROR: Neither the jovyan user nor '${NB_USER}' exists. This could be the result of stopping and starting, the container with a different NB_USER environment variable."
< exit 1
< fi
< |
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@bernt-matthias The other (unneccessary) Try sed -i '118,122d' /usr/local/bin/start.sh
sed -i '82,93d' /usr/local/bin/start.sh
start.sh |
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This seems to solve this issue (running in the next): |
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I have created image @bernt-matthias Try podman run --rm \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_ALLOW_INSECURE_WRITES=true \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpc |
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Still If I |
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I found the culprit. Please command podman pull glcr.b-data.ch/jupyterlab/r/base:test-hpcand then podman run --rm \
-p 8888:8888 \
-u root \
-e NB_USER=root \
-e NB_UID=0 \
-e NB_GID=0 \
-e JUPYTER_ALLOW_INSECURE_WRITES=true \
-e NOTEBOOK_ARGS="--allow-root" \
glcr.b-data.ch/jupyterlab/r/base:test-hpc |
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This solved the error and fails now at: |
@bernt-matthias What does id
ls -aln $HOME
ls -aln /usr/local/lib/R/etc/Renviron.sitereturn? |
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I could but |
Oddly writing to |
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What does |
Indeed.
Does not exist, its |
benz0li
added a commit
that referenced
this issue
Jan 31, 2025
- Do not add to default group when run with rootless triplet - #5
benz0li
added a commit
that referenced
this issue
Jan 31, 2025
- Set HOME="/home/root" when run with rootless triplet - #5
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Closed in favour of containers/podman#25177. |
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With the fixed configuration (see) the following command was now successful: |
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@bernt-matthias What about #5 (comment), i.e. not being able to start RStudio. Does is work now? |
Sorry for the delay. Had technical difficulties to get a browser running on the machine. Everything -- including RStudio and VSCode -- runs now with |
This is great news! Thank you for confirming. |
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This just gives me:
Error: OCI runtime error: crun: cannot setresgid to `100`: Invalid argumentThis seems to do much more:
But there is an error in the "end":
runuser: cannot set groups: Operation not permittedOriginally posted by @bernt-matthias in rocker-org/rocker-versioned2#838 (comment)
The text was updated successfully, but these errors were encountered: