changed target folder for slurm-config.ini in description #10
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
TorecLuik
reviewed
Apr 22, 2024
| @@ -101,8 +101,10 @@ To connect an OMERO processor to a Slurm cluster using the `biomero` library, us | |||
| - `/etc/slurm-config.ini` | |||
| - `~/slurm-config.ini` | |||
|
|
|||
| *Note*: Make sure to place the `slurm-config.ini` in the target folder at build time of your docker container instead of mounting it at runtime. This is because the library reads the config file at import time, and if it is not found, it will not work. | |||
There was a problem hiding this comment.
Are you sure?
This seem questionable to me, because as of yet we do not run any part of this library automatically (e.g. when starting OMERO), so why would the SlurmClient already be started anywhere?
However, we do add it to the container also, just override it with the mount. So your note might still be applicable.
For example, we use
# Run the biomero container
echo "Starting BIOMERO..."
podman run -d --rm --name biomero \
-e CONFIG_omero_master_host=omeroserver \
-e OMERO_WORKER_NAME=biomero \
-e CONFIG_omero_scripts_timeout=604800000 \
--network omero \
--volume /mnt/...:/OMERO \
--volume /mnt/...:/data \
--volume /.../slurm-config.ini:/etc/slurm-config.ini \
--secret ssh-config,target=/tmp/.ssh/config --secret ssh-key,target=/tmp/.ssh/id_rsa --secret ssh-pubkey,target=/tmp/.ssh/id_rsa.pub --secret ssh-known_hosts,target=/tmp/.ssh/known_hosts \
--userns=keep-id:uid=1000,gid=997 \
cellularimagingcf/biomero:"$NL_BIOMERO_VERSION"
Where we mount the specific config for that environment at runtime.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Some minor additions to the documentation according to what was discussed in this image.sc issue