6570 slurm job state query #6579
Closed
Conversation
This file contains hidden or 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
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io>
This reverts commit 9e9476f. Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
…-io#6272) Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Ben Sherman <bentshermann@gmail.com> * Bump org.apache.commons:commons-lang3 from 3.12.0 to 3.18.0 Bumps org.apache.commons:commons-lang3 from 3.12.0 to 3.18.0. --- updated-dependencies: - dependency-name: org.apache.commons:commons-lang3 dependency-version: 3.18.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> --------- Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Chris Hakkaart <chris.hakkaart@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…flow-io#6266) [ci fast] Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io> Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Nikhil Kumar <nikhilkumar516@gmail.com>
…nextflow-io#6284) Signed-off-by: Author Name <nathan.johnson@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Nathan Johnson <nathanjohnson@Nathans-MBP.fritz.box> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io>
Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io>
…i fast] Changed Azure API call from JSON-embedded content to direct binary download using 'download: true' parameter. This prevents binary data corruption that occurred when converting JSON-escaped strings back to bytes. Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Nathan Johnson <nathan.johnson@seqera.io> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Claude <noreply@anthropic.com>
--------- Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Chris Hakkaart <chris.hakkaart@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: jorgee <jorge.ejarque@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Richard Scott <5149834+richard-scott@users.noreply.github.com>
Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com>
nextflow-io#6303) [ci fast] Signed-off-by: jorgee <jorge.ejarque@seqera.io>
… [ci fast] Signed-off-by: Nathan Johnson <nathan.johnson@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Nathan Johnson <nathanjohnson@Nathans-MBP.fritz.box> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
--------- Signed-off-by: jorgee <jorge.ejarque@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: jorgee <jorge.ejarque@seqera.io> Signed-off-by: Ben Sherman <bentshermann@gmail.com>
--------- Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com> Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Ben Sherman <bentshermann@gmail.com>
…4299) Signed-off-by: Ben Sherman <bentshermann@gmail.com> Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com>
…ow-io#6558)" This reverts commit cda4ac1. Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Add synchronized to writeObject method to prevent concurrent modification of the shared stack field when multiple executor threads serialize JSON simultaneously. Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
…xtflow-io#6618) [ci fast] * Add stageFileEnabled flag to control .command.stage file creation (nextflow-io#4279) Improvement of nextflow-io#6558 providing: 1. More declarative approach 2. Better control on enabling/disabling stage file capability 3. Fix Google Batch stage file method - Add stageFileEnabled field to TaskBean - Add isStageFileEnabled() to TaskRun delegating to executor - Add isStageFileEnabled() to Executor with NXF_WRAPPER_STAGE_FILE_ENABLED env var support, defaulting to true for AbstractGridExecutor - Enable stageFileEnabled for GoogleBatchExecutor - Add comprehensive tests Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
…low-io#6581) Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Co-authored-by: Chris Hakkaart <chris.hakkaart@seqera.io> Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
jorgee
reviewed
Dec 12, 2025
jorgee
reviewed
Dec 12, 2025
jorgee
reviewed
Dec 12, 2025
jorgee
reviewed
Dec 12, 2025
Contributor
There was a problem hiding this comment.
I have tested with a local Slurm installation, and it works fine.
In the squeue documentation, it doesn't mention that can't be used with -u or -p. I have tested it and despite the command doesn't fail, it is not returning any value. So, ignoring this flags when using --only-job-state is correct.
Changes look fine to me, I just have added some suggestions in docs to make versionadded blocks point to the next edge release and links to the Slurm documentation. @christopher-hakkaart and @tcutts look at them and accept if they are correct.
@tcutts there is a commit that is not signed-off. Could you fix it?
jorgee
reviewed
Dec 12, 2025
jorgee
reviewed
Dec 12, 2025
Signed-off-by: Tim Cutts <tim.cutts@astrazeneca.com>
tcutts
force-pushed
the
6570-slurm-job-state-query
branch
from
e34ef6f to
3c36143
Compare
Contributor
Author
|
I've made a mess in my git trying to update the attestations. I'll close this pull request and start again. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
20 participants
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.
This patch adds support for the squeue --only-job-state option, which allows admins of recent SLURM versions to enable job state caching, and thereby reduce the RPC call load on SLURM. Because not all SLURM versions support this, and it does cause other filtering options (-p and -u) to be ignored, this has a new config parameter for the executor, onlyJobState, which defaults to "false" to stay the same as current nextflow behaviour.
I have written unit tests for the code, included in the PR, plus some docs for the users.
I have run the code on AstraZeneca's SLURM cluster, and it appears to behave correctly, at least for a very simple test workflow.