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Use small tower compute env #113

Merged
merged 2 commits into from
Sep 16, 2024
Merged

Use small tower compute env #113

merged 2 commits into from
Sep 16, 2024

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gq1
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@gq1 gq1 commented Sep 13, 2024

Use small 1.2G for base nextflow job

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@gq1
Update sanger_test_full.yml
2584645 
Use small 1.2G for base nextflow job
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This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @gq1,

It looks like this pull-request is has been made against the sanger-tol/blobtoolkit main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the sanger-tol/blobtoolkit dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Sep 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ea1b05a

+| ✅ 133 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2024-09-16 11:05:03

@gq1 gq1 marked this pull request as draft September 13, 2024 14:36
@gq1 gq1 self-assigned this Sep 13, 2024
@gq1 gq1 requested a review from muffato September 13, 2024 14:37
@gq1 gq1 changed the base branch from main to dev September 13, 2024 14:51
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gq1 commented Sep 13, 2024 •
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This is just test PR, probably no need to merge.

We have default TOWER_COMPUTE_ENV with 4G memory for nextflow head job before we set export NXF_OPTS='-Xms128m -Xmx1024m' , all our pipelines use the variable set in the github org level.

Then we had problems to run BTK pipeline, therefore we created TOWER_COMPUTE_ENV_LAERGE secret in repo level with 6G memory, just for this pipeline.

Now I have set export NXF_OPTS='-Xms128m -Xmx1024m'in usertoldevbashrc and tower agent should pick up this now. And also addTOWER_COMPUTE_ENV_SMALL` secret in the repo level with 1.2G memory. That is why I created this PR to test, the full test will only be triggered after merging. and that why I triggered it manually:
https://github.com/sanger-tol/blobtoolkit/actions/runs/10851051619

 bjobs -w 699899
JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
699899  toldev  RUN   oversubscribed tol22-head2 tol22-oversubscribed04 nf-workflow-4xCJISjF4Rfoq Sep 13 15:34

I also triggered a pipeline on the dev branch after I updated TOWER_COMPUTE_ENV_LAERGE to small one.
https://github.com/sanger-tol/blobtoolkit/actions/runs/10851299237

bjobs -w 700191
JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
700191  toldev  RUN   oversubscribed tol22-head2 tol22-oversubscribed04 nf-workflow-4XPhE81lwXYSCR Sep 13 15:50

Both jobs are running with 1.2G memory now.
I don't have permission to update the secrets on org level. @muffato can you update the value for secret TOWER_COMPUTE_ENV' to TOL_farm_LSF_Small`, then we don't need to update any pipeline, just tidy up this one.

@gq1
Update sanger_test_full.yml
ea1b05a 
Use the org level variable TOWER_COMPUTE_ENV which point to  small actually with 1.2G memory.
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gq1 commented Sep 16, 2024

Manually trigger a full test run on farm via tower:
https://github.com/sanger-tol/blobtoolkit/actions/runs/10882505974/job/30193691802

bjobs -u toldev -l 711960

Mon Sep 16 12:05:00: Submitted from host , CWD </lustre/scratch123
/tol/teams/tolit/nf-tower-agent>, Output File </lustre/scr
atch123/tol/teams/tolit/nf-tower-agent/nf-5VFUEos54CFlPx.l
og>, Requested Resources <select[mem>1200] rusage[mem=1200
] span[hosts=1]>, memory/swap limit enforced per-job/per-h
ost;

@gq1 gq1 marked this pull request as ready for review September 16, 2024 11:19
@gq1 gq1 merged commit e0bf8ba into dev Sep 16, 2024
7 checks passed
@muffato muffato deleted the small_tower_compute_env branch September 18, 2024 14:51
@muffato muffato mentioned this pull request Oct 2, 2024
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