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fixed msgfdb index memory bug #420

Merged
merged 5 commits into from
Sep 19, 2024
Merged

fixed msgfdb index memory bug #420

merged 5 commits into from
Sep 19, 2024

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daichengxin
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@daichengxin daichengxin commented Sep 19, 2024 •
edited by codiumai-pr-agent-pro bot
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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
  • If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.
  • 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).

PR Type

Bug fix

Description

  • Fixed a memory allocation bug in the MSGFDBINDEXING process by adding -Xmx and -Xms parameters to the msgf_plus command.
  • The memory settings are now dynamically set based on the task.memory value, improving resource management.

Changes walkthrough 📝

Relevant files
Bug fix
main.nf
Fix memory allocation in MSGFDBINDEXING process                   

modules/local/openms/thirdparty/msgfdb_indexing/main.nf

  • Added memory allocation parameters -Xmx and -Xms to the msgf_plus
    command.
  • Ensured memory settings are dynamically set based on task.memory.
    		•  +2/-0     

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    PR Reviewer Guide 🔍

    ⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪
    🧪 No relevant tests
    🔒 No security concerns identified
    ⚡ Key issues to review

    Memory Allocation
    The PR adds memory allocation parameters to the msgf_plus command, but it's unclear if this change has been tested with various memory configurations to ensure it works as expected.

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    codiumai-pr-agent-pro bot commented Sep 19, 2024 •
    edited
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    PR Code Suggestions ✨

    CategorySuggestion                                                                                                                                    Score
    Possible issue
    Add a safeguard to prevent memory allocation from exceeding system limits

    Add error handling to ensure that the memory allocation doesn't exceed the available
    system memory. This can prevent potential out-of-memory errors.

    modules/local/openms/thirdparty/msgfdb_indexing/main.nf [25-26]

    --Xmx ${task.memory.toMega()} \
--Xms ${task.memory.toMega()} \
+-Xmx ${Math.min(task.memory.toMega(), Runtime.getRuntime().maxMemory() / (1024 * 1024))} \
+-Xms ${Math.min(task.memory.toMega(), Runtime.getRuntime().maxMemory() / (1024 * 1024)) / 4} \
    • Apply this suggestion
    Suggestion importance[1-10]: 9

    Why: This suggestion addresses a potential issue by adding error handling to prevent memory allocation from exceeding system limits, which is crucial for avoiding out-of-memory errors.

    		9
    Performance
    Adjust the initial heap size to a fraction of the maximum heap size for better memory management

    Consider using a fraction of the total memory for the initial heap size (-Xms) to
    allow for better memory management. A common practice is to set it to 25% of the
    maximum heap size.

    modules/local/openms/thirdparty/msgfdb_indexing/main.nf [25-26]

     -Xmx ${task.memory.toMega()} \
--Xms ${task.memory.toMega()} \
+-Xms ${task.memory.toMega() / 4} \
    • Apply this suggestion
    Suggestion importance[1-10]: 8

    Why: This suggestion improves memory management by setting the initial heap size to 25% of the maximum, which is a common practice and can lead to better performance and resource utilization.

    		8
    Maintainability
    Use a more universal method for memory unit conversion to ensure cross-system compatibility

    Consider adding memory unit conversion to ensure consistency across different
    systems. The toMega() method might not be available on all Nextflow versions or
    configurations.

    modules/local/openms/thirdparty/msgfdb_indexing/main.nf [25-26]

    --Xmx ${task.memory.toMega()} \
--Xms ${task.memory.toMega()} \
+-Xmx ${task.memory.toBytes() / (1024 * 1024)}m \
+-Xms ${task.memory.toBytes() / (1024 * 1024) / 4}m \
    • Apply this suggestion
    Suggestion importance[1-10]: 7

    Why: This suggestion enhances maintainability by using a more universal method for memory unit conversion, ensuring compatibility across different systems and Nextflow versions.

    		7

    💡 Need additional feedback ? start a PR chat

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    github-actions bot commented Sep 19, 2024 •
    edited
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    nf-core lint overall result: Passed ✅

    Posted for pipeline commit 5e685df

    +| ✅ 278 tests passed       |+
#| ❔  10 tests were ignored |#

    ❔ Tests ignored:

    • files_exist - File is ignored: conf/igenomes.config
    • files_exist - File is ignored: conf/test_full.config
    • files_exist - File is ignored: conf/test.config
    • files_exist - File is ignored: .github/workflows/awstest.yml
    • files_exist - File is ignored: .github/workflows/awsfulltest.yml
    • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
    • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
    • files_unchanged - File ignored due to lint config: docs/README.md
    • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
    • multiqc_config - multiqc_config

    ✅ Tests passed:

    Run details

    • nf-core/tools version 2.14.1
    • Run at 2024-09-19 11:46:21

    @ypriverol ypriverol merged commit 7734f96 into bigbio:dev Sep 19, 2024
    17 checks passed
    @ypriverol ypriverol mentioned this pull request Sep 20, 2024
    Closed
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    @ypriverol ypriverol ypriverol approved these changes

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