Closed daichengxin closed 1 week ago
โฑ๏ธ Estimated effort to review: 2 ๐ต๐ตโชโชโช |
๐งช No relevant tests |
๐ No security concerns identified |
โก 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. |
Category | Suggestion | 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 availablesystem memory. This can prevent potential out-of-memory errors.** [modules/local/openms/thirdparty/msgfdb_indexing/main.nf [25-26]](https://github.com/bigbio/quantms/pull/420/files#diff-3dbb08a2c4597937a8f88758401b3adb18bf3180c3a7203ea29c61702033f822R25-R26) ```diff --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]: 9Why: 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) toallow 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]](https://github.com/bigbio/quantms/pull/420/files#diff-3dbb08a2c4597937a8f88758401b3adb18bf3180c3a7203ea29c61702033f822R25-R26) ```diff -Xmx ${task.memory.toMega()} \ --Xms ${task.memory.toMega()} \ +-Xms ${task.memory.toMega() / 4} \ ``` - [ ] **Apply this suggestion** Suggestion importance[1-10]: 8Why: 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 differentsystems. The toMega() method might not be available on all Nextflow versions or configurations.** [modules/local/openms/thirdparty/msgfdb_indexing/main.nf [25-26]](https://github.com/bigbio/quantms/pull/420/files#diff-3dbb08a2c4597937a8f88758401b3adb18bf3180c3a7203ea29c61702033f822R25-R26) ```diff --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]: 7Why: This suggestion enhances maintainability by using a more universal method for memory unit conversion, ensuring compatibility across different systems and Nextflow versions. | 7 |
๐ก Need additional feedback ? start a PR chat
nf-core lint
overall result: Passed :white_check_mark:Posted for pipeline commit 5e685df
+| โ
278 tests passed |+
#| โ 10 tests were ignored |#
User description
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.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
MSGFDBINDEXING
process by adding-Xmx
and-Xms
parameters to themsgf_plus
command.task.memory
value, improving resource management.Changes walkthrough ๐
main.nf
Fix memory allocation in MSGFDBINDEXING process
modules/local/openms/thirdparty/msgfdb_indexing/main.nf
-Xmx
and-Xms
to themsgf_plus
command.
task.memory
.