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deepmodeling / dpdispatcher

generate HPC scheduler systems jobs input scripts and submit these scripts to HPC systems and poke until they finish
https://docs.deepmodeling.com/projects/dpdispatcher/
GNU Lesser General Public License v3.0
42 stars 56 forks source link

improve SGE system #446

Closed thangckt closed 3 months ago

thangckt commented 5 months ago

Summary by CodeRabbit

coderabbitai[bot] commented 3 months ago

Walkthrough

The recent changes primarily focus on refining script generation and resource management within the dpdispatcher package. Key updates include simplifying source file handling, modifying job name and resource directives in PBS scripts, and enhancing the Resources class with new parameters for SGE parallel environment names. Additionally, test files have been updated to align with these changes, ensuring consistency and correctness in script generation and resource allocation.

Changes

File(s) Change Summary
dpdispatcher/machine.py Simplified source file handling in gen_script_env method by removing intermediate variable.
dpdispatcher/machines/pbs.py Modified PBS script header generation, job name, node selection, and queue handling. Added custom script header logic and script execution commands.
dpdispatcher/submission.py Added sge_pe_name parameter to Resources class and updated related methods.
tests/sample_class.py Updated get_sample_resources and get_sample_resources_dict functions to include sge_pe_name parameter.
tests/test_argcheck.py Added sge_pe_name key in test setup dictionary for resource allocation.
tests/test_lsf_script_generation.py Removed double curly braces around source commands in test_shell_trival function.

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thangckt commented 3 months ago

@njzjz

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 41.17647% with 10 lines in your changes missing coverage. Please review.

Project coverage is 47.50%. Comparing base (20a872d) to head (09a17a8). Report is 20 commits behind head on master.

Files with missing lines Patch % Lines
dpdispatcher/machines/pbs.py 37.50% 10 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (20a872d) and HEAD (09a17a8). Click for more details.

HEAD has 6 uploads less than BASE | Flag | BASE (20a872d) | HEAD (09a17a8) | |------|------|------| ||15|9|
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #446 +/- ## =========================================== - Coverage 60.03% 47.50% -12.54% =========================================== Files 39 39 Lines 3826 3840 +14 =========================================== - Hits 2297 1824 -473 - Misses 1529 2016 +487 ```

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