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Implement HPC execution #192

Merged
merged 13 commits into from
Dec 10, 2021
Merged

Implement HPC execution #192

merged 13 commits into from
Dec 10, 2021

Commits on Dec 9, 2021

  1. implement HPC execution

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  2. Create docking-protein-protein-hpc.cfg

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  3. add adaptive timer 

    and fix typo in percentage calculation
    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  4. Update libhpc.py

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  5. linting

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  6. fix the complete check

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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  7. Update libhpc.py

    @rvhonorato
    rvhonorato committed Dec 9, 2021
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Commits on Dec 10, 2021

  1. Merging benchmark functionalities with hpc 

    Also, modularized functions for better testing.

TODO
testing if it reproduces what @rvhonorate implemented
    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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  2. add get_engine factory

    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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  3. correct imports

    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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  4. lint

    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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  5. Merge branch 'hpc-improve' into hpc 

    A small touch over @rvhonorato implementation. Good work m8!

Done:

* brings some variables to parameters render things more configurable and testable
* leverages what was done in `benchmark` regarding job heading creation.
* Creates a small factory for the `Engine` in the modules `_run`.
* defines default variables at the module level so they are synchronized in `libworkflow` and `libhpc`
    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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  6. add default variable for mode

    @joaomcteixeira
    joaomcteixeira committed Dec 10, 2021
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