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salilab / IHMValidation

Validation software for integrative models deposited to PDB
MIT License
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Hardcoded paths prevent parallel execution #44

Open aozalevsky opened 2 years ago

aozalevsky commented 2 years ago

It would be nice to have the ability to update the PDB-Dev in parallel. Together with the recent updates in #38 it would allow to rebuild the whole repo (with recalculated values) in under 2 minutes on a modern 32-128 core node.

So far I identified several places which interfere with parallel execution:

https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/__init__.py#L737-L739

uses a hardcoded test.cif as a temporary filename

https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/utility.py#L475-L490

removes any temp files by mask, including temp files generated for other structures. It specifically hits sascif processing (looks like other files are not reread again. at least when molprobity and excluded volume are already recalculated).

https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/sas.py#L86 https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/sas.py#L134 https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/sas.py#L370-L372 https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/sas.py#L379

https://github.com/salilab/IHMValidation/blob/f1aec61bc2f8de7717f20024b7fb712d94733d4f/master/pyext/src/validation/sas.py#L381-L382

temp files for sas processing.