Parallel read and preprocess the data #371
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…tps://github.com/alchemistry/alchemlyb into 359-speed-up-the-readpreprocess-in-abfe-workflow
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| import pytest | ||
| from alchemtest.amber import load_bace_example | ||
| from alchemtest.gmx import load_ABFE | ||
| from joblib import parallel_config |
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Maybe just import joblib so that it's clearer below what comes from joblib? In this way any un-qualified functions and classes are alchemlyb and everything else is external.
| suffix="xvg", | ||
| T=310, | ||
| ) | ||
| with parallel_config(backend="threading"): |
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I find
| with parallel_config(backend="threading"): | |
| with joblib.parallel_config(backend="threading"): |
clearer when quickly reading the code.
src/alchemlyb/workflows/abfe.py
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| @@ -115,7 +116,7 @@ def __init__( | |||
| else: | |||
| raise NotImplementedError(f"{software} parser not found.") | |||
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| def read(self, read_u_nk=True, read_dHdl=True): | |||
| def read(self, read_u_nk=True, read_dHdl=True, n_jobs=-1): | |||
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Is default -1 really always the best choice? Did you try on a machine with, say, 16 cores, and 16 hyperthreaded cores (or really anything with hyperthreads)?
I am willing to make -1 the default if this is not throwing surprises for users. Otherwise the conservative 1 would be better and users can then explicitly enable.
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Add a paragraph about parallelization: how to enable it, what it does (for each file), any potential problems...
src/alchemlyb/workflows/abfe.py
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| @@ -201,6 +219,7 @@ def run( | |||
| overlap="O_MBAR.pdf", | |||
| breakdown=True, | |||
| forwrev=None, | |||
| n_jobs=-1, | |||
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see above
- Is -1 safe as new default?
- add docs (explanation)
- add versionchanged
src/alchemlyb/workflows/abfe.py
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| @@ -307,7 +329,7 @@ def update_units(self, units=None): | |||
| logger.info(f"Set unit to {units}.") | |||
| self.units = units or None | |||
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| def preprocess(self, skiptime=0, uncorr="dE", threshold=50): | |||
| def preprocess(self, skiptime=0, uncorr="dE", threshold=50, n_jobs=-1): | |||
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see above
- Is -1 safe as new default?
- add docs (explanation)
- add versionchanged
Use joblib to parallelise the read and preprocess.