release 2.9.0 blog post #449
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@hmacdope should we emphasize more that people should try and install to make use of the much faster distance calculations? Or should we include it as a conda package run time dependency for x86 architectures? |
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Distopia works on my old x86 macOS: In [1]: import MDAnalysis as mda; import MDAnalysisTests.datafiles as data
In [2]: u = mda.Universe(data.TPR, data.TRR)
In [3]: u.atoms.n_atoms
Out[3]: 47681
In [10]: %timeit d = mda.lib.distances.distance_array(u.atoms[:5000], u.atoms[500:4000],
⋮ box=u.dimensions)
629 ms ± 2.78 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [11]: %timeit d = mda.lib.distances.distance_array(u.atoms[:5000], u.atoms[500:4000],
⋮ box=u.dimensions, backend="distopia")
324 ms ± 163 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)and gives 2x speed-up for a medium-sized problem. For all 47k atoms ... In [14]: %timeit d = mda.lib.distances.distance_array(u.atoms, u.atoms, box=u.dimensions, backend="distopia")
Segmentation fault: 11oops.... but in all fairness, the serial version ran my laptop out of its 16 GB of memory but completed In [4]: %timeit d = mda.lib.distances.distance_array(u.atoms, u.atoms, box=u.dimensions,
⋮ backend="serial")
1min 36s ± 3.02 s per loop (mean ± std. dev. of 7 runs, 1 loop each) |
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The post could now be published in principle (edit: because we now have 3.13 cf packages) but let’s wait until at least tomorrow in case anyone wants to make any changes. |
Co-authored-by: Irfan Alibay <[email protected]>
(MDAnalysis/mdanalysis#4805) (or it will have them soon enough so that I can remove the limitation)
Co-authored-by: Jenna M Swarthout Goddard <[email protected]>
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| * Support for Gromacs v2024.4 and v2025 TPR files. | ||
| * A new "water" keyword for selecting water residues. | ||
| * Support for **[distopia][] 0.4.0** as an optional distance library |
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@hmacdope can you look over the distopia part, please?
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see also PR MDAnalysis/mdanalysis#4970 for doc update
- installation instructions - link to docs for backends - mini example - mention (currently undocumented) MDAnalysis.lib.distances.HAS_DISTOPIA
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@jennaswa with release post up, are you able to put out announcements (LinkedIn, bsky, discussions)? (Not sure if I have any time soon) |
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