release 2.9.0 blog post

[orbeckst]

No description provided.

[IAlibay]

thanks @orbeckst !

[p-j-smith]

Thank you!

[orbeckst]

@hmacdope should we emphasize more that people should try and install

mamba install distopia

to make use of the much faster distance calculations? Or should we include it as a conda package run time dependency for x86 architectures?

[orbeckst]

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: 11

oops.... 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)

[orbeckst]

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.

[orbeckst]

@hmacdope can you look over the distopia part, please?

[orbeckst]

see also PR MDAnalysis/mdanalysis#4970 for doc update

[orbeckst]

@jennaswa with release post up, are you able to put out announcements (LinkedIn, bsky, discussions)? (Not sure if I have any time soon)

[jennaswa]

Done:

• Discord: https://discord.com/channels/807348386012987462/811409277964386344/1351093728156057661
• Discussions: Release of MDAnalysis 2.9.0 mdanalysis#4976
• LinkedIn: https://www.linkedin.com/feed/update/urn:li:activity:7307303370254393345
• Bluesky: https://bsky.app/profile/mdanalysis.bsky.social/post/3lkkntpmo4c2x