Release 4.9.0 - Githubissues

joaander commented 1 week ago

Minor and major releases:

[x] Update tutorial submodule.
[x] Check for new or duplicate contributors since the last release: comm -13 (git log $(git describe --tags --abbrev=0) --format="%aN <%aE>" | sort | uniq | psub) (git log --format="%aN <%aE>" | sort | uniq | psub). Add entries to .mailmap to remove duplicates.
[x] Ensure that added features have Sybil examples.
[x] Run hoomd-benchmarks, check for performance regressions with the previous release, and post the tables in the release pull request.
[x] Run hoomd-validation.

All releases:

[x] Update change log.
- git log --format=oneline --first-parent $(git log -n 1 --pretty=format:%H -- CHANGELOG.rst)...
[x] Check readthedocs build, especially change log formatting.
[x] Run bumpversion.
[x] Tag and push.
[x] Update conda-forge recipe.
[x] Update glotzerlab-software.
[x] Update hoomd-component-template.
[x] Update hpmc-energy-template.

joaander commented 1 week ago

TODO:

[x] Make trunk-major branches on hoomd-examples and hoomd-validation.

joaander commented 1 week ago

Benchmark results: hoomd-benchmarks results using hoomd-benchmarks@aa0a49619ae7d7a3014041580734c7bf506cc878

A100 GPU:

                                       4.4.0         4.5.0         4.6.0         4.7.0         4.8.2         4.9.0
GSD                             4.791792e+02  4.731964e+02  4.553129e+02  5.100473e+02  4.931779e+02  2.066046e+02
GSDLog                          4.363332e+04  5.617271e+04  4.517247e+04  9.929403e+04  1.048745e+05  1.049983e+05
HDF5Log                         2.893153e+03  2.876746e+03  2.838468e+03  3.035536e+03  3.067277e+03  2.857904e+03
HPMCOctahedron                  8.682262e+02  1.151776e+03  1.144427e+03  1.137270e+03  1.146105e+03  1.131344e+03
HPMCSphere                      1.713513e+03  1.727364e+03  1.722474e+03  1.723051e+03  1.723319e+03  1.693258e+03
MDPairLJ                        4.246912e+03  4.308015e+03  4.380430e+03  4.399601e+03  4.381139e+03  4.356096e+03
MDPairOPP                       2.231376e+03  2.235057e+03  2.231965e+03  2.244641e+03  2.224166e+03  2.228840e+03
MDPairTable                     3.181794e+03  3.176203e+03  3.168321e+03  3.177067e+03  3.169898e+03  3.148561e+03
MDPairWCA                       9.236660e+03  9.588624e+03  9.195625e+03  9.313692e+03  9.376735e+03  9.241932e+03
MicrobenchmarkBoxResize         9.892524e+04  9.718413e+04  1.006777e+05  1.008278e+05  1.012290e+05  9.991252e+04
MicrobenchmarkCustomTrigger     3.355987e+06  3.401013e+06  3.376825e+06  2.944161e+06  2.970443e+06  2.928140e+06
MicrobenchmarkCustomUpdater     7.484706e+06  7.076594e+06  7.661491e+06  5.376681e+06  5.881132e+06  5.959842e+06
MicrobenchmarkEmptySimulation   2.000430e+07  2.025979e+07  2.007140e+07  2.040640e+07  2.028346e+07  2.021539e+07
MicrobenchmarkForceArrayAccess  5.090195e+02  5.153541e+02  5.111711e+02  4.694176e+02  4.952243e+02  4.909943e+02
MicrobenchmarkGetSnapshot       6.369185e+02  5.986899e+02  6.074992e+02  6.209972e+02  6.284500e+02  6.055712e+02
MicrobenchmarkSetSnapshot       9.885144e+01  9.964724e+01  9.213005e+01  8.694488e+01  8.974944e+01  8.781282e+01

AMD EPYC 7763 (16 cores used)

                                       4.4.0         4.5.0         4.6.0         4.7.0         4.8.2         4.9.0
GSD                             2.751245e+02  2.700695e+02  2.718832e+02  2.929055e+02  3.084674e+02  1.686356e+02
GSDLog                          1.395534e+04  1.268620e+04  1.352679e+04  1.796345e+04  1.785674e+04  1.741646e+04
HDF5Log                         2.671884e+03  2.653186e+03  2.648474e+03  2.756567e+03  2.812777e+03  2.614108e+03
HPMCOctahedron                  9.490398e+01  1.525612e+02  1.530392e+02  1.537280e+02  1.607360e+02  1.609572e+02
HPMCPairKernFrenkel                      NaN           NaN  8.285537e+01  8.404953e+01  8.424805e+01  8.307501e+01
HPMCPairLJ                               NaN  2.490526e+01  2.522094e+01  2.512821e+01  2.519707e+01  2.474059e+01
HPMCPairStep                             NaN           NaN  1.381667e+02  1.361902e+02  1.385008e+02  1.279315e+02
HPMCPairUnionWCA                         NaN           NaN  3.155201e+01  3.230026e+01  3.219535e+01  2.896644e+01
HPMCSphere                      1.828604e+02  3.161800e+02  3.142426e+02  3.139931e+02  3.084222e+02  3.135341e+02
MDPairLJ                        1.489196e+02  1.472301e+02  1.482793e+02  1.474038e+02  1.508971e+02  1.584694e+02
MDPairOPP                       4.444242e+01  4.476899e+01  4.449167e+01  4.458091e+01  4.467470e+01  4.456193e+01
MDPairTable                     1.272132e+02  1.267520e+02  1.263354e+02  1.264216e+02  1.293265e+02  1.337697e+02
MDPairWCA                       5.927040e+02  5.882546e+02  5.910454e+02  5.869398e+02  6.114920e+02  6.585349e+02
MicrobenchmarkBoxResize         1.196068e+04  1.198899e+04  1.184958e+04  1.193219e+04  1.191606e+04  1.193472e+04
MicrobenchmarkCustomForce       3.106380e+03  3.126629e+03  3.125996e+03  3.151540e+03  3.218497e+03  3.238602e+03
MicrobenchmarkCustomTrigger     3.545734e+06  3.671073e+06  3.509753e+06  2.966529e+06  3.069516e+06  3.167667e+06
MicrobenchmarkCustomUpdater     8.046831e+06  7.765310e+06  7.432404e+06  5.629433e+06  6.023337e+06  6.108036e+06
MicrobenchmarkEmptySimulation   1.506374e+07  1.529829e+07  1.485701e+07  1.493459e+07  1.477044e+07  1.504979e+07
MicrobenchmarkForceArrayAccess  1.571391e+02  1.581153e+02  1.573185e+02  1.508361e+02  1.603869e+02  1.473952e+02
MicrobenchmarkGetSnapshot       2.500562e+01  2.520764e+01  2.525337e+01  2.591139e+01  2.527913e+01  1.625160e+01
MicrobenchmarkSetSnapshot       1.749779e+01  1.756731e+01  1.721007e+01  1.772079e+01  1.774450e+01  1.380459e+01

Note: The change in GSD performance comes from moving the benchmarks to scratch.

glotzerlab / hoomd-blue

Release 4.9.0 #1916