Last active
March 31, 2017 21:48
-
-
Save dotsdl/0e0fbd409e3e102d0458 to your computer and use it in GitHub Desktop.
MDAnalysis performance improvements under new topology model
The notebook says that the benchmark system are not available but we recently put them on figshare (as also mentioned in the updated README for the vesicle_library):
A set of large vesicle systems, ranging in size from 1.75 M to 10 M particles are made available under doi:10.6084/m9.figshare.3406708.
@dotsdl please fix the notebook as it holds up MDAnalysis/MDAnalysis.github.io#41 (see also MDAnalysis/MDAnalysis.github.io#41 (comment) )
- fix availability of vesicle library
- remove stupid json warnings
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
@jandom sorry didn't see this until now. Since the
Topology
is a collection ofnumpy
arrays instead of a list ofAtom
objects, it should perform better for many smaller systems, too, and each one also has a smaller memory footprint since we only have as many attributes as we need, no duplication of data, etc.. We already see that we get a decent speedup on parsing a GRO file with this new scheme, but we also omitted guessing from it, too, so perhaps it's not a fair comparison.Does that kinda answer your question?