Oineus is an implementation of shared-memory parallel computation of persistent homology published in D. Morozov and A. Nigmetov. "Towards lockfree persistent homology." Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures. 2020.
It also contains an implementation of the critical set method from A. Nigmetov and D. Morozov, "Topological Optimization with Big Steps." arXiv preprint arXiv:2203.16748 (2022)."
Currently it supports computation of lower-star persistence of scalar functions on regular grids or of user-defined filtrations (where each simplex needs to be created manually). It is written in C++ with python bindings (pybind11).
Oineus requires C++17 standard and python3.
Pybind11
is included as a submodule.
Other dependencies are Boost and TBB,
install them before compiling Oineus.
E.g., on Ubuntu
$ sudo apt-get install libtbb-dev
$ sudo apt-get install libboost-all-dev
After that compilation is standard:
$ git clone --recurse-submodules [email protected]:anigmetov/oineus.git
$ cd oineus
$ mkdir build
$ cd build
$ cmake ..
$ make -j4
Compiled Oineus python package is located in [build_directory]/python/bindings
.
The oineus
directory there contains the __init__.py
and the binary
with C++ bindings whose name is platform-dependent, say, _oineus.cpython-311-x86_64-linux-gnu.so
.
If you get an error similar to
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/narn/code/oineus/bindings/python/oineus/__init__.py", line 7, in <module>
from . import _oineus
ImportError: cannot import name '_oineus' from partially initialized module 'oineus' (most likely due to a circular import) (/home/narn/code/oineus/bindings/python/oineus/__init__.py)
you are most probably trying to import Oineus from the source directory oineus/bindings/python
,
which contains only the __init__.py
. Make sure that PYTHONPATH
contains the directory oineus/build/bindings/python
.
Another possibility can be that Pybind11 did not pick up the correct Python
executable. Suppose that you have system-wide Python, version 3.11,
but you want to compile for your virtual environment, venv
or conda
,
in which you have Python 3.9. Sometimes, even you activated your Python
virtual environment, pybind11 chooses a different Python (you can see which one
in the output of cmake ..
; also, the name of the binary
_oineus.cpython-311-x86_64-linux-gnu.so
contains the version).
In this case, remove CMakeCache.txt and run
$ cmake .. -DPYTHON_EXECUTABLE=path_to_correct_python
If the command which python
shows you the right Python,
the easiest is
$ cmake .. -DPYTHON_EXECUTABLE=$(which python)
Python packages needed by Oineus are numpy
and scipy
. Some of the examples
require torch
for optimization and matplotlib
, plotly
and dash
for
visualization. File requirements.txt
contains all of these; if you do not
need to run examples, it is simpler to just pip install numpy scipy
in your virtual
environment.
See Tutorial.
Oineus is a free program distributed under modified BSD license. See legal.txt for details.