Welcome to the HOPS library, the Highly Optimized Polytope Sampling library - a powerful open-source C++17 library for efficient and scalable MCMC algorithms. HOPS provides a versatile framework for sampling convex-constrained spaces equipped with arbitrary target functions. With HOPS, you can achieve optimized and scalable performance in your MCMC algorithms, making it a valuable tool for various applications.
The library is fully documented, with interactive demos and further resources available to help you get started quickly. Whether you're working on a research project or an industrial application, HOPS provides the performance and flexibility you need to efficiently sample your data.
You can also use HOPS with Python interface available at https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy. We hope that the HOPS library will prove to be an invaluable tool in your work, and we invite you to explore its many features and benefits.
For details and benchmarks see the application note https://doi.org/10.1093/bioinformatics/btaa872. Test data from the application note is downloadable at https://doi.org/10.26165/JUELICH-DATA/YXLFKJ.
Documentation, interactive demos and further resources can be found at https://modsim.github.io/hops/.
HOPS contains git submodules that point to third-party libraries. For this reason, HOPS should be fetched recursively:
git clone git@jugit.fz-juelich.de:IBG-1/ModSim/hops.git --recursive
HOPS uses CMake as build system.
See the Dockerfile for a demonstration on installing HOPS and its dependencies on Ubuntu 20.4.
Python interface is available at https://github.com/modsim/hopsy.
| Option Name | Default | Description |
|---|---|---|
| HOPS_BENCHMARKS | OFF | Enables compilation of Benchmarks (Requires Celero). |
| HOPS_DOCS | ON | Enables generation of documentation. |
| HOPS_BINARIES | OFF | Enables compilation of hops executables |
| HOPS_IO | ON | Enables compilation of module for reading and writing csv |
| HOPS_TESTS | ON | Enables compilation of unit tests |
| HOPS_LIBRARY_TYPE | SHARED | Type of library to build. Options are STATIC, SHARED or HEADER_ONLY (deprecated) |
For more options, check CMakeLists.txt
$ mkdir cmake-build-release cd cmake-build-release # create and switch into
# directory for out-of-source build
$ cmake .. -DCMAKE_BUILD_TYPE=Release # run cmake
$ make # build hops
$ make test # run Tests
$ sudo make install # install
Use an IDE (e.g. CLion) to parse the project and its CMakeLists.txt. Note: Much easier to compile with clang than with MSCV.
See the examples directory for demonstrations on how to use the library.
- g++
- Clang
- Microsoft Visual C++
-
If you run into trouble finding CLP on Linux (e.g. Ubuntu 20.04), try extending the cmake prefix path:
-DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu -
In case something went wrong fetching the git lfs content, try:
git lfs pull -
Compare to the Dockerfile to see if dependencies are missing in your local environment.
The development of HOPS primarily takes place on (JuGit)[https://jugit.fz-juelich.de/IBG-1/ModSim/hops], where we have access to powerful continuous integration and a Docker registry. The GitHub repository is only a mirror, so please report issues and make pull requests on JuGit.