Science Score: 57.0%
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Low similarity (14.5%) to scientific vocabulary
Repository
AnyBEM - Nonlocal Protein Electrostatics in Impala
Basic Info
- Host: GitHub
- Owner: tkemmer
- License: mit
- Language: C++
- Default Branch: master
- Size: 225 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
AnyBEM - Nonlocal Protein Electrostatics in Impala
The AnyBEM library provides domain-specific variants of the implicit representations and matrix-vector products from NESSie.jl and CuNESSie.jl for the Impala language.
Getting started
Requirements
- CMake 3.12 (or above)
- GCC or Clang (C++14-compatible)
- AnyDSL Runtime Library
- clipp (optional, for tools only)
- Badhron (optional, for testing only)
Installation
sh
git clone https://github.com/tkemmer/anybem.git
mkdir anybem/build
cd anybem/build
cmake ..
make
If you installed the AnyDSL runtime library according to the build
instructions in the project's README file, you'll probably need to tell
CMake its location, e.g., by replacing the above cmake command by
sh
cmake .. -DAnyDSL_runtime_DIR=/<path to anydsl>/runtime/build/share/anydsl/cmake
Configuration options
Configuration options can be provided by appending the respective option-value tuples in the form -D<option>=<value> to the above cmake command:
|Option | Values | Description |
|--------------------|---------------|-----------------------------------------------|
|AnyBEM_BACKEND | cpu, cuda | Back end to be used for matrix multiplication |
|AnyBEM_DEVICE | 0, ... | ID of device to be used with CUDA back end |
|AnyBEM_INTRINSICS | f32, f64 | Floating-point precision level for intrinsics |
Default values are denoted by a bold font.
Features
Most functionality currently provided by AnyBEM is showcased through the anybem tool, which is built automatically alongside the AnyBEM libraries. The tool can be found in the tools/cli directory.
``` NAME AnyBEM - Nonlocal Protein Electrostatics in Impala
SYNOPSIS
./cli/anybem
OPTIONS
Citing
If you use AnyBEM in your research, please cite the following publications:
T. Kemmer, S. Hack, B. Schmidt, A. Hildebrandt. CUDA-accelerated protein electrostatics in linear space. Journal of Computational Science 70 (2023) 102022. https://doi.org/10.1016/j.jocs.2023.102022
T. Kemmer. Space-efficient and exact system representations for the nonlocal protein electrostatics problem. Ph. D. thesis (2021), Johannes Gutenberg University Mainz. Mainz, Germany. https://doi.org/10.25358/openscience-5689
Citation items for BibTeX can be found in CITATION.bib.
Owner
- Name: Thomas Kemmer
- Login: tkemmer
- Kind: user
- Location: Germany
- Company: University of Mainz
- Repositories: 5
- Profile: https://github.com/tkemmer
Computer scientist and Gentoo Linux enthusiast
Citation (CITATION.bib)
@article{anybem-2023,
author = {Thomas Kemmer and Sebastian Hack and Bertil Schmidt and Andreas Hildebrandt},
title = {CUDA-accelerated protein electrostatics in linear space},
year = {2023},
journal = {Journal of Computational Science},
volume = {70},
pages = {102022},
doi = {https://doi.org/10.1016/j.jocs.2023.102022}
}
@phdthesis{anybem-2021,
author = {Kemmer, Thomas},
title = {{Space-efficient and exact system representations for the nonlocal protein electrostatics problem}},
year = {2021},
school = {Johannes Gutenberg University Mainz},
address = {Mainz, Germany},
doi = {10.25358/openscience-5689}
}
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