Most of the software worked on by BioExcel have their own upstream source repositories and separate release cycles managed within each software project. BioExcel project snapshots of these are provided below. BioExcel is also developing additional tooling maintained in GitHub at https://github.com/bioexcel
Exascale co-design benchmark cases
BioExcel has extracted four benchmark cases either drawn from or illustrative of key functionality of the core applications GROMACS, HADDOCK, and CP2K and made them available in a form suitable for co-design of the full stack of dependencies they require. These will be useful for e.g. processor design or benchmarking of new hardware. For a detailed description see https://doi.org/10.5281/zenodo.3354707. The official release of the benchmark cases is found there, and any interim updates can be found at https://github.com/bioexcel/bioexcel-exascale-co-design-benchmarks/.
Project releases
This section lists the BioExcel software releases, which are snapshots of the upstream sources at particular points in time and may not correspond to particular upstream versions. Each part of these releases is covered by separate open source licenses.
Fifth Software Release (Dec 2023)
The individual components that make up this project release are archived and available separately on Zenodo:
- GROMACS
- GROMACS 2023.3
source code 10.5281/zenodo.10017686
manual 10.5281/zenodo.10017699 - GROMACS 2023.2
source code 10.5281/zenodo.8134397
manual 10.5281/zenodo.8134388 - GROMACS 2023.1
source code 10.5281/zenodo.7852175
manual 10.5281/zenodo.7852189 - GROMACS 2023
source code 10.5281/zenodo.7588619
manual 10.5281/zenodo.7588711 - GROMACS 2022.6
source code 10.5281/zenodo.8134375
manual 10.5281/zenodo.8134358 - GROMACS 2022. 5
source code 10.5281/zenodo.7586780
manual 10.5281/zenodo.7586765 - GROMACS 2021.7
source code 10.5281/zenodo.7586728
manual 10.5281/zenodo.7586709
- GROMACS 2023.3
- HADDOCK
- HADDOCK-3 beta
https://zenodo.org/records/10527751
- HADDOCK-3 beta
- PMX
- DOI: 10.5281/zenodo.10477399, https://zenodo.org/records/10477399
- BioBB
Fourth Software Release (June 2022)
This final project release from BioExcel-2 is available permanently archived on Zenodo:
- BioExcel-Software-Release-4.zip
https://doi.org/10.5281/zenodo.6761700
The individual components that make up this project release are also archived and available separately on Zenodo:
- GROMACS
- GROMACS 2022.1 source code (includes QM/MM interface to CP2K)
https://doi.org/10.5281/zenodo.6451564 - GROMACS 2022.1 manual
https://doi.org/10.5281/zenodo.6451567 - GROMACS 2021.5 source code (maintenance release)
https://doi.org/10.5281/zenodo.5850051 - GROMACS 2021.5 manual (maintenance release)
https://doi.org/10.5281/zenodo.5849961 - GROMACS 2020.7 source code (maintenance release)
https://doi.org/10.5281/zenodo.5938877 - GROMACS 2020.7 manual (maintenance release)
https://doi.org/10.5281/zenodo.5938884
- GROMACS 2022.1 source code (includes QM/MM interface to CP2K)
- PMX
- pmx release June2022
https://doi.org/10.5281/zenodo.6671368
- pmx release June2022
- HADDOCK
- HADDOCK v3.0.0-beta.1
https://doi.org/10.5281/zenodo.6593819 - 1st stable release of haddock-pilot
https://doi.org/10.5281/zenodo.6593427 - 3rd stable release of the haddock-tools
https://doi.org/10.5281/zenodo.6593626 - 1st release of benchmark-tools
https://doi.org/10.5281/zenodo.6593526
- HADDOCK v3.0.0-beta.1
- QM/MM w/ CP2K
- CP2K v9.1 release incorporating BioExcel QM/MM contributions reported in D1.6
https://doi.org/10.5281/zenodo.6760368 - Software to analyse and visualise CP2K parallel MD performance
https://doi.org/10.5281/zenodo.6670413 - D1.6 release of BioExcel QM/MM Benchmark Suite
https://doi.org/10.5281/zenodo.6676034 - CP2K biomolecular QM/MM benchmarking data
https://doi.org/10.5281/zenodo.6675865 - Report on CP2K biomolecular QM/MM performance profiling
https://doi.org/10.5281/zenodo.6591574
- CP2K v9.1 release incorporating BioExcel QM/MM contributions reported in D1.6
Third Software Release (June 2020)
This project release is available permanently archived on Zenodo (https://doi.org/10.5281/zenodo.3906457). Here are direct links to the packaged software, collected together as the BioExcel Software Release, and also available for different core codes, for your convenience. Note that the BioExcel-Software-Release is the union of the other four downloads
BioExcel-Software-Release-3.tar.gz
sha1sum:da39a3ee5e6b4b0d3255bfef95601890afd80709
sha256sum: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
D1.4 release of CP2K QM/MM optimisations
sha1sum: 8448097e8d1880eb0639840c15f15e32aadeff20
sha256sum: 5a91087fb5ca4ba46effccaa607724d32effc225da91e65442255f69380dd606
gromacs-2020.2.tar.gz
sha1sum: 95dd99c253065aaba8a0d8da4913e124cbe4032a
sha256sum: 7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3
HADDOCK v3.0.alpha2
sha1sum: d41bebe5fdf193da698009297b12bd5b7ddf4f7d
sha256sum: 48878d4b0db99ea6c3fc005a02d47fd925bdc54d9bf7fe86275fb83926f00139
D1.4 release of BioExcel QM/MM Benchmark Suite
sha1sum: 157ed008b6472d24ed9dcd8af63555b3cd6024c6
sha256sum: d2a3a3216698c2f6b75db58f01ea58c9e55f4f143f27220faf0ac38bcf9893ed
D1.4 release of PMX
sha1sum: b83ae71cf43f664fe3162130d2002fffb5690e5d
sha256sum: 0a69f1f9d2b307d7dc7acad32205f330903b6c27164a6b4dc7ade3097a899c54
Second Software Release (October 2018)
This project release is available permanently archived on Zenodo (https://doi.org/10.5281/zenodo.1473685). Here are direct links to the packaged software, collected together as the BioExcel Software Release, and also available for different pilot codes, for your convenience. Note that the BioExcel-Software-Release is the union of the other three downloads.
BioExcel-Software-Release-2.tar.gz
sha1sum: da39a3ee5e6b4b0d3255bfef95601890afd80709
sha256sum: 7ae05d146a0387e7237ca5ebada32966e02b2434841b10ee2efa582baf9febad
BioExcel-CPMD-MiMiC-2.tar.gz
sha1sum: 188fc84a3d4cee08745a707b4cbc82f40fe88420
sha256sum: a4602f461a3f57db9ffcc02152651bbc1c2db3d221f14be6621ab795456258fa
BioExcel-GROMACS-2019-beta1-1.tar.gz
sha1sum: da39a3ee5e6b4b0d3255bfef95601890afd80709
sha256sum: b52338291e2132617e771ae9f0943dad5e5f3322385a06061808c4e29855fe0d
BioExcel-HADDOCK-20181016-1.tar.gz
sha1sum: 319b04d72c95cbd81ed35ba73996c4c41caf0ac9
sha256sum: ab96e1982963a1046ab6edf44417a03d8834f2cb32df072d380600aca5dc8a7e
First Software Release (April 2017)
Here are direct links to the packaged software, collected together as the first BioExcel Software Release, and also available for different pilot codes.
BioExcel-Software-Release-1.tar.gz
sha1sum: b71ef73870364439811c22c10803905d301c1ed2
sha256sum: 375428003742eee9a15c681c151f76a70e39d57af15e42ecfafd8ffd4d188da4
BioExcel-CPMD-MiMiC-0.1.0-1.tar.gz
sha1sum: af9a085b70d5b38a08aeb35ca5cee68a760b2769
sha256sum: 76edf4b541b6ef7d20f79918e779c07ef84a0b93fb6694fd159006093b642d8b
BioExcel-GROMACS-2016.3-1.tar.gz
sha1sum: fdb44e6eb349e05be06c878e566c760fc77f633b
sha256sum: 048c78deef807a23fbc42a11016c138b5c721a4b4323c872de3ab841d1e1e998
BioExcel-HADDOCK-20170426-1.tar.gz
sha1sum: 179c4461d7a3fbcfd8f71281628ac1ac0768b989
sha256sum: 9cded8d93f0a25e5b6a03e7721579f0e919a941dea0bbb8e15ff86cb435ac4c6
GitHub
Various other tools (including the workflow blocks biobb), which are under development by the center, can be downloaded from our GitHub repository:
Upstream sources
The project release tar-balls above are maintained in GitHub, and are sourced from multiple upstream repositories managed by each software project.
GROMACS
Releases:
Development:
- https://github.com/gromacs/gromacs
- https://github.com/gromacs/regressiontests
- https://github.com/gromacs/manual
- https://github.com/deGrootLab/pmx
HADDOCK
Releases:
- http://haddocking.com/ (license form required)
- https://sbgrid.org/software/titles/pdb-tools
- https://github.com/haddocking/pdb-tools/releases
- https://github.com/haddocking/haddock-tools/releases
Development:
- https://github.com/haddocking/
- https://github.com/haddocking/pdb-tools
- https://github.com/haddocking/haddock-tools
- https://github.com/haddocking/disvis
- https://github.com/haddocking/powerfit
- https://github.com/haddocking/haddock-webserver-flask (to be published)
CPMD / MiMiC
Releases:
- http://www.cpmd.org/download (registration and/or commercial license needed)
Development: