Code Repositories

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.

Third Software Release (June 2020)

The latest 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)

The latest 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:

https://github.com/bioexcel

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:

HADDOCK

Releases:

Development:

CPMD / MiMiC

Releases:

Development: