Commit Graph

12 Commits

Author SHA1 Message Date
751a4b8612 Add support for --seq_limit in Jackhmmer - significantly reduces peak RAM use
* See https://github.com/EddyRivasLab/hmmer/issues/323 for more context.
* We observed 75.6 GB -> 13.6 GB peak RAM reduction for one of our queries.

PiperOrigin-RevId: 782808687
Change-Id: I4306dc6921015c88c5f8ced69a4ef46e10574a57
2025-07-14 02:00:15 -07:00
06d28cad2e Update to Ubuntu 24.04 / CUDA 12.6.3 base image and use Python 3.12
PiperOrigin-RevId: 765229057
Change-Id: I7b1c8234fd1b067e62e308116d603f0e3d375972
2025-06-04 05:20:40 -07:00
6cc6364a8d Internal change
PiperOrigin-RevId: 765224124
Change-Id: I1aad4e6d7cee2e27e3f360c1845b4c4111b4eeec
2025-06-04 05:20:24 -07:00
64723739f5 Update to Ubuntu 24.04 / CUDA 12.6.3 base image and use Python 3.12
PiperOrigin-RevId: 765219906
Change-Id: I271f442012ee30356ef316eda87abd231319a673
2025-05-30 09:49:16 -07:00
935d47f8d4 Reduce the size of the Docker/Singularity container
PiperOrigin-RevId: 765209187
Change-Id: I075874b51b243a3e75bc8078ea81920f1984dbc5
2025-05-30 17:12:44 +01:00
17afe151ea Improve AlphaFold 3 Dockerfile
* Use `apt-get` instead of `apt`. Should not make much difference since we set the `--quiet` flag though.
* Document better the rationale behind building HMMER from scratch.
* Check SHA-256 hash of the downloaded HMMER tar file.
* Addresses critique from https://www.linkedin.com/pulse/getting-alphafold-3-run-amd-gpus-owain-kenway-egite/.

PiperOrigin-RevId: 763703614
Change-Id: Ibc231b8c31d1d891f537e2765094c1710a76eaea
2025-05-27 02:54:58 -07:00
2d466dc791 Do not limit parallelism of make when building HMMER
PiperOrigin-RevId: 759516856
Change-Id: I1c926a30edf87f0d3e6feccb42e474ff96c06d6d
2025-05-16 02:07:09 -07:00
4158f7a246 Add a comment that HMMER can also be installed using apt instead of building it from source
PiperOrigin-RevId: 708206092
2024-12-20 10:59:39 +00:00
781d8d04f9 Add XLA flag workaround for CUDA Capability 7.x GPUs
PiperOrigin-RevId: 705559274
2024-12-13 06:35:21 +00:00
1558f06eb3 Document additional dependencies in Dockerfile
PiperOrigin-RevId: 698386882
2024-11-21 10:30:17 +00:00
899b16d8d0 Update pip in the virtual environment
PiperOrigin-RevId: 697911731
2024-11-19 10:44:50 +00:00
4f52a3bb62 Initial release of AlphaFold 3
PiperOrigin-RevId: 695257954
2024-11-11 10:42:47 +00:00