73 Commits

Author	SHA1	Message	Date
Sachin Kadyan	1b5813df76	Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.	2023-01-09 20:55:03 -05:00
Gustaf Ahdritz	f362ebffa7	Undo DeepSpeed config change	2022-03-29 20:38:31 -04:00
Gustaf Ahdritz	9f5581781e	Fix DeepSpeed config builder	2022-03-29 15:19:30 -04:00
Gustaf Ahdritz	c83c42e81c	Fix bug in mmCIF cache script	2022-03-14 16:31:02 -04:00
Gustaf Ahdritz	950b02f040	One last adjustment to generate_chain_data_cache.py	2022-02-22 17:46:20 -05:00
Gustaf Ahdritz	39860f936c	Adjust default behavior of generate_chain_data_cache.py	2022-02-22 17:42:22 -05:00
Gustaf Ahdritz	4c7c30b1d7	Fix chain data cache script bug, improve logging	2022-02-22 17:37:52 -05:00
Gustaf Ahdritz	70362e4b1f	Fix bugs in chain data cache script	2022-02-05 00:17:17 -05:00
Gustaf Ahdritz	3b82ddb793	Add chain data cache generator	2022-02-04 23:55:45 -05:00
Gustaf Ahdritz	a46f1b1218	Revert changes to mmcif cache gen script	2022-02-04 15:59:37 -05:00
Gustaf Ahdritz	7f3a48ee80	Un-comment lines in alignment script	2022-02-04 15:17:48 -05:00
Gustaf Ahdritz	84f45ee1bf	Fix bug in cache script	2022-02-04 15:10:16 -05:00
Gustaf Ahdritz	54deee17c6	Restore cache generation script	2022-02-04 15:07:12 -05:00
Gustaf Ahdritz	721e43be8d	Add GPU relaxation	2022-02-03 22:50:34 -05:00
Gustaf Ahdritz	998155e9b6	Merge branch 'main' of github.com:aqlaboratory/openfold into chunking_experiment	2022-02-03 17:09:26 -05:00
Gustaf Ahdritz	fb341b174c	Merge	2022-02-03 17:09:18 -05:00
Gustaf Ahdritz	f30d77b7d7	Prep for training	2022-02-03 17:07:10 -05:00
Gustaf Ahdritz	6ce8cfe31e	Fixes	2022-02-03 17:06:45 -05:00
Gustaf Ahdritz	02fc43762b	Beef up alignment script	2022-02-03 17:06:30 -05:00
Gustaf Ahdritz	81ebd4a8d3	Fix NVIDIA loggier issue in install script	2022-02-01 16:20:58 -05:00
Gustaf Ahdritz	52a8b8f313	Update AlphaFold parameter download link	2022-02-01 12:36:55 -05:00
Karl Leswing	ffd154146b	Source the environment because it is reccomended that this is called via source	2022-01-20 10:57:37 -05:00
Karl Leswing	74675b7358	Ready For PR	2022-01-20 10:50:59 -05:00
Gustaf Ahdritz	36b9a8ea9c	Add script for generating sample feature dict	2021-12-30 19:51:50 -05:00
Gustaf Ahdritz	f4701ffa91	Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py	2021-12-20 00:50:20 -05:00
Gustaf Ahdritz	edffead3c4	Make AlignmentRunner more flexible	2021-12-19 22:08:04 -05:00
Gustaf Ahdritz	f4316dc084	Fix AlphaFold DB download script	2021-12-19 15:44:13 -05:00
Gustaf Ahdritz	96709588dd	Add low-memory attention (still needs to be incorporated)	2021-12-17 18:00:06 -05:00
Gustaf Ahdritz	71fabe1e3b	Fix mmseqs script bug	2021-12-10 18:33:23 -05:00
Sachin Kadyan	ddf922df6f	Made initialization consistent for template_featurizer in all modules. ... Added obsolete_pdbs_file and release_dates_path in all initialization points.	2021-12-10 18:58:56 -04:00
Gustaf Ahdritz	57720ec78e	Merge pull request #24 from yuzhiguo07/patch-1 ... Update precompute_alignments_mmseqs.py	2021-11-29 22:02:34 -05:00
Gustaf Ahdritz	ca810168d9	Add bfloat16 support to DeepSpeed config script	2021-11-29 19:03:40 -05:00
yuzhiguo07	1bfb1e1b2a	Update precompute_alignments_mmseqs.py	2021-11-29 15:11:41 -06:00
Gustaf Ahdritz	78e7996227	Fix bugs in MMseqs DB script	2021-11-29 13:53:27 -05:00
Gustaf Ahdritz	52800ff027	Add alternative fasta file extension	2021-11-22 16:26:05 -05:00
Gustaf Ahdritz	6e5c619c38	Fix bug in alignment precomputation script	2021-11-15 16:16:08 -05:00
Gustaf	8c95493f1a	Update documention for ProteinNet use case	2021-11-10 02:08:58 -05:00
Gustaf	e7b239c9e4	Add missing variable	2021-11-10 02:05:50 -05:00
Gustaf	2c7ce956e8	Add more ProteinNet functionality	2021-11-10 01:53:46 -05:00
Gustaf	22cc45a85a	Begin to add ProteinNet support (WIP)	2021-11-09 23:53:14 -05:00
Gustaf	36f317bef9	Add MMseqs2 MSA generation	2021-11-09 02:57:53 -05:00
Gustaf Ahdritz	1feca912a7	Merge pull request #2 from aqlaboratory/marta-sd/nan-loss ... Fix NaN loss bug + add development env for Nvidians	2021-11-03 12:14:11 -04:00
Marta	6c14c76a1b	add dllogger to conda env	2021-11-02 06:03:49 -07:00
Gustaf Ahdritz	9d4c9357c5	Speed up template featurizer	2021-10-29 23:18:06 -04:00
Gustaf Ahdritz	a9a19b78a9	Fix model checkpointing bug	2021-10-26 16:16:25 -04:00
Gustaf Ahdritz	98b2c663c5	Add description to ProteinNet MSA script	2021-10-26 00:40:37 -04:00
Gustaf Ahdritz	b5f885d0ff	Add ProteinNet support to parser	2021-10-26 00:39:07 -04:00
Gustaf Ahdritz	94ab346e40	Merge pull request #1 from aqlaboratory/mpvenkatesh/changes ... minor fixes	2021-10-24 14:21:28 -04:00
sft-managed	04fa3548e9	minor fixes	2021-10-24 10:21:12 -07:00
Gustaf Ahdritz	5b9cfdafa6	Add script for installing the HH-suite	2021-10-22 18:01:58 -04:00