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Author	SHA1	Message	Date
Jennifer	870e0db32b	Adds experiment_config_json for setting custom configurations with a json.	2024-05-02 02:54:06 -04:00
jnwei	0ba7e7f9b5	removes outputs from OpenFold.ipynb	2024-05-02 02:53:35 -04:00
Jennifer	d4ed0b0c8f	Add log statement to weight conversion script	2024-05-02 02:52:45 -04:00
Jennifer	67454c3982	bugfixes and adds a section to convert optim files	2024-05-02 02:52:04 -04:00
jnwei	638fbaf600	Updates commit value for OpenFold notebook.	2024-05-02 02:36:13 -04:00
Jennifer	2dd481e12d	fix path error in scripts/utils.py and logging fix	2024-05-02 02:36:13 -04:00
jnwei	cfb4c19cac	run_pretrained_openfold.py: Change default paths of binary to be conda environment bin	2024-05-02 02:36:13 -04:00
Jennifer	f4e54ec7ed	clear up some space for docker ci	2024-05-02 02:36:13 -04:00
Jennifer Wei	60fbe53990	changes required for pytorch2	2024-05-02 02:36:13 -04:00
Jennifer	ec6058cd56	DNS: Local profiler changes	2024-05-02 02:36:12 -04:00
jnwei	2a4818a340	update license file	2024-05-02 02:36:12 -04:00
Jennifer	6b77062dd9	adds config recording to wandb	2024-05-02 02:36:12 -04:00
Jennifer	0f2b292913	Adds experiment_config_json for setting custom configurations with a json.	2024-05-02 02:36:12 -04:00
Jennifer	5bfad07412	Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.	2024-05-02 02:36:12 -04:00
jnwei	521bc6e910	removes outputs from OpenFold.ipynb	2024-05-02 02:36:12 -04:00
Jennifer	a7216c73cf	changes reloading weights to account for possible state_dict headers.	2024-05-02 02:36:12 -04:00
Jennifer	711ba0abe2	Add log statement to weight conversion script	2024-05-02 02:36:12 -04:00
Jennifer	dd1dd64137	bugfixes and adds a section to convert optim files	2024-05-02 02:36:12 -04:00
Jennifer	0a0dbb3960	Adjust weight conversion and add a script for converting checkpoints.	2024-05-02 02:36:12 -04:00
Jennifer	d9d4bf1427	updates zero_to_fp32.py for new deepspeed version and import_weight bugfix	2024-05-02 02:36:12 -04:00
jnwei	08276f0faa	Updates commit value for OpenFold notebook.	2024-05-02 02:36:12 -04:00
Lukas Jarosch	eb4d1e57af	Add improved alignment-db creation script ... - much faster due to the use of threading and mp - also supports sharding	2024-05-02 02:36:12 -04:00
Christina Floristean	76b1ec98e2	Scripts from Lukas to be used in improved setup process	2024-05-02 02:36:12 -04:00
jnwei	4ee9943e16	Remove nvcc compute capability 37 which caused kernel build issues	2024-05-02 02:00:52 -04:00
Jennifer Wei	2625e0b29e	Merge pull request #437 from jnwei/mkl-fix ... Adds mkl version to environment.yml	2024-04-30 22:36:22 +07:00
Jennifer	64631f0c61	Adds mkl version to environment.yml	2024-04-30 09:46:12 -04:00
Jennifer	09e74c7613	fix path error in scripts/utils.py and logging fix	2024-04-29 06:26:05 -04:00
Vaclav Hanzl	30813a36b6	Fix Colab by using OF commit from pl_upgrades ... The commit used so far now fails with Colab's numpy. (Commit from current main does not work either.)	2024-04-27 19:45:44 +02:00
jnwei	cb3ff410c3	run_pretrained_openfold.py: Change default paths of binary to be conda environment bin	2024-04-23 16:40:17 +07:00
Jennifer	81c847b173	clear up some space for docker ci	2024-04-22 06:05:09 -04:00
Jennifer	12eb81bac5	Reset miniforge version to 23.3.1-1	2024-04-22 05:14:04 -04:00
Jennifer	cf0cc8bcc5	small edit to Dockerfile	2024-04-22 05:00:06 -04:00
Jennifer	1d2237347e	upgrading hmmer hhsuite and kalign2 packages	2024-04-22 04:48:05 -04:00
jnwei	0b11ced1d8	change mamba version	2024-04-22 14:55:43 +07:00
jnwei	ed5261f880	Split cuda install commands in Dockerfile	2024-04-22 14:32:22 +07:00
Jennifer	ad34fc3c5d	updates Bio.PDBData call and environment.yml	2024-04-22 02:55:09 -04:00
jnwei	793eb966b2	adjust pytorch version number	2024-04-20 16:52:06 +07:00
jnwei	addb80a849	changes to Dockerfile ane pin mkl to 2024	2024-04-20 16:36:54 +07:00
jnwei	866477a268	Update gpg keys for Docker build	2024-04-20 14:09:58 +07:00
jnwei	3cab807e06	fix mkl version to 2024.0.0	2024-04-19 18:13:33 +07:00
jnwei	5ccb7de370	updates Dockerfile	2024-04-19 17:51:25 +07:00
Jennifer	ea142a0a68	fixes deepspeed function definition.	2024-04-19 06:40:37 -04:00
Jennifer	1ae833bfc8	Updates low_precision check to use current precision settings.	2024-04-19 06:14:08 -04:00
Jennifer	80e6341022	change message for test_model.py compare	2024-04-17 06:47:13 -04:00
Jennifer	bbf989a7bf	psivant local pl2 upgrades without mpi configuration	2024-04-16 20:48:33 -04:00
Jennifer Wei	ce000c6061	changes required for pytorch2	2024-04-12 10:14:57 +00:00
Jennifer	523adaf448	adds reload_dataloaders_every_n_epochs flag	2024-04-11 02:57:49 -04:00
Jennifer	577219c112	Removes OF copy of zero_to_fp32.py favoring deepspeed.util version	2024-04-02 05:01:33 -04:00
Jennifer	862635834a	add paren to save_hyperparameters	2024-04-02 02:49:16 -04:00
Jennifer	5ff5177bc6	more logging changes	2024-04-01 04:36:34 -04:00