Commits · 1d2237347e0201cac8f77d46a1e96d339349ca8d · OpenDAS / OpenFold

22 Apr, 2024 4 commits
- upgrading hmmer hhsuite and kalign2 packages · 1d223734
  Jennifer authored Apr 22, 2024
  
  1d223734
- change mamba version · 0b11ced1
  jnwei authored Apr 22, 2024
  
  0b11ced1
- Split cuda install commands in Dockerfile · ed5261f8
  jnwei authored Apr 22, 2024
  
  ed5261f8
- updates Bio.PDBData call and environment.yml · ad34fc3c
  Jennifer authored Apr 22, 2024
  
  ad34fc3c
20 Apr, 2024 3 commits
- adjust pytorch version number · 793eb966
  jnwei authored Apr 20, 2024
  
  793eb966
- changes to Dockerfile ane pin mkl to 2024 · addb80a8
  jnwei authored Apr 20, 2024
  
  addb80a8
- Update gpg keys for Docker build · 866477a2
  jnwei authored Apr 20, 2024
  
  866477a2
19 Apr, 2024 4 commits
- fix mkl version to 2024.0.0 · 3cab807e
  jnwei authored Apr 19, 2024
  
  3cab807e
- updates Dockerfile · 5ccb7de3
  jnwei authored Apr 19, 2024
  
  5ccb7de3
- fixes deepspeed function definition. · ea142a0a
  Jennifer authored Apr 19, 2024
  
  ea142a0a
- Updates low_precision check to use current precision settings. · 1ae833bf
  Jennifer authored Apr 19, 2024
  
  1ae833bf
17 Apr, 2024 1 commit
- change message for test_model.py compare · 80e63410
  Jennifer authored Apr 17, 2024
  
  80e63410
11 Apr, 2024 1 commit
- adds reload_dataloaders_every_n_epochs flag · 523adaf4
  Jennifer authored Apr 11, 2024
  
  523adaf4
02 Apr, 2024 2 commits
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 577219c1
  Jennifer authored Apr 02, 2024
  
  577219c1
- add paren to save_hyperparameters · 86263583
  Jennifer authored Apr 02, 2024
  
  86263583
01 Apr, 2024 1 commit
- more logging changes · 5ff5177b
  Jennifer authored Mar 27, 2024
  
  5ff5177b
27 Mar, 2024 1 commit
- add metric logging to progress bar. · 0c3435cc
  Jennifer authored Mar 25, 2024
  
  0c3435cc
25 Mar, 2024 1 commit
- seed workers fix and validation_epoch_end extra argument · cfd2e719
  Jennifer authored Mar 25, 2024
  
  cfd2e719
21 Mar, 2024 1 commit
- superimposition fix from Aymen · a317ad27
  Jennifer authored Mar 21, 2024
  
  a317ad27
19 Mar, 2024 3 commits
- Merge branch 'pl_upgrades' of https://github.com/jnwei/openfold into pl_upgrades · 36cd9eb0
  Jennifer authored Mar 19, 2024
  
  36cd9eb0
- first pass changes to run with pl 2.1 · 6dc34d71
  Jennifer authored Jan 24, 2024
  
  6dc34d71
- initial compatibility changes for upgrading multimer · 5f5a79a7
  Jennifer authored Jan 12, 2024
  
  5f5a79a7
13 Mar, 2024 2 commits
- adds config recording to wandb · 6ba0a594
  Jennifer authored Mar 13, 2024
  
  6ba0a594
- Adds `experiment_config_json` for setting custom configurations with a json. · d1fe024b
  Jennifer authored Mar 13, 2024
  
  d1fe024b
22 Feb, 2024 1 commit
- Changes resume_model_weights_only flag in train_openfold to reload weights... · f4df7217
  Jennifer authored Feb 22, 2024
```
Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.
```
  f4df7217
21 Feb, 2024 3 commits
- removes outputs from OpenFold.ipynb · f1cd1381
  jnwei authored Feb 21, 2024
  
  f1cd1381
- Merge weight-loading changes into setup-improvements · 9776b696
  jnwei authored Feb 21, 2024
  
  9776b696
- Updates commit value for OpenFold notebook. · 9f346d35
  jnwei authored Feb 21, 2024
  
  9f346d35
20 Feb, 2024 4 commits
- Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold... · 11952997
  Christina Floristean authored Feb 20, 2024
```
Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements
```
  11952997
- Add improved alignment-db creation script · 70918209
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  70918209
- Scripts from Lukas to be used in improved setup process · 50949b9a
  Christina Floristean authored Sep 08, 2023
  
  50949b9a
- changes reloading weights to account for possible state_dict headers. · ddfccd56
  Jennifer authored Feb 14, 2024
  
  ddfccd56
19 Feb, 2024 3 commits
- merging changes from main · f0fc7d91
  Jennifer authored Feb 19, 2024
  
  f0fc7d91
- first pass changes to run with pl 2.1 · ff368008
  Jennifer authored Jan 24, 2024
  
  ff368008
- initial compatibility changes for upgrading multimer · 456103da
  Jennifer authored Jan 12, 2024
  
  456103da
14 Feb, 2024 1 commit
- Add log statement to weight conversion script · e31e0378
  Jennifer authored Feb 13, 2024
  
  e31e0378
12 Feb, 2024 1 commit
- bugfixes and adds a section to convert optim files · 775f77dd
  Jennifer authored Feb 12, 2024
  
  775f77dd
09 Feb, 2024 1 commit
- Adjust weight conversion and add a script for converting checkpoints. · 260592e0
  Jennifer authored Feb 09, 2024
  
  260592e0
08 Feb, 2024 2 commits
- updates zero_to_fp32.py for new deepspeed version and import_weight bugfix · 1df591b0
  Jennifer authored Feb 08, 2024
  
  1df591b0
- Merge pull request #405 from aqlaboratory/multimer · bb3f51e5
  Christina Floristean authored Feb 07, 2024
```
Full multimer merge
```
  bb3f51e5