Commits · 7de0ab00dba3c7b2ea30dcc6dff8cf894abccbd6 · OpenDAS / OpenFold · GitLab

06 May, 2024 3 commits
- first pass changes to run with pl 2.1 · 7de0ab00
  Jennifer authored Jan 24, 2024
  
  7de0ab00
- initial compatibility changes for upgrading multimer · a51b08cd
  Jennifer authored Jan 12, 2024
  
  a51b08cd
- adds mpi4py to environment and removes stray print statements from test · af457b95
  Jennifer Wei authored May 06, 2024
  
  af457b95
02 May, 2024 33 commits
- Updates environment.yml to unpin wandb version · 9b6c1dac
  Jennifer authored May 02, 2024
  
  9b6c1dac
- Updates organization of command line flags for pl.Trainer · 142c5e65
  Jennifer authored May 02, 2024
  
  142c5e65
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 2eda3215
  Jennifer authored Apr 02, 2024
  
  2eda3215
- Removes OF copy of zero_to_fp32.py favoring deepspeed.util version · 3a4ed753
  Jennifer authored Apr 02, 2024
  
  3a4ed753
- Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold... · e4f9af23
  Jennifer authored May 02, 2024
```
Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements
```
  e4f9af23
- updates Bio.PDBData call and environment.yml · 02cb7711
  Jennifer authored Apr 22, 2024
  
  02cb7711
- adds deepspeed_evoformer flag to inference script. · c4cccb6b
  Jennifer authored Apr 30, 2024
  
  c4cccb6b
- changes required for pytorch2 · 19525826
  Jennifer Wei authored Apr 12, 2024
  
  19525826
- DNS: Local profiler changes · 226c7bac
  Jennifer authored Mar 29, 2024
  
  226c7bac
- adds config recording to wandb · eba00d85
  Jennifer authored Mar 13, 2024
  
  eba00d85
- Adds `experiment_config_json` for setting custom configurations with a json. · 870e0db3
  Jennifer authored Mar 13, 2024
  
  870e0db3
- removes outputs from OpenFold.ipynb · 0ba7e7f9
  jnwei authored Feb 21, 2024
  
  0ba7e7f9
- Add log statement to weight conversion script · d4ed0b0c
  Jennifer authored Feb 13, 2024
  
  d4ed0b0c
- bugfixes and adds a section to convert optim files · 67454c39
  Jennifer authored Feb 12, 2024
  
  67454c39
- Updates commit value for OpenFold notebook. · 638fbaf6
  jnwei authored Feb 21, 2024
  
  638fbaf6
- fix path error in scripts/utils.py and logging fix · 2dd481e1
  Jennifer authored Apr 29, 2024
  
  2dd481e1
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cfb4c19c
  jnwei authored Apr 23, 2024
  
  cfb4c19c
- clear up some space for docker ci · f4e54ec7
  Jennifer authored Apr 22, 2024
  
  f4e54ec7
- changes required for pytorch2 · 60fbe539
  Jennifer Wei authored Apr 12, 2024
  
  60fbe539
- DNS: Local profiler changes · ec6058cd
  Jennifer authored Mar 29, 2024
  
  ec6058cd
- update license file · 2a4818a3
  jnwei authored Mar 21, 2024
  
  2a4818a3
- adds config recording to wandb · 6b77062d
  Jennifer authored Mar 13, 2024
  
  6b77062d
- Adds `experiment_config_json` for setting custom configurations with a json. · 0f2b2929
  Jennifer authored Mar 13, 2024
  
  0f2b2929
- Changes resume_model_weights_only flag in train_openfold to reload weights... · 5bfad074
  Jennifer authored Feb 22, 2024
```
Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.
```
  5bfad074
- removes outputs from OpenFold.ipynb · 521bc6e9
  jnwei authored Feb 21, 2024
  
  521bc6e9
- changes reloading weights to account for possible state_dict headers. · a7216c73
  Jennifer authored Feb 14, 2024
  
  a7216c73
- Add log statement to weight conversion script · 711ba0ab
  Jennifer authored Feb 13, 2024
  
  711ba0ab
- bugfixes and adds a section to convert optim files · dd1dd641
  Jennifer authored Feb 12, 2024
  
  dd1dd641
- Adjust weight conversion and add a script for converting checkpoints. · 0a0dbb39
  Jennifer authored Feb 09, 2024
  
  0a0dbb39
- updates zero_to_fp32.py for new deepspeed version and import_weight bugfix · d9d4bf14
  Jennifer authored Feb 08, 2024
  
  d9d4bf14
- Updates commit value for OpenFold notebook. · 08276f0f
  jnwei authored Feb 21, 2024
  
  08276f0f
- Add improved alignment-db creation script · eb4d1e57
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  eb4d1e57
- Scripts from Lukas to be used in improved setup process · 76b1ec98
  Christina Floristean authored Sep 08, 2023
  
  76b1ec98
30 Apr, 2024 2 commits
- Merge pull request #437 from jnwei/mkl-fix · 2625e0b2
  Jennifer Wei authored Apr 30, 2024
```
Adds mkl version to environment.yml
```
  2625e0b2
- Adds mkl version to environment.yml · 64631f0c
  Jennifer authored Apr 30, 2024
  
  64631f0c
29 Apr, 2024 1 commit
- fix path error in scripts/utils.py and logging fix · 09e74c76
  Jennifer authored Apr 29, 2024
  
  09e74c76
23 Apr, 2024 1 commit
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cb3ff410
  jnwei authored Apr 23, 2024
  
  cb3ff410