Commits · 78fa6c6ea9fd3724125fcf32ace3e9e8a0304f1d · OpenDAS / OpenFold

10 Nov, 2021 3 commits
- Use a more reasonable default for dataloader workers · 78fa6c6e
  Gustaf Ahdritz authored Nov 09, 2021
  
  78fa6c6e
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · da88b6bd
  Gustaf authored Nov 09, 2021
  
  da88b6bd
- Begin to add ProteinNet support (WIP) · 22cc45a8
  Gustaf authored Nov 09, 2021
  
  22cc45a8
09 Nov, 2021 3 commits
- Disable training-time chunking in default config · d03fc112
  Gustaf Ahdritz authored Nov 09, 2021
  
  d03fc112
- Fix confusing terminology · ed9ca30d
  Gustaf authored Nov 09, 2021
  
  ed9ca30d
- Add MMseqs2 MSA generation · 36f317be
  Gustaf authored Nov 09, 2021
  
  36f317be
04 Nov, 2021 4 commits
- Greatly speed up MSA processing code · 99361481
  Gustaf Ahdritz authored Nov 04, 2021
  
  99361481
- Fix batched loss · fd56fb0a
  Gustaf Ahdritz authored Nov 04, 2021
  
  fd56fb0a
- Merge pull request #3 from aqlaboratory/marta-sd/slurm · 793362fb
  Gustaf Ahdritz authored Nov 04, 2021
```
Manually specify cluster_environment for DeepSpeed if running with SLURM
```
  793362fb
- specify cluster_environment for DeepSpeed if running with SLURM · cb4eecb0
  Marta authored Nov 04, 2021
  
  cb4eecb0
03 Nov, 2021 2 commits
- Fix typo in loss message · 4b1c4488
  Gustaf Ahdritz authored Nov 03, 2021
  
  4b1c4488
- Merge pull request #2 from aqlaboratory/marta-sd/nan-loss · 1feca912
  Gustaf Ahdritz authored Nov 03, 2021
```
Fix NaN loss bug + add development env for Nvidians
```
  1feca912
02 Nov, 2021 8 commits
- add missing import · 709b144c
  Marta authored Nov 02, 2021
  
  709b144c
- pass callbacks to trainer · 005e6125
  Marta authored Nov 02, 2021
  
  005e6125
- add dllogger to conda env · 6c14c76a
  Marta authored Nov 02, 2021
  
  6c14c76a
- dont wait until 2nd epoch to measure perf · a9d3dc9f
  Marta authored Nov 02, 2021
  
  a9d3dc9f
- log_dir -> log_file for dllogger · f1a9d2b4
  Marta authored Nov 02, 2021
  
  f1a9d2b4
- fix bool args parsing bug · 3a65a7c9
  Marta authored Nov 02, 2021
  
  3a65a7c9
- dont try to use ddp for single-gpu single-node training · cd5a1e13
  Marta authored Nov 02, 2021
  
  cd5a1e13
- perf callback · 35449bf1
  Marta authored Oct 29, 2021
  
  35449bf1
30 Oct, 2021 2 commits
- Remove warning · 56f0a8a0
  Gustaf Ahdritz authored Oct 29, 2021
  
  56f0a8a0
- Speed up template featurizer · 9d4c9357
  Gustaf Ahdritz authored Oct 29, 2021
  
  9d4c9357
29 Oct, 2021 7 commits
- zero out nan components in loss · 5a004f04
  Marta authored Oct 29, 2021
  
  5a004f04
- center coordinates at 0 · 45a98436
  Marta authored Oct 29, 2021
  
  45a98436
- add resources to dockerfile + .dockerignore · 1c4d2c71
  Marta authored Oct 29, 2021
  
  1c4d2c71
- Dockerfile with minimal env needed for training · f86fc334
  Marta authored Oct 29, 2021
  
  f86fc334
- Remove debugging print statement · e69b2a11
  Gustaf Ahdritz authored Oct 29, 2021
  
  e69b2a11
- Remove experimental features committed by mistake · 9df2af52
  Gustaf Ahdritz authored Oct 29, 2021
  
  9df2af52
- Fix horrible in-place operation bug · d5480cbe
  Gustaf Ahdritz authored Oct 29, 2021
  
  d5480cbe
28 Oct, 2021 5 commits
- Make template code use less memory during inference · 2faff451
  Gustaf Ahdritz authored Oct 28, 2021
  
  2faff451
- Add empty template handling to inference pipeline · 407d9924
  Gustaf Ahdritz authored Oct 28, 2021
  
  407d9924
- Add PyTorch Lightning note in README · 8f7e90d6
  Gustaf Ahdritz authored Oct 27, 2021
  
  8f7e90d6
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · 5941d584
  Gustaf Ahdritz authored Oct 27, 2021
  
  5941d584
- Fix empty template feature bug · d71d37ff
  Gustaf Ahdritz authored Oct 27, 2021
  
  d71d37ff
26 Oct, 2021 6 commits
- Fix model checkpointing bug · a9a19b78
  Gustaf Ahdritz authored Oct 26, 2021
  
  a9a19b78
- Make template parsing optional · 81ae777d
  Gustaf Ahdritz authored Oct 26, 2021
  
  81ae777d
- Add section on ProteinNet to README · ea484b71
  Gustaf Ahdritz authored Oct 26, 2021
  
  ea484b71
- Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main · f7ed4a4b
  Gustaf Ahdritz authored Oct 26, 2021
  
  f7ed4a4b
- Add description to ProteinNet MSA script · 98b2c663
  Gustaf Ahdritz authored Oct 26, 2021
  
  98b2c663
- Add ProteinNet support to parser · b5f885d0
  Gustaf Ahdritz authored Oct 26, 2021
  
  b5f885d0