Commits · cb4eecb08c4441b1b5fec1dcd8f1613943dfc4b1 · OpenDAS / OpenFold

04 Nov, 2021 1 commit
- 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
25 Oct, 2021 3 commits
- Tweak README formatting · 0fb5b743
  Gustaf Ahdritz authored Oct 25, 2021
  
  0fb5b743
- Remove a pair of outdated comments · f03be78f
  Gustaf Ahdritz authored Oct 25, 2021
  
  f03be78f
- Fix bug in dummy dataset · 428d90ce
  Gustaf Ahdritz authored Oct 25, 2021
  
  428d90ce
24 Oct, 2021 2 commits
- Merge pull request #1 from aqlaboratory/mpvenkatesh/changes · 94ab346e
  Gustaf Ahdritz authored Oct 24, 2021
```
minor fixes
```
  94ab346e
- minor fixes · 04fa3548
  sft-managed authored Oct 24, 2021
  
  04fa3548
23 Oct, 2021 3 commits
- Fix PDB parsing, add distillation MSA cropping · 6298a3e6
  Gustaf Ahdritz authored Oct 23, 2021
  
  6298a3e6
- Fix bug in MSA loss · 4d40ce80
  Gustaf Ahdritz authored Oct 23, 2021
  
  4d40ce80
- Add training callbacks · 4c9d372d
  Gustaf Ahdritz authored Oct 23, 2021
  
  4c9d372d
22 Oct, 2021 1 commit
- Clarify checkpointing comment · 727e68c2
  Gustaf Ahdritz authored Oct 22, 2021
  
  727e68c2