Commits · 1efccb6c8814d0b39ffa4b4fd20cba6ddc023096 · OpenDAS / FastFold

30 Aug, 2022 1 commit
- add faster extraMSA and templateStack (#53) · 1efccb6c
  LuGY authored Aug 30, 2022
```
* add faster extraMSA and templateStack

* add license
```
  1efccb6c
29 Aug, 2022 2 commits

support ray2.0 (#52) · 369f3e70
Fazzie-Maqianli authored Aug 29, 2022

369f3e70

Add more parameter functionality to HHBlits and HHSearch runners (#51) · 56a32c3b

Yuanqi Wang authored Aug 28, 2022



* [ray] use ray for DB queries

* patched openmm

* add test exec script

* remove output before exec

* [tools] add coverage param to HHBlits

* [tools] add more param options to HHSearch

* [tools] remove ray from JackHmmer runner

* [tools] add comment for cov param in hhblits

* [tools] cleanup all debug code

* [tools] restore original files
Co-authored-by: shenggan <csg19971016@gmail.com>

56a32c3b

23 Aug, 2022 3 commits
- fix typo in readme · ae44a3b7
  lclgy authored Aug 23, 2022
  
  ae44a3b7
- merge data workflow to main (#48) · b254d465
  LuGY authored Aug 23, 2022
```
Added data workflow for fastfold
```
  b254d465
- modify reading data way and add inference test (#50) · a37c8b4c
  LuGY authored Aug 23, 2022
  
  a37c8b4c
19 Aug, 2022 2 commits
- upload dockerfile, workflow and update readme · 03a24ef9
  LuGY authored Aug 19, 2022
  
  03a24ef9
- update README (#40) · 4afdd475
  Fazzie-Maqianli authored Aug 12, 2022
  
  4afdd475
29 Jul, 2022 1 commit
- add chunk for self_att and opm (#38) · 665e6c97
  shenggan authored Jul 29, 2022
  
  665e6c97
28 Jul, 2022 1 commit
- fix backward return for fused softmax torch function (#36) · 48ae1b08
  shenggan authored Jul 28, 2022
  
  48ae1b08
27 Jul, 2022 2 commits
- remove scale in fused softmax kernel (#34) · ded582b2
  shenggan authored Jul 27, 2022
  
  ded582b2
- fix pointer assignment error in softmax_cuda_kernel.cu · ad7f0cb5
  Shenggan authored Jul 27, 2022
  
  ad7f0cb5
25 Jul, 2022 2 commits
- use torch.multiprocess to launch multi-gpu inference · 9924e7be
  Shenggan authored Jul 25, 2022
  
  9924e7be
- refactor softmax kernel · f44557ed
  shenggan authored Jul 25, 2022
  
  f44557ed
03 Jun, 2022 3 commits
- use template for fused softmax & add unittest for fused softmax (#26) · a65d5009
  shenggan authored Jun 03, 2022
  
  a65d5009
- use template in layernorm kernel & add unittest for fastnn layernorm (#25) · 771d4b83
  shenggan authored Jun 03, 2022
  
  771d4b83
- fix dap init in benchmark (#24) · ad1bbc52
  shenggan authored Jun 03, 2022
  
  ad1bbc52
26 Apr, 2022 1 commit
- fix overflow for softmax kernel (#20) · 259b6c87
  shenggan authored Apr 26, 2022
  
  259b6c87
21 Apr, 2022 2 commits
- Merge pull request #18 from hpcaitech/sync_openfold_591d10d · 92e6cf49
  shenggan authored Apr 21, 2022
```
sync with openfold 591d10d
```
  92e6cf49
- sync with openfold 591d10d · 5f052a0a
  Shenggan authored Apr 21, 2022
  
  5f052a0a
18 Apr, 2022 3 commits
- Merge pull request #15 from hpcaitech/openmm_patch · 72444d5b
  shenggan authored Apr 18, 2022
```
add openmm patch and readme
```
  72444d5b
- add openmm patch and readme · c2e8357f
  Shenggan authored Apr 18, 2022
  
  c2e8357f
- Merge pull request #14 from hpcaitech/inference_pipeline · eecadd36
  shenggan authored Apr 18, 2022
```
add inference pipeline from openfold/alphafold
```
  eecadd36
14 Apr, 2022 1 commit
- add inference pipeline from openfold/alphafold · 42427a1c
  Shenggan authored Apr 14, 2022
  
  42427a1c
12 Apr, 2022 1 commit
- Merge pull request #13 from hpcaitech/colossalai_distributed · b3b3b445
  shenggan authored Apr 12, 2022
```
use colossalai as distributed core
```
  b3b3b445
11 Apr, 2022 1 commit
- use colossalai as distributed core · aa140059
  Shenggan authored Apr 11, 2022
  
  aa140059
08 Apr, 2022 2 commits
- Merge pull request #12 from hpcaitech/fix_mask · 3b0299c2
  shenggan authored Apr 08, 2022
```
fix mask softmax and support inference for arbitrary length sequences
```
  3b0299c2
- fix mask softmax and support inference for arbitrary length sequences · ed759cf4
  Shenggan authored Apr 08, 2022
  
  ed759cf4
09 Mar, 2022 2 commits
- Merge pull request #6 from hpcaitech/inject_openfold · 16d10d6a
  shenggan authored Mar 09, 2022
```
add inject_openfold
```
  16d10d6a
- add inject_openfold · 8e75ab95
  Shenggan authored Mar 07, 2022
  
  8e75ab95
07 Mar, 2022 2 commits
- Merge pull request #4 from hpcaitech/fix_gather · 90019096
  shenggan authored Mar 07, 2022
```
fix minor bug in gather
```
  90019096
- fix minor bug in gather · 77642096
  Shenggan authored Mar 07, 2022
  
  77642096
03 Mar, 2022 4 commits
- Merge pull request #1 from hpcaitech/refactor_kernel · e96b76b0
  shenggan authored Mar 03, 2022
```
refactor kernel implementation
```
  e96b76b0
- refactor kernel implementation · f206de08
  shenggan authored Mar 03, 2022
  
  f206de08
- add acknowledge · 1c0a3d39
  Shenggan authored Mar 03, 2022
  
  1c0a3d39
- add paper link and citation · f6d59be5
  Shenggan authored Mar 03, 2022
  
  f6d59be5
02 Mar, 2022 1 commit
- remove cuda ext option in setup.py · cce4ec63
  Shenggan authored Mar 02, 2022
  
  cce4ec63
28 Feb, 2022 2 commits
- init commit · 53143f58
  Shenggan authored Feb 28, 2022
  
  53143f58
- init commit · d5f3875c
  Shenggan authored Feb 28, 2022
  
  d5f3875c
27 Feb, 2022 1 commit
- Initial commit · 62ed1c4a
  shenggan authored Feb 27, 2022
  
  62ed1c4a