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Pl upgrades #1

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@jnwei jnwei commented Apr 20, 2024

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jnwei and others added 30 commits January 12, 2024 04:27
@jnwei
initial compatibility changes for upgrading multimer
2ed8115
@jnwei
np type update in openfold.np.relax
201eafd
@jnwei
initial compatibility changes for upgrading multimer
e71c1b1
@jnwei
np type update in openfold.np.relax
91776cd
@jnwei
update deprecated jax.numpy.DeviceArray to jax.Array
427a6ee
@jnwei
Merge branch 'multimer-pytorch-update' of https://github.com/aqlabora…
9c94078 
…tory/openfold into multimer-pytorch-update
@christinaflo @jnwei
Additional fix for multimer deepspeed test
e813bb5
@jnwei
first pass changes to run with pl 2.1
df4dfac
@jnwei
initial compatibility changes for upgrading multimer
456103d
@jnwei
first pass changes to run with pl 2.1
ff36800
@jnwei
merging changes from main
f0fc7d9
@jnwei
Merge pull request aqlaboratory#407 from jnwei/pl_upgrades
49ab053 
Pytorch lightning upgrades
@rostro36
Added custom template folder
17f24bd
@rostro36
Fix always is_custom_template.
10b6838
@rostro36
Less dependent on input sequnece, use template length instead
e9bacd8
@rostro36
Support for multiple custom templates.
50f8617
@jnwei
initial compatibility changes for upgrading multimer
5f5a79a
@jnwei
first pass changes to run with pl 2.1
6dc34d7
@jnwei
Merge branch 'pl_upgrades' of https://github.com/jnwei/openfold into …
36cd9eb 
…pl_upgrades
@rostro36
Fixed documentation according to comments.
295d0d5
@jnwei
superimposition fix from Aymen
a317ad2
@jnwei
seed workers fix and validation_epoch_end extra argument
cfd2e71
@rostro36
Added alignment method.
6b4f167
@jnwei
add metric logging to progress bar.
0c3435c
@jnwei
more logging changes
5ff5177
@jnwei
add paren to save_hyperparameters
8626358
@jnwei
Removes OF copy of zero_to_fp32.py favoring deepspeed.util version
577219c
@jnwei
adds reload_dataloaders_every_n_epochs flag
523adaf
@jnwei
change message for test_model.py compare
80e6341
@jnwei
Updates low_precision check to use current precision settings.
1ae833b
jnwei and others added 30 commits November 7, 2024 15:42
@jnwei
Merge pull request aqlaboratory#479 from vaclavhanzl/patch-3
b79ca29 
Update Installation.md - fix pl_upgrades clone instructions
@etowahadams
add environment variables
cde001f
@jnwei
Merge pull request aqlaboratory#502 from etowahadams/etowahadams/inst…
8ece4f3 
…all-docs

docs: Add env var instructions to install guide
@jnwei
Revert "docs: Add env var instructions to install guide "
625ade9
@ljarosch
Merge pull request aqlaboratory#504 from aqlaboratory/revert-502-etow…
e605ec8 
…ahadams/install-docs

Revert "docs: Add env var instructions to install guide  "
@etowahadams
docs: env variable
a01a60f
@etowahadams
fix: formatting
9f09442
@etowahadams
fix: formatting
6a43510
@etowahadams
try quotes
f1d0ae7
@etowahadams
fix: formatting
c05a354
@etowahadams
fix: formatting
56277ea
@jnwei
Merge pull request aqlaboratory#505 from etowahadams/update-install
a1192c8 
docs: Add env var to install guide
@nenuadrian
Minor typo fix in Installation.md
a364def
@etowahadams
updated script
e8d3558
@jnwei
Merge pull request aqlaboratory#520 from etowahadams/etowahadams/upda…
26d1a5d 
…te-script

Fix RODA flatten script
@jnwei
Merge pull request aqlaboratory#516 from nenuadrian/patch-1
815a042 
Minor typo fix in Installation.md
@jnwei
Maintainance to pl_upgrades
100a309
@jnwei
Merge branch 'main' into pl_upgrades
ab4a245
@jnwei
fix environment to support tests
0c2d455
@jnwei
Change casting for deepspeed compare model test to fp32
9caf30a
@jnwei
support openmm>8 and fix tolerance units in amber minimization
7e06ed9
@jnwei
Merge pull request #2 from aqlaboratory/pl_upgrades
cb899a5 
merge changes from upstream pl_upgrades
@jnwei
Allow numpy>2 and support compute capability >9
da37880
@jnwei
Add link to issue for deepspeed_evo_attention test.
4312aec
@jnwei
Update installation docs to build CUDA12 version
0672517
@jnwei
fix inference documentation
16af434
@jnwei
update version number.
fe10216
@jnwei
Update config.py
a5433c3 
small fix to spacing
@jnwei
Update amber_minimize.py
620a54f 
small fix to spacing
@jnwei
Update OpenFold notebook to updated pytorch2 commit
dbc2d30
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10 participants

@jnwei @christinaflo @rostro36 @dingquanyu @ljarosch @ryan-attunely @vaclavhanzl @etowahadams @nenuadrian