Skip to content

Initial version porting the eden configs over to the new evo2 recipe #1502

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jstjohn wants to merge 11 commits into
base: main
Choose a base branch
from
+5,909 −1,769
Open

Initial version porting the eden configs over to the new evo2 recipe #1502

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
0a1c3ce
Initial version porting the eden configs over to the new evo2 recipe
jstjohn Mar 9, 2026
ea7fdba
Cleanup the environment between tests
jstjohn Mar 9, 2026
7cd8ede
Work on test failures and making sure we are following mbridge conven…
jstjohn Mar 10, 2026
7761d54
Fix test related to savanna -> mbridge -> vortex checkpoint test
jstjohn Mar 10, 2026
7899f46
Get eden tests passing
jstjohn Mar 11, 2026
f9026a0
Merge branch 'main' of github.com:NVIDIA/bionemo-framework into jstjo…
jstjohn Mar 11, 2026
12f01b3
Address PR feedback and adding docs and 20b checkpoint
jstjohn Mar 11, 2026
9e24137
Updates to readme and adding independent scripts for conversion
jstjohn Mar 11, 2026
0cacf51
Add validation for the finetune checkpoint path
jstjohn Mar 11, 2026
4709e95
Cleanup unused commented out code
jstjohn Mar 11, 2026
d2dd38b
Fix the parameterization for the 20b model
jstjohn Mar 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
484 changes: 440 additions & 44 deletions bionemo-recipes/recipes/evo2_megatron/README.md
View file
Open in desktop

Large diffs are not rendered by default.

3 changes: 3 additions & 0 deletions bionemo-recipes/recipes/evo2_megatron/examples/.dockerignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,10 @@
*.yaml

# directories created during these notebook runs.
evo2_20b_finetune/
savanna_20b_download/
nemo2_evo2_1b_8k/
evo2_1b_bf16_mbridge/
preprocessed_data/
pretraining_demo/
brca1_fasta_files/
Expand Down
2 changes: 2 additions & 0 deletions bionemo-recipes/recipes/evo2_megatron/examples/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
*.yaml

# directories created during these notebook runs.
evo2_20b_finetune/
savanna_20b_download/
nemo2_evo2_1b_8k/
evo2_1b_bf16_mbridge/
preprocessed_data/
Expand Down
934 changes: 934 additions & 0 deletions bionemo-recipes/recipes/evo2_megatron/examples/evo2_20b_finetune_and_export.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

2,300 changes: 1,145 additions & 1,155 deletions bionemo-recipes/recipes/evo2_megatron/examples/fine-tuning-tutorial.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading
Loading