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Evo2#694

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jstjohn wants to merge 149 commits intomainNVIDIA/bionemo-framework:mainfrom evo2NVIDIA/bionemo-framework:evo2Copy head branch name to clipboard

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Commits on Nov 16, 2024

• [cye/evo2-llm-dev] Private internal development branch for Evo2 in BioNeMo.

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Commits on Dec 4, 2024

• [cye/evo2-llm-dev] Add rough draft of data preprocessing for Evo2.

  

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• Add manual data test for evo2

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Commits on Dec 5, 2024

• Change remotes for submodules for now

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• Cye/nemo2 fixes

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Commits on Dec 10, 2024

• Write model checkpoint context and set Evo2Dataset in the pre-training.

  

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Commits on Dec 11, 2024

• Fix inference script to make sense, i.e. no seq parallelism for decoding, default 0 for topk/topp.

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Commits on Dec 16, 2024

• Cye/fix Hyena species biases

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Commits on Dec 19, 2024

• Hyena golden value test

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Commits on Dec 21, 2024

• [cye/blended-training] Expose blended weights for training Hyena.

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Commits on Dec 23, 2024

• Changes for 256 node training run

  

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Commits on Dec 24, 2024

• Integrate BioNeMo Noodles into Hyena data preprocessing.

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Commits on Jan 3, 2025

• [cye/lineage-str] Clean up interface for taxonomic lineage tokens in Hyena.

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• Changes made on 256 node branch

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• Cye/hyena flops

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• Fix broken import of blended training config.

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• Cye/import fix

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Commits on Jan 6, 2025

• Add improved nsys profiling support

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Commits on Jan 7, 2025

• [cye/hyena-doc-update] Add data preprocessing documentation, fix tech debt in tokenizer and config, remove unused args in infer.py.

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Commits on Jan 8, 2025

• [cye/transcript-readme] Add main documentation snippets for Hyena, and add transcript splicing script for preprocessing.

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Commits on Jan 10, 2025

• Bump nemo version to the new context length insensitive code, and update test to use new checkpoint

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Commits on Jan 13, 2025

• added flag for tflops callback

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• [cye/evo2-ckpt-utils] Add Evo2 ZeRO-1/3 to NeMo checkpointing utils.

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Commits on Jan 14, 2025

• Add test for evo2 tokenizer.

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• Fix nemo-savanna repo build in CI

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• fixing format issues on evo2-dev

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• Add tests for parallel hyena operators used in evo2

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• Rebase on OSS.

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Commits on Jan 15, 2025

• [cye/tp-comm-fix] Fix TP communication overlap inconsistency.

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Commits on Jan 16, 2025

• Add temporary fix for shard-tensor bug in Megatron-LM

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Commits on Jan 17, 2025

• Add initial test for preprocess.py

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• Bump NeMo to pick up FLOPS calculations.

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Commits on Jan 21, 2025

• [cye/z3-log-fix] Fix parameter count log.

  

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Commits on Jan 22, 2025

• [cye/docker-patch-fix] Move Megatron patch to BioNeMo base image in Dockerfile.

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Commits on Jan 24, 2025

• shipping hotfix for dockers built locally - fix from main 17c6b20

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• [cye/1m-ckpt-config] Add HyenaConfig options for 1M context length dimensions.

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• [cye/fix-tp-comm-overlap] Fix default tp_comm_overlap=True being used in inference, which is not appropriate.

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Commits on Jan 27, 2025

• reducing scope of tested folders for evo2-dev

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Commits on Jan 28, 2025

• Adds basic inference test

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• [cye/deactivate-infer-tpcomm] Deactivate TP communication during inference to support those checkpoints.

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• fix: ensure test looks in test file dir for required data

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Commits on Jan 29, 2025

• m2.5 accuracy 7b runs

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Commits on Jan 30, 2025

• Fixes test_evo2.py unit test and adds enhancements to existing unit tests for Evo2 inference.

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• Fix bug in wandb logger argparse.

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Commits on Feb 3, 2025

• [cye/pad-loss-mask] Fixes TP comm overlap bug with sequence parallel and reduce the size of torch_dist checkpoints.

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• Add longphase dataset config to repo

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Commits on Feb 5, 2025

• bump Megatron-LM, nemo-savanna and rebase to main OSS

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Commits on Feb 7, 2025

• CI hotfix

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• test: Create tests for Evo2Dataset mask_phylogenetic_tags

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Commits on Feb 11, 2025

• [cye/torch_dist_fix] Remove torch_dist patch and bump Megatron, reorganize tests.

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• Changes related to accuracy and perf with new nemo2 changes

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Commits on Feb 12, 2025

• [cye/tp-comm-fp8-wgrad-fix]Require --fp8-wgrad when using TP communication overlap.

  

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Commits on Feb 13, 2025

• Adding evo2 to JET

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• Remove sample data from evo2-dev branch

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• [BUGFIX] evo2-dev CI

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Commits on Feb 14, 2025

• Remove test_mask_phylogenetic tags (moving to nemo repo)

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• attempt at merge -- nemo matches github main. Dockerfile has major bump to pytorch.

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• Bump nemo to fix forward bug

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• Add required changes to work with NeMo upstream

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• Add back new context manager for parallel state cleanup

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• Move test_config into nemo where the code is

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Commits on Feb 15, 2025

• Fix arg name mismatch

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• add new license

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• remove tab from license

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• Bump nemo to fix bug in dataset

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Commits on Feb 18, 2025

• Bump NeMo commit for perf improved loss mask

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• Adding options for controlling dropout to train.py

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• Bump nemo and remove nograd decorator

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• Bump nemo with latest tag masking

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• Cover non-DNA case due to bug in preprocessing, never have non-dna unmasked in loss other than pad/eod

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• Try reverting some of the recent fixes related to TP

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• Bump nemo version with better tested

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• Revert loss mask updates

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• handle 0 token case more gracefully

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Commits on Feb 19, 2025

• bump NeMo with proper handling of control character containing sequences and handling divide by zero in loss

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• Update remote pointers to new public NeMo branches

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• Remove unused Megatron torch_dist sizing patch.

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• Remove fasta from test and replace with synthetic sequence

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• Move fasta creation utility into testing sub-package

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• Add a test that verifies that the new phylo tag masking code is faster than the old code

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• Move phylo tag benchmark to NeMo testing

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Commits on Feb 20, 2025

• Merge in main

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• Update Megatron-LM submodule to commit 62529f1d (has 1M context fix) (#697)

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Commits on Feb 21, 2025

• fix config typo in test

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• bump NeMo to latest PR version

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• Fix issue causing gh-docs-deploy failure (#698)

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• Update nemo pointer with PR updates

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• Add new license to new files (failing ci) (#699)

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• Change kingdom to domain in tag description

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• Merge in upstream

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• Merge branch 'main' of github.com:NVIDIA/bionemo-framework into evo2

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Commits on Feb 22, 2025

• Make new versions of the files available freshly converted from HF

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• bump nemo version to fix broken import

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• bump nemo to top of tree

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Commits on Feb 24, 2025

• Adding in the predict method and test

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• Merge branch 'main' of github.com:NVIDIA/bionemo-framework into evo2

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• bump NeMo commit

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• Fix multipart download naming in nemo

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• Update docs for checkpoint conversion

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• shrink tests down to 1b case

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Commits on Feb 25, 2025

• add end to end fine-tuning tutorial

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• ignore object hashes in precommit

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• Bump nemo pointer to latest PR pointer

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• Update ci/benchmarks/partial-conv/evo2_pretrain.yaml

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• Update ci/benchmarks/perf/evo2_pretrain.yaml

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• Slightly smaller test_train.py

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• Add missing main function for inference cli

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• Add --batch-size option to predict

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• Fixing the description of the 1b model

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Commits on Feb 26, 2025

• remove hard-coded PBSS

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• Remove comment block from code

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Commits on Feb 27, 2025

• evo2 train unit test (#704)

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Commits on Feb 28, 2025

• Updates to benchmarks: evo2 (#705)

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Commits on Mar 4, 2025

• Add brca1 zeroshot example + predict and scoring updates to evo2.

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• Add vortex style fp8 support to predict

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• Update the brca notebook with a run on an fp8 supporting machine

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• Merge in upstream changes to bionemo

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• add missing/new NGC urls

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• Remove fasta from pre commit

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• Remove TODOs related to PBSS

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• Moved test config into the tests/config dir with the other configs

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• Address yaml location feedback

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• Add new test covering padding and seq dims

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• Address comments on documentation

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• Run pre-commit on docs

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• Address PR feedback on test naming

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• Refactor out fasta dataset, add tests for it (#716)

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• Bump nemo commit with predict changes

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• no longer needed since we do not have committed fastas

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• Reformat to pass pre-commit

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• update readme to mention predict (#717)

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• Fix parallel short hyena operator test

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• Add slow tests for 7b

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• Update faster 1b test with lower precision so it passes in CI

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• Merge branch 'evo2' of github.com:NVIDIA/bionemo-framework into evo2

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• Address formatting issues

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• Leave megatron-lm as is and add more stringent slow test along with less stringent fast test

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• Bump nemo as well

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• Merge branch 'main' of github.com:NVIDIA/bionemo-framework into evo2

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Commits on Mar 5, 2025

• Update pointer to evo2 test file

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• only run most stringent comparison with h100

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• add missing ngc link for new 7b-8k checkpoint

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• Fixing sahpe issue in parallel short hyena test

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• Address issue with pycache when there are tests with the same name in different submodules

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• Move to per-package tests for slow as well as fast tests

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• Handle no tests found case

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• Add option for allowing no slow tests for a submodule

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• Handle exit code capturing within the context of a pipefail script properly

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• Merge branch 'main' into evo2

  jstjohn

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  46fee2c

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