NVIDIA BioNeMo Framework v2.3

New Features

• Distributed Inference Support for ESM2 and Geneformer
  • Enables linear inference throughput as GPU number is increased
  • See ESM2 inference notebook and use --num-gpus parameter.

Updates & Improvements

• Prior Geneformer inference on H100 accuracy regression fixed.
• Base image updated to nvcr.io/nvidia/pytorch:24.12-py3; python updated to 3.12 among other core dependency upgrades (base container release notes here).

Changes

• Distributed Inference Support for ESM2/Geneformer by @farhadrgh in #482
• Flexible memory management to avoid fragmentation-related CUDA OOM by @farhadrgh in #524
• Update nightly Docker image tag by @tshimko-nv in #539
• set UV_NO_CACHE by @pstjohn in #529
• RowFeatureIndex Optimization by @polinabinder1 in #531
• Updates to NvFaidx, Fasta Noodles, and Sequence Accessor by @skothenhill-nv in #532
• Fix csv dataset by @holgerroth in #543
• Run all pytests even if submodules fail by @pstjohn in #545
• xFail known bad tests on H100 and fix CVEs by @gagank1 in #549
• Fully Integrate SCDL into Geneformer by @savitha-eng in #480
• Fix MLM loss ignore idx by @farhadrgh in #552
• Attempts to bump the base image to pytorch:24.07 by @pstjohn in #544
• Pstjohn/update base image 2410 by @pstjohn in #551
• [BUFIX] fail when passed fastas with duplicate sequence ids by @skothenhill-nv in #555
• Update ddp config to improve ESM-2 15B MFU by @sichu2023 in #520
• add temporary mistune pin to fix docs build issue by @pstjohn in #559
• Bump 3rdparty/Megatron-LM from 99f23d2 to 2da43ef by @dependabot in #558
• Bump 3rdparty/NeMo from 06e6703 to 06a1491 by @dependabot in #538
• update base image to 24.12 by @pstjohn in #553
• Un-xfail geneformer on H100 test by @trvachov in #563
• update devcontainer for new ubuntu base image by @pstjohn in #566
• don't eagerly download esm2 checkpoints by @pstjohn in #567
• run pytest with or without docs and notebooks in run_pytest.sh by @dorotat-nv in #569
• Jwilber/bionemo example small updates by @jwilber in #561
• remove unused file from repo by @jwilber in #562
• add initial configs for perf testing on ESM2 in JET (bionemo2) by @dorotat-nv in #497
• Add pre-training page for ESM-2 by @pstjohn in #578
• Edits to README and CONTRIBUTING.md, moving some text around by @pstjohn in #577
• Refactor dockerfile for better caching and avoid pbss download in notebook test by @pstjohn in #573
• Bump 3rdparty/NeMo from 06a1491 to d44ed44 by @dependabot in #580
• Simplify ESM2 finetune test by @farhadrgh in #576
• default to overlap_param_gather by @sichu2023 in #582
• Bump 3rdparty/Megatron-LM from 2da43ef to 65720c8 by @dependabot in #579
• Add self-hosted azure runner workflows by @pstjohn in #587
• ARM docker build with 24.12 pytorch fw image by @trvachov in #581
• Add gpu target identificator to JET configs by @dorotat-nv in #586
• add codecov badge by @pstjohn in #588
• Add support for marking and skipping slow tests, temporarily mark pydantic tests as slow by @pstjohn in #589
• pin cdifflib version by @pstjohn in #593
• Remove outdated note on very large datasets in MultiEpochDataset by @pstjohn in #521
• Bump 3rdparty/NeMo from eb9848b to abd4bf7 by @dependabot in #597
• Revert "pin cdifflib version (#593)" by @pstjohn in #599
• fix esm2_pretrain.yaml by @dorotat-nv in #600
• add myself to ci by @nvdreidenbach in #594
• Bump virtualenv from 20.26.3 to 20.26.6 by @dependabot in #596
• Bump 3rdparty/Megatron-LM from 65720c8 to c76410a by @dependabot in #592
• move load calls, rename test for better readibility by @pstjohn in #601
• Only run cleanup if tests ran, adds pytest marker config for slow tests by @pstjohn in #595
• only run trufflehog on diff by @pstjohn in #604
• run trufflehog on entire main branch on push action by @pstjohn in #605
• add comments to the unit-test.yaml file by @pstjohn in #606
• Remove v2.0 from README title by @pstjohn in #602
• ESM2 Finetuning refactor by @farhadrgh in #574
• fix image links in esm2 model card by @pstjohn in #584
• Release of v1.0 of BioNeMo Modular Co-Design (MoCo) by @nvdreidenbach in #575
• fix devcontainer paths in ubuntu 24 by @pstjohn in #610
• Bump rsync and other dockerfile lints by @pstjohn in #603
• Jm/codeowners revamp by @jomitchellnv in #617
• Update MoCo notebooks by @nvdreidenbach in #614
• set min seq len by default by @pstjohn in #621
• hotfix for some failing python tests due to NGC files being moved around by @pstjohn in #626
• Bump 3rdparty/Megatron-LM from c76410a to 4fb4c3d by @dependabot in #624
• revert ESM2 Finetuning refactor (#574) by @farhadrgh in #628

New Contributors

• @holgerroth made their first contribution in #543
• @nvdreidenbach made their first contribution in #594

Full Changelog: v2.2...v2.3