add wandb group and model size in Geneformer configs: benchmarks#859
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polinabinder1
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May 5, 2025
Signed-off-by: dorotat <dorotat@nvidia.com>
Signed-off-by: dorotat <dorotat@nvidia.com>
Signed-off-by: dorotat <dorotat@nvidia.com>
### Description NVIDIA-NeMo/NeMo#12856 introduces code reduction and perf improvements including standardizing input/output shapes for Hyena operators and consequentially reducing rearrangement overhead. This PR updates the EVO2 test to comply with those changes, ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [ ] Documentation update - [ ] Other (please describe): ### CI Pipeline Configuration Configure CI behavior by applying the relevant labels: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### Usage <!--- How does a user interact with the changed code --> ```python TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [ ] I have tested these changes locally - [ ] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully --------- Signed-off-by: Farhad Ramezanghorbani <farhadr@nvidia.com> Signed-off-by: Cory Ye <cye@nvidia.com> Signed-off-by: cspades <cory0ye@gmail.com> Signed-off-by: Timur Rvachov <trvachov@nvidia.com> Signed-off-by: Danny <dreidenbach@nvidia.com> Signed-off-by: Cory Ye <44509866+cspades@users.noreply.github.com> Signed-off-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Signed-off-by: Peter St. John <pstjohn@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Polina Binder <pbinder@nvidia.com> Signed-off-by: polinabinder1 <pbinder@nvidia.com> Signed-off-by: dorotat <dorotat@nvidia.com> Signed-off-by: Truong Nguyen <tgnguyen@nvidia.com> Signed-off-by: Jonathan Mitchell <jomitchell@nvidia.com> Signed-off-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Signed-off-by: Steven <skothenhill@nvidia.com> Co-authored-by: Dorota Toczydlowska <115542912+dorotat-nv@users.noreply.github.com> Co-authored-by: Cory Ye <44509866+cspades@users.noreply.github.com> Co-authored-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Co-authored-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Co-authored-by: Steven Kothen-Hill <148821680+skothenhill-nv@users.noreply.github.com> Co-authored-by: Peter St. John <pstjohn@nvidia.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: polinabinder1 <pbinder@nvidia.com> Co-authored-by: Truong Nguyen <tgnguyen@nvidia.com> Co-authored-by: jomitchellnv <148147880+jomitchellnv@users.noreply.github.com> Co-authored-by: lvojtku <lvojtku@nvidia.com> Signed-off-by: dorotat <dorotat@nvidia.com>
### Description This addresses: #757 ### Type of changes In the original code the optimizer was not saved in the checkpoint, but it is expected in the megatron strategy. Saving the optimizer is added to the checkpoint callback and the test has been updated. Changes were made to have the checkpointing callback in the nemo logger. This is the same as the training path in sub-packages/bionemo-llm/src/bionemo/llm/train.py. --------- Signed-off-by: Polina Binder <pbinder@nvidia.com> Signed-off-by: polinabinder1 <pbinder@nvidia.com> Signed-off-by: dorotat <dorotat@nvidia.com>
Signed-off-by: dorotat <dorotat@nvidia.com>
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### Description Adding the required grouping to fix Geneformer-specific group in wandb  ### Type of changes <!-- Mark the relevant option with an [x] --> - [x] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [ ] Documentation update - [ ] Other (please describe): ### CI Pipeline Configuration Configure CI behavior by applying the relevant labels: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### Usage <!--- How does a user interact with the changed code --> ```python TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [ ] I have tested these changes locally - [ ] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully --------- Signed-off-by: dorotat <dorotat@nvidia.com> Signed-off-by: Farhad Ramezanghorbani <farhadr@nvidia.com> Signed-off-by: Cory Ye <cye@nvidia.com> Signed-off-by: cspades <cory0ye@gmail.com> Signed-off-by: Timur Rvachov <trvachov@nvidia.com> Signed-off-by: Danny <dreidenbach@nvidia.com> Signed-off-by: Cory Ye <44509866+cspades@users.noreply.github.com> Signed-off-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Signed-off-by: Peter St. John <pstjohn@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Polina Binder <pbinder@nvidia.com> Signed-off-by: polinabinder1 <pbinder@nvidia.com> Signed-off-by: Truong Nguyen <tgnguyen@nvidia.com> Signed-off-by: Jonathan Mitchell <jomitchell@nvidia.com> Signed-off-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Signed-off-by: Steven <skothenhill@nvidia.com> Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com> Co-authored-by: Cory Ye <44509866+cspades@users.noreply.github.com> Co-authored-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Co-authored-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Co-authored-by: Steven Kothen-Hill <148821680+skothenhill-nv@users.noreply.github.com> Co-authored-by: Peter St. John <pstjohn@nvidia.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: polinabinder1 <pbinder@nvidia.com> Co-authored-by: Truong Nguyen <tgnguyen@nvidia.com> Co-authored-by: jomitchellnv <148147880+jomitchellnv@users.noreply.github.com> Co-authored-by: lvojtku <lvojtku@nvidia.com>
camirr-nv
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Jun 26, 2025
### Description Adding the required grouping to fix Geneformer-specific group in wandb  ### Type of changes <!-- Mark the relevant option with an [x] --> - [x] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [ ] Documentation update - [ ] Other (please describe): ### CI Pipeline Configuration Configure CI behavior by applying the relevant labels: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### Usage <!--- How does a user interact with the changed code --> ```python TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [ ] I have tested these changes locally - [ ] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully --------- Signed-off-by: dorotat <dorotat@nvidia.com> Signed-off-by: Farhad Ramezanghorbani <farhadr@nvidia.com> Signed-off-by: Cory Ye <cye@nvidia.com> Signed-off-by: cspades <cory0ye@gmail.com> Signed-off-by: Timur Rvachov <trvachov@nvidia.com> Signed-off-by: Danny <dreidenbach@nvidia.com> Signed-off-by: Cory Ye <44509866+cspades@users.noreply.github.com> Signed-off-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Signed-off-by: Peter St. John <pstjohn@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Polina Binder <pbinder@nvidia.com> Signed-off-by: polinabinder1 <pbinder@nvidia.com> Signed-off-by: Truong Nguyen <tgnguyen@nvidia.com> Signed-off-by: Jonathan Mitchell <jomitchell@nvidia.com> Signed-off-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Signed-off-by: Steven <skothenhill@nvidia.com> Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com> Co-authored-by: Cory Ye <44509866+cspades@users.noreply.github.com> Co-authored-by: Timur Rvachov <120140748+trvachov@users.noreply.github.com> Co-authored-by: nvdreidenbach <97637601+nvdreidenbach@users.noreply.github.com> Co-authored-by: Steven Kothen-Hill <148821680+skothenhill-nv@users.noreply.github.com> Co-authored-by: Peter St. John <pstjohn@nvidia.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: polinabinder1 <pbinder@nvidia.com> Co-authored-by: Truong Nguyen <tgnguyen@nvidia.com> Co-authored-by: jomitchellnv <148147880+jomitchellnv@users.noreply.github.com> Co-authored-by: lvojtku <lvojtku@nvidia.com> Signed-off-by: Ubuntu <camirr@nvidia.com>
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Description
Adding the required grouping to fix Geneformer-specific group in wandb
Type of changes
CI Pipeline Configuration
Configure CI behavior by applying the relevant labels:
Note
By default, the notebooks validation tests are skipped unless explicitly enabled.
Authorizing CI Runs
We use copy-pr-bot to manage authorization of CI
runs on NVIDIA's compute resources.
automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123)
/ok to testcomment on the pull request to trigger CI. This will need to be done for each new commit.Usage
Pre-submit Checklist