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--- a/README.md +++ b/README.md @@ -1,96 +1,96 @@ -# BioNeMo Framework - -[](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU) -[](https://nvidia.github.io/bionemo-framework) -[](https://github.com/NVIDIA/bionemo-framework/actions/workflows/unit-tests.yml) -[](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework/tags) -[](https://codecov.io/gh/NVIDIA/bionemo-framework) - -NVIDIA BioNeMo Framework is a is a comprehensive suite of programming tools, libraries, and models designed for computational drug discovery. -It accelerates the most time-consuming and costly stages of building and adapting biomolecular AI models by providing -domain-specific, optimized models and tooling that are easily integrated into GPU-based computational resources for the -fastest performance on the market. You can access BioNeMo Framework as a free community resource here in this repository -or learn more at <https://www.nvidia.com/en-us/clara/bionemo/> about getting an enterprise license for improved -expert-level support. - -BioNeMo Framework is part of a larger ecosystem of NVIDIA Biopharma products. Get notified of new releases, bug fixes, critical security updates, and more for biopharma. [Subscribe.](https://www.nvidia.com/en-us/clara/biopharma/product-updates/) - -## Structure of the Framework - -The `bionemo-framework` is organized into independently installable namespace packages. These are located under the -`sub-packages/` directory. Please refer to [PEP 420 – Implicit Namespace Packages](https://peps.python.org/pep-0420/) -for details. - - -## Documentation Resources - -- **Official Documentation:** For user guides, API references, and troubleshooting, visit our [official documentation](https://docs.nvidia.com/bionemo-framework/latest/). -- **In-Progress Documentation:** To explore the latest features and developments, check the documentation reflecting the current state of the `main` branch [here](https://nvidia.github.io/bionemo-framework/). Note that this may include references to features or APIs that are not yet finalized. - -## Getting Started with BioNeMo Framework - -Full documentation on using the BioNeMo Framework is provided in our documentation: -<https://docs.nvidia.com/bionemo-framework/latest/user-guide/>. To simplify the integration of optimized third-party dependencies, BioNeMo is primarily distributed as a containerized library. You can download the latest released container for the BioNeMo Framework from -[NGC](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework). To launch a pre-built container, you can use the brev.dev launchable [](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU) or execute the following command: - -```bash -docker run --rm -it \ - --gpus=all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \ - nvcr.io/nvidia/clara/bionemo-framework:nightly \ - /bin/bash -``` - -### Setting up a local development environment - -#### Initializing 3rd-party dependencies as git submodules - -The NeMo and Megatron-LM dependencies are included as git submodules in bionemo2. The pinned commits for these submodules represent the "last-known-good" versions of these packages -that are confirmed to be working with bionemo2 (and those that are tested in CI). - -To initialize these sub-modules when cloning the repo, add the `--recursive` flag to the git clone command: - -```bash -git clone --recursive git@github.com:NVIDIA/bionemo-framework.git -cd bionemo-framework -``` - -To download the pinned versions of these submodules within an existing git repository, run - -```bash -git submodule update --init --recursive -``` - -Different branches of the repo can have different pinned versions of these third-party submodules. Ensure submodules are automatically updated after switching branches or pulling updates by configuring git with: - - -```bash -git config submodule.recurse true -``` - -**NOTE**: this setting will not download **new** or remove **old** submodules with the branch's changes. -You will have to run the full `git submodule update --init --recursive` command in these situations. - -#### Build the Docker Image Locally - - -With a locally cloned repository and initialized submodules, build the BioNeMo container using: - -```bash -docker buildx build . -t my-container-tag -``` - - -#### VSCode Devcontainer for Interactive Debugging - -We distribute a [development container](https://devcontainers.github.io/) configuration for vscode -(`.devcontainer/devcontainer.json`) that simplifies the process of local testing and development. Opening the -bionemo-framework folder with VSCode should prompt you to re-open the folder inside the devcontainer environment. - -> [!NOTE] -> The first time you launch the devcontainer, it may take a long time to build the image. Building the image locally -> (using the command shown above) will ensure that most of the layers are present in the local docker cache. - -### Quick Start - -See the [tutorials pages](https://docs.nvidia.com/bionemo-framework/latest/user-guide/examples/bionemo-esm2/pretrain/) -for example applications and getting started guides. +# BioNeMo Framework + +[](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU) +[](https://nvidia.github.io/bionemo-framework) +[](https://github.com/NVIDIA/bionemo-framework/actions/workflows/unit-tests.yml) +[](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework/tags) +[](https://codecov.io/gh/NVIDIA/bionemo-framework) + +NVIDIA BioNeMo Framework is a is a comprehensive suite of programming tools, libraries, and models designed for computational drug discovery. +It accelerates the most time-consuming and costly stages of building and adapting biomolecular AI models by providing +domain-specific, optimized models and tooling that are easily integrated into GPU-based computational resources for the +fastest performance on the market. You can access BioNeMo Framework as a free community resource here in this repository +or learn more at <https://www.nvidia.com/en-us/clara/bionemo/> about getting an enterprise license for improved +expert-level support. + +BioNeMo Framework is part of a larger ecosystem of NVIDIA Biopharma products. Get notified of new releases, bug fixes, critical security updates, and more for biopharma. [Subscribe.](https://www.nvidia.com/en-us/clara/biopharma/product-updates/) + +## Structure of the Framework + +The `bionemo-framework` is organized into independently installable namespace packages. These are located under the +`sub-packages/` directory. Please refer to [PEP 420 – Implicit Namespace Packages](https://peps.python.org/pep-0420/) +for details. + + +## Documentation Resources + +- **Official Documentation:** For user guides, API references, and troubleshooting, visit our [official documentation](https://docs.nvidia.com/bionemo-framework/latest/). +- **In-Progress Documentation:** To explore the latest features and developments, check the documentation reflecting the current state of the `main` branch [here](https://nvidia.github.io/bionemo-framework/). Note that this may include references to features or APIs that are not yet finalized. + +## Getting Started with BioNeMo Framework + +Full documentation on using the BioNeMo Framework is provided in our documentation: +<https://docs.nvidia.com/bionemo-framework/latest/user-guide/>. To simplify the integration of optimized third-party dependencies, BioNeMo is primarily distributed as a containerized library. You can download the latest released container for the BioNeMo Framework from +[NGC](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework). To launch a pre-built container, you can use the brev.dev launchable [](https://console.brev.dev/launchable/deploy/now?launchableID=env-2pPDA4sJyTuFf3KsCv5KWRbuVlU) or execute the following command: + +```bash +docker run --rm -it \ + --gpus=all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \ + nvcr.io/nvidia/clara/bionemo-framework:nightly \ + /bin/bash +``` + +### Setting up a local development environment + +#### Initializing 3rd-party dependencies as git submodules + +The NeMo and Megatron-LM dependencies are included as git submodules in bionemo2. The pinned commits for these submodules represent the "last-known-good" versions of these packages +that are confirmed to be working with bionemo2 (and those that are tested in CI). + +To initialize these sub-modules when cloning the repo, add the `--recursive` flag to the git clone command: + +```bash +git clone --recursive git@github.com:NVIDIA/bionemo-framework.git +cd bionemo-framework +``` + +To download the pinned versions of these submodules within an existing git repository, run + +```bash +git submodule update --init --recursive +``` + +Different branches of the repo can have different pinned versions of these third-party submodules. Ensure submodules are automatically updated after switching branches or pulling updates by configuring git with: + + +```bash +git config submodule.recurse true +``` + +**NOTE**: this setting will not download **new** or remove **old** submodules with the branch's changes. +You will have to run the full `git submodule update --init --recursive` command in these situations. + +#### Build the Docker Image Locally + + +With a locally cloned repository and initialized submodules, build the BioNeMo container using: + +```bash +docker buildx build . -t my-container-tag +``` + + +#### VSCode Devcontainer for Interactive Debugging + +We distribute a [development container](https://devcontainers.github.io/) configuration for vscode +(`.devcontainer/devcontainer.json`) that simplifies the process of local testing and development. Opening the +bionemo-framework folder with VSCode should prompt you to re-open the folder inside the devcontainer environment. + +### NOTE +The first time you launch the devcontainer, it may take a long time to build the image. Building the image locally +(using the command shown above) will ensure that most of the layers are present in the local docker cache. + +### Quick Start + +See the [tutorials pages](https://docs.nvidia.com/bionemo-framework/latest/user-guide/examples/bionemo-esm2/pretrain/) +for example applications and getting started guides.