> This page is for Boltz-2, version 1.9.0.
> For other versions, use one of these documentation indexes:
> - 1.10.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/boltz2/1.10.0/llms.txt
> - 1.9.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.9.0/llms.txt
> - 1.8.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.8.0/llms.txt
> - 1.7.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.7.0/llms.txt
> - 1.6.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.6.0/llms.txt
> - 1.5.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.5.0/llms.txt
> - 1.4.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.4.0/llms.txt
> - 1.3.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.3.0/llms.txt
> - 1.2.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.2.0/llms.txt
> - 1.1.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.1.0/llms.txt
> - 1.0.0: https://docs.nvidia.com/nim/bionemo/boltz2/1.0.0/llms.txt

> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/nim/bionemo/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/nim/bionemo/_mcp/server.

# Configuring the Boltz-2 NIM

The Boltz-2 NIM uses Docker containers.
Each NIM has its own Docker container and there are several ways to configure it.
The section below describes how to configure a NIM container.

## GPU Selection

By default, Docker can use all available GPUs on the system when it starts with the NVIDIA Container Runtime:

```bash
docker run --runtime=nvidia ...
```

In environments with a combination of GPUs, you can only expose specific GPUs inside the container using either:

- The `--gpus` flag. For example, `docker run --gpus='"device=1"' ...`
- The environment variable `NVIDIA_VISIBLE_DEVICES`. For example, to expose only Device 1, pass `-e NVIDIA_VISIBLE_DEVICES=1`. To expose GPU IDs 1 and 4, pass`-e NVIDIA_VISIBLE_DEVICES=1,4`.

The device IDs to use as inputs are listed in the output of `nvidia-smi -L`:

```
GPU 0: Tesla H100 80GB HBM3 (UUID: GPU-aaaaaaaa-bbbb-cccc-dddd-111111111111)
GPU 1: Tesla H100 80GB HBM3 (UUID: GPU-eeeeeeee-ffff-0000-1111-222222222222)
```

Refer to the [NVIDIA Container Toolkit documentation](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/docker-specialized.html#gpu-enumeration) for more instructions.

## Environment Variables

The Boltz-2 NIM container image on NVIDIA Container Registry is **`nvcr.io/nim/mit/boltz2:<version>`** (NGC org **nim**, team **mit**). Examples on this page use the substituted form `nvcr.io/nim/mit/boltz2:1.9.0`, which resolves to that path.


The following table describes the environment variables that can be passed into a NIM as a `-e` argument added to a `docker run` command:

| ENV | Required? | Default | Notes |
| --- | --------- | ------- | ----- |
| `NGC_API_KEY` | Yes | None | You must set this variable to the value of your personal NGC API key. |
| `NIM_CACHE_PATH` | No | `/opt/nim/.cache` | Location (in container) where the container caches model artifacts. |
| `NIM_HTTP_API_PORT` | No | `8000` | Publish the NIM service to the prescribed port inside the container. Make sure to adjust the port passed to the `-p/--publish` flag of Docker run to reflect that (ex: `-p $NIM_HTTP_API_PORT:$NIM_HTTP_API_PORT`). The left-hand side of this `:` is your host address:port, and does NOT have to match with `$NIM_HTTP_API_PORT`. The right-hand side of the `:` is the port inside the container and MUST match the port the NIM listens on: use the value of `NIM_HTTP_API_PORT` when set, otherwise **8000** (the default in this column—not a different port). Supported endpoints are `/v1/license` (Returns the license information), `/v1/metadata` (Returns metadata including asset information, license information, model information, and version) and `/v1/metrics` (Exposes Prometheus metrics using an ASGI app endpoint). |
| `NIM_LOG` | No | `INFO` | Controls NIM service logging. Available options are `DEBUG`, `INFO`, `WARNING`, `ERROR`, and `CRITICAL`. |
| `NIM_LOG_LEVEL` | No | `INFO` | Alternative NIM logging level control. Available options are `DEBUG`, `INFO`, `WARNING`, `ERROR`, and `CRITICAL`. |
| `MODEL_PATH` | No | Unset | Hard override of the NIM model root. When set, checkpoints and supporting assets are loaded from this directory instead of the NGC cache. Used for [custom / fine-tuned checkpoints](/nim/bionemo/boltz2/1.9.0/custom-checkpoints). |
| `NIM_DISABLE_MODEL_DOWNLOAD` | No | Unset | When set to `1`/`true`, skip downloading model artifacts from NGC. Use together with `MODEL_PATH` when serving local checkpoints. |
| `NIM_BOLTZ_CONF_CKPT_FILE` | No | `boltz2_conf.ckpt` | Filename of the structure checkpoint inside `MODEL_PATH` or the NGC cache root. |
| `NIM_BOLTZ_AFFINITY_CKPT_FILE` | No | `boltz2_aff.ckpt` | Filename of the affinity checkpoint inside `MODEL_PATH` or the NGC cache root. |
| `NIM_DEFAULT_RANDOM_SEED` | No | `42` | Controls the random seed used for inference. |
| `NIM_TELEMETRY_MODE` | No | `0` | String **`0`** disables telemetry (default). **`1`** enables baseline collection (hardware and NIM information). On RTX GPUs, collection stays off unless you also set `NIM_TELEMETRY_ENABLE_ON_RTX=true`. Refer to [NIM Telemetry](#nim-telemetry). For privacy and full configuration details, refer to [NVIDIA's Privacy Policy](https://www.nvidia.com/en-us/about-nvidia/privacy-policy/) and [NIM Telemetry Settings](https://developer.nvidia.com/docs/nim-tools/latest/templates/nimlib/nim-telemetry.html). |
| `NIM_TELEMETRY_ENABLE_ON_RTX` | No | `false` | String **`true`** allows telemetry on RTX GPUs when `NIM_TELEMETRY_MODE` is not **`0`**. Default **`false`**. Has no effect when telemetry is disabled. Refer to [NIM Telemetry](#nim-telemetry). |
| `NIM_TELEMETRY_ENABLE_LOGGING` | No | `true` | Enables logging for telemetry operations when set to `true`. Only applicable when `NIM_TELEMETRY_MODE=1`. |
| `NIM_OUTPUT_PATH` | No | `/opt/nim/output` | Root directory for exposed prediction artifacts (`prediction_*/{confidence_scores,pae,pde}/`). Falls back to `NIM_CACHE_PATH` when unset. Mount a host directory here when persisting confidence JSONs or full PAE/PDE `.npz` files. |
| `NIM_EXPOSE_CONFIDENCE_SCORES` | No | `false` | Controls whether to expose per-sample confidence JSON files (`confidence_*_model_*.json`) under `$NIM_OUTPUT_PATH/prediction_*/confidence_scores/`. Set to `true` to persist files (including scalar metrics such as `complex_pde` and `complex_ipde`), set to `false` to disable (default). This setting does not write full PAE or PDE matrices; use `write_full_pae` and `write_full_pde` in predict requests to write full matrices as `.npz` files under `$NIM_OUTPUT_PATH`. |
| `NIM_MAX_MSA_SEQS` | No | `4096` | Cap on MSA sequences retained when parsing request MSAs. Raise this to allow deeper MSAs (for example `8192`). |
| `NIM_MAX_POLYMER_INPUTS` | No | `12` | Maximum number of polymer chains allowed in a single predict request. |
| `NIM_MAX_LIGAND_INPUTS` | No | `20` | Maximum number of ligands allowed in a single predict request. |
| `NIM_MAX_POLYMER_LENGTH` | No | `4096` | Maximum length for an individual polymer sequence. |
| `NIM_MAX_TEMPLATES_PER_POLYMER` | No | `4` | Maximum number of structural templates allowed per protein polymer. |

For additional Boltz-2 tuning variables such as `NIM_MODEL_PROFILE`, refer to [Optimization](/nim/bionemo/boltz2/1.9.0/optimization).

## NIM Telemetry

NIM Telemetry collects minimal host and NIM information to help improve performance, reliability, and compatibility across deployments. Collection is **disabled by default on RTX GPUs** and can be enabled explicitly when you opt in.

### `NIM_TELEMETRY_MODE`

Controls telemetry collection mode.

- **`0`** — Disables telemetry.
- **`1`** — Enables baseline collection (hardware and NIM information).

**Default:** `0`

### `NIM_TELEMETRY_ENABLE_ON_RTX`

Set to **`true`** to allow telemetry collection on RTX GPUs. This setting applies only when `NIM_TELEMETRY_MODE` is not **`0`** (for example, when baseline collection is enabled on the deployment).

**Default:** `false`

For what is collected, retention, and advanced options, refer to [NIM Telemetry Settings](https://developer.nvidia.com/docs/nim-tools/latest/templates/nimlib/nim-telemetry.html) and [NVIDIA's Privacy Policy](https://www.nvidia.com/en-us/about-nvidia/privacy-policy/).

## Volumes

The following table describes the paths inside the container into which local paths can be mounted.

| Container path | Required | Notes | Docker argument example |
| -------------- | -------- | ----- | ----------------------- |
| `/opt/nim/.cache` (or `NIM_CACHE_PATH` if present) | Not required, but if this volume is not mounted, the container will do a fresh download of the model each time it is brought up. | This is the directory within which models are downloaded inside the container. It is very important that this directory can be accessed from inside the container. This can be achieved by setting the permissions of the local directory to `read-write-execute` (`777`). For example, to use `~/.cache/nim` as the host machine directory for caching models, first do `mkdir -p ~/.cache/nim`, then `chmod 777 ~/.cache/nim` before running the `docker run command`. | `-v ~/.cache/nim:/opt/nim/.cache ` |
| `/opt/nim/output` (or `NIM_OUTPUT_PATH` if present) | Not required | Destination for exposed prediction artifacts such as confidence JSONs and full PAE/PDE `.npz` files under `prediction_*/`. Keep this separate from the model cache so large matrices do not fill `NIM_CACHE_PATH`. | `-v ./output:/opt/nim/output -e NIM_OUTPUT_PATH=/opt/nim/output` |

## Logging Configuration

The Boltz-2 NIM provides logging environment variables to control verbosity for different components. You can configure these when starting the container to adjust the level of detail in logs for debugging or production use.

### Example: Running with Logging Configuration

The following example shows how to run the NIM with standard logging configuration:

```bash
export LOCAL_NIM_CACHE=~/.cache/nim
export NGC_API_KEY=<Your NGC API Key>
```

```bash
docker run --rm --name boltz2 --runtime=nvidia \
    --shm-size=16G \
    -e NGC_API_KEY \
    -e NIM_LOG=INFO \
    -e NIM_LOG_LEVEL=INFO \
    -v $LOCAL_NIM_CACHE:/opt/nim/.cache \
    -p 8000:8000 \
    nvcr.io/nim/mit/boltz2:1.9.0
```


### Example: Debug Logging for Troubleshooting

To enable verbose logging for troubleshooting issues, set the log levels to their most detailed settings:

```bash
export LOCAL_NIM_CACHE=~/.cache/nim
export NGC_API_KEY=<Your NGC API Key>
```

```bash
docker run --rm --name boltz2 --runtime=nvidia \
    --shm-size=16G \
    -e NGC_API_KEY \
    -e NIM_LOG=DEBUG \
    -e NIM_LOG_LEVEL=DEBUG \
    -v $LOCAL_NIM_CACHE:/opt/nim/.cache \
    -p 8000:8000 \
    nvcr.io/nim/mit/boltz2:1.9.0
```