# Containerization

Atomic runs with all permissions by default. To restrict which directories it can write to and what it can access, choose one of two approaches:

1. Run the whole `atomic` process inside an isolated environment.
2. Run `atomic` on the host and route tool execution into an isolated environment.

Containerization is the outer boundary, not the only one. [Security](/security) covers the project-trust prompt that gates which project-scoped extensions, skills, and settings load in the first place; read it alongside this page when you are deciding what an untrusted repository is allowed to do.

## Choose a pattern

| Pattern | What is isolated | Best for | Notes |
| --- | --- | --- | --- |
| Gondolin extension | Selected file tools, shell execution, and `!` commands | Local micro-VM tool routing while keeping auth on host | Other tools, including `search`, remain on the host. See [`examples/extensions/gondolin/`](https://github.com/bastani-inc/atomic/tree/main/packages/coding-agent/examples/extensions/gondolin). |
| Plain Docker | Whole `atomic` process in a local container | Simple local isolation | Provider API keys enter the container. |
| OpenShell | Whole `atomic` process in a policy-controlled sandbox | Local or remote managed sandbox | Requires an OpenShell gateway. |

Extensions run wherever the `atomic` process runs. If you run host `atomic` with a tool-routing extension, other custom extension tools still run on the host unless they also delegate their operations.

## Gondolin

[Gondolin](https://github.com/earendil-works/gondolin) is a local Linux micro-VM.
Use the [example extension](https://github.com/bastani-inc/atomic/tree/main/packages/coding-agent/examples/extensions/gondolin) when you want `atomic` on the host with selected file tools and shell execution routed into the VM. This is not isolation for the entire session.

Setup:

```bash
cp -R packages/coding-agent/examples/extensions/gondolin ~/.atomic/agent/extensions/gondolin
cd ~/.atomic/agent/extensions/gondolin
npm ci --ignore-scripts
```

Run from the project you want mounted:

```bash
cd /path/to/project
atomic -e ~/.atomic/agent/extensions/gondolin
```

The extension mounts the host cwd at `/workspace` in the VM and overrides `read`, `write`, `edit`, `bash`, `find`, and `ls`.
User `!` commands are routed into the VM, as well.
File changes under `/workspace` write through to the host.

`search` remains a host tool; it is not redirected into the VM. The removed `grep` tool is not registered. For guest-only content searches, use a shell command through the routed `bash` tool or `!` command. To expose only these routed tools, start with `atomic --tools read,write,edit,bash,find,ls -e ~/.atomic/agent/extensions/gondolin`; other loaded extensions can still supply host-side tools. Use whole-process isolation instead when host filesystem access must be prevented.

Requirements: npm for dependency installation, Node.js >= 23.6.0 for `@earendil-works/gondolin`, plus QEMU (requires installation through your package manager).

## Plain Docker

Run the whole `atomic` process in Docker when you want the simplest local container boundary.

`Dockerfile.atomic`:

```dockerfile
FROM node:24-bookworm-slim

RUN apt-get update \
  && apt-get install -y --no-install-recommends bash ca-certificates git ripgrep \
  && rm -rf /var/lib/apt/lists/*
RUN npm install -g --ignore-scripts @bastani/atomic

WORKDIR /workspace
ENTRYPOINT ["atomic"]
```

For an image without Node.js or npm, use the release-archive installer instead:

```dockerfile
FROM debian:bookworm-slim

RUN apt-get update \
  && apt-get install -y --no-install-recommends bash ca-certificates curl git ripgrep tar \
  && rm -rf /var/lib/apt/lists/*
RUN curl -fsSL https://raw.githubusercontent.com/bastani-inc/atomic/main/install.sh | sh

ENV PATH="/root/.local/bin:${PATH}"
WORKDIR /workspace
ENTRYPOINT ["atomic"]
```

The archive path installs the full prebuilt payload and needs no JavaScript runtime or package manager. The other packages in this example support Atomic's shell and common coding tasks.

Build and run:

```bash
docker build -t atomic-sandbox -f Dockerfile.atomic .

docker run --rm -it \
  -e ANTHROPIC_API_KEY \
  -v "$PWD:/workspace" \
  -v atomic-agent-home:/root/.atomic/agent \
  atomic-sandbox
```

The `-v "$PWD:/workspace"` option mounts your current directory at /workspace in the container. Reads and writes in `/workspace` directly affect your host files, as in the Gondolin example.

Use a named volume for `/root/.atomic/agent` if you want container-local settings and sessions. Mounting your host `~/.atomic/agent` exposes host auth and session files to the container.

## OpenShell

Use [NVIDIA OpenShell](https://docs.nvidia.com/openshell/about/overview) when you want a policy-controlled sandbox with filesystem, process, network, credential, and inference controls.
OpenShell can run sandboxes through a local gateway backed by Docker, Podman, or a VM runtime, or through a remote Kubernetes gateway.

Every sandbox requires an active gateway.
Register and select one before creating a sandbox:

```bash
openshell gateway add <gateway-url> --name <name>
openshell gateway select <name>
```

Launch `atomic` inside an OpenShell sandbox:

```bash
openshell sandbox create --name atomic-sandbox --from atomic -- atomic
```

In this pattern, the whole `atomic` process runs inside the sandbox.
Built-in tools, `!` commands, and extension tools execute inside the OpenShell boundary.

If the gateway is remote, project files are not bind-mounted from the host, meaning writes in the sandbox are not reflected on your machine.
Clone the repository inside the sandbox or use OpenShell file transfer commands:

```bash
openshell sandbox upload atomic-sandbox ./repo /workspace
openshell sandbox download atomic-sandbox /workspace/repo ./repo-out
```

OpenShell providers can keep raw model API keys outside the sandbox.
When inference routing is configured, code inside the sandbox can call `https://inference.local`, and the gateway injects the configured provider credentials upstream.
Configure Atomic to use the corresponding OpenAI-compatible or Anthropic-compatible endpoint if you want model traffic to use this route.