mcp-sandbox

MCP server for isolated scientific script execution. Run R, Python, GMT, GRASS GIS, LaTeX, Octave, Julia, and more in disposable containers — fully stateless, no host filesystem access.

Tools

Tool	Description
run_script	Execute a script in an isolated sandbox container
list_runtimes	List available scientific runtimes

Supported Runtimes

Runtime	Tools
r	R + ggplot2, dplyr, tidyr, jsonlite
python	Python 3 + numpy, scipy, pandas, matplotlib, sympy, scikit-learn, geopandas, pyproj, rasterio, obspy
gmt	Generic Mapping Tools
grass	GRASS GIS — headless; each run gets a throwaway location
latex	pdflatex (texlive)
octave	GNU Octave
julia	Julia
gnuplot	Gnuplot
bash	Bash scripts

Design

• Each run spawns a fresh container — fully stateless, no reuse
• Container deleted after execution (--rm)
• Network access enabled
• Memory limit: 2GB, CPU limit: 2 cores
• Input files injected at /sandbox/input/ (base64)
• Output files collected from /sandbox/output/, returned by reference: a capability URL plus metadata (name, bytes, SHA-256, MIME, expiry). Small text outputs (< 4 KB) are still inlined. See "Output handling" below.

Install

The sandbox runs containers rootless, as a dedicated sandbox user. The image and the running service must live in that user's podman store. This is the single most important thing to get right — see Troubleshooting.

1. Create the service user

useradd -r -m -d /var/lib/mcp-sandbox -s /bin/bash sandbox
echo "sandbox:100000:65536" >> /etc/subuid
echo "sandbox:100000:65536" >> /etc/subgid
# rootless podman needs a runtime dir (/run/user/<uid>) present at boot:
loginctl enable-linger sandbox

2. Build the image — as the sandbox user

Build into the sandbox user's rootless store. Not your login user's, not root's — the server only ever reads sandbox's store:

sudo -u sandbox -H podman build -t mcp-sandbox:latest -f Containerfile .

Already built the image elsewhere? Don't rebuild — transfer it across the store boundary:

podman save mcp-sandbox:latest | sudo -u sandbox -H podman load

3. Install the server

python3 -m venv venv
venv/bin/pip install -e .

Running as a service

Run the server as sandbox so it reads that user's image store. Minimal unit (adjust the checkout path and entrypoint to your install):

# /etc/systemd/system/mcp-sandbox.service
[Unit]
Description=mcp-sandbox MCP server
After=network.target

[Service]
User=sandbox
ExecStart=/var/lib/mcp-sandbox/mcp-sandbox/venv/bin/mcp-sandbox
Restart=on-failure

[Install]
WantedBy=multi-user.target

Adding dependencies

The image is the single source of truth for what a runtime can do. Because every run is a fresh --rm container, a runtime pip install inside a sandbox does not persist — it re-downloads and rebuilds on every invocation, and on current Fedora it hits PEP 668 (externally-managed-environment) anyway. So:

• Missing package? Add the python3-* (or R-*, etc.) RPM to the Containerfile and rebuild the image — don't pip-install at runtime. Prefer Fedora RPMs; they keep the image reproducible and versioned in git.
• No Fedora RPM for it? Add a build-time RUN pip install … layer to the Containerfile, baked into the image — never a runtime install in the sandbox.

Rebuild after any change (as the sandbox user — see Install/Troubleshooting):

sudo -u sandbox -H podman build -t mcp-sandbox:latest -f Containerfile .

Output handling

Files written to /sandbox/output/ are returned by reference, not inlined as base64. After a run, the server stages each output under a fresh unguessable token and returns a compact metadata record in place of the bytes:

{
  "name": "figure.png",
  "bytes": 29901,
  "sha256": "…",
  "mime": "image/png",
  "url": "https://host.example/sandbox-out/<token>/figure.png",
  "expires_in": 3600
}

• Capability URL. Each file is staged at /<token>/<name>, where <token> is ~256 bits from a CSPRNG (secrets.token_urlsafe(32)). Possessing the URL is the authorization to fetch it — there is no separate credential.
• Small text is still inlined. Text outputs below 4 KB come back inline; a round-trip to read three lines isn't worth it. Everything else is referenced.
• Bounded lifetime. Staged files live for a TTL (default 60 min), after which the GC timer deletes them and the URL 404s — this bounds the exposure window of any leaked URL.
• Integrity. The sha256 lets a consumer verify the bytes, or confirm a file's identity without fetching it.

Serving the staged outputs

nginx serves the staging directory read-only, with listing, logging, and auth off (the token is the authentication):

location /sandbox-out/ {
    alias /var/cache/mcp-sandbox/outputs/;
    auth_basic off;      # the capability token is the authorization
    autoindex off;       # non-enumerable: no directory listing
    access_log off;      # keep tokens out of logs
    add_header X-Robots-Tag "noindex" always;
}

On SELinux, the staging dir must carry httpd_sys_content_t, applied before it is populated:

semanage fcontext -a -t httpd_sys_content_t "/var/cache/mcp-sandbox/outputs(/.*)?"
restorecon -RFv /var/cache/mcp-sandbox/outputs

Expiry is a systemd .timer firing every 15 min that deletes token directories older than the TTL.

Configuration

HOST=127.0.0.1
PORT=8815
SANDBOX_IMAGE=mcp-sandbox:latest
DEFAULT_TIMEOUT=60
MAX_TIMEOUT=300
# Output-by-reference — REPLACE names with the actual ones from the code:
SANDBOX_PUBLIC_URL=https://host.example    # base for capability links
OUTPUT_DIR=/var/cache/mcp-sandbox/outputs  # staging directory
OUTPUT_TTL=3600                            # seconds; keep in sync with GC timer

Troubleshooting

Rebuilt the image but the server still runs the old one? You almost certainly built into the wrong podman store. Containers run rootless as sandbox, which reads its own store under /var/lib/mcp-sandbox/.local/share/containers. An image built as your login user or as root lands in a different store the server never reads — so the build "succeeds" and changes nothing.

Confirm what the service actually sees, and rebuild/load into that store:

sudo -u sandbox -H podman images mcp-sandbox
sudo -u sandbox -H podman build -t mcp-sandbox:latest -f Containerfile .
# or: podman save mcp-sandbox:latest | sudo -u sandbox -H podman load

No MCP restart is needed afterwards — each run is a fresh --rm container that resolves mcp-sandbox:latest from the sandbox store at launch. Restart the service only when you change the server code or RUNTIMES.

License

Apache-2.0