Project Bourne MCP Server

Project Bourne

Project Bourne is open-source execution and provenance infrastructure for reproducible scientific and engineering workloads.

It answers: Exactly how did this scientific result come to exist?

Keep AI off the cluster

Researcher's workstation
  Linux / macOS
        │
  AI / Agent (optional)
        │ local stdio MCP
        ▼
  Bourne Control Plane
        │
        ├─ freezes immutable ExecutionPlan
        ├─ builds/stages versioned Bourne workers
        └─ uses existing VPN / OpenSSH
        ▼

HPC login / access node
  one-shot Bourne Remote Worker
        │
        ├─ validates the plan
        ├─ verifies staged file digests
        ├─ stages the execution bundle
        └─ submits with sbatch / qsub / bsub
        ▼

Slurm / PBS / IBM LSF
        │
        │ allocates resources
        ▼

Compute allocation
  execution-scoped Bourne Compute Worker
        │
        ├─ reads immutable ExecutionPlan
        ├─ observes actual allocation
        ├─ reproduces selected environment
        ├─ performs compute-side preflight
        ├─ executes exact scientific argv
        └─ writes durable result evidence
        ▼

Scientific workload

Later:

Researcher's workstation
        │
        │ existing SSH
        ▼
Remote Worker: reconcile
        │
        ├─ exact Bourne-owned scheduler job state
        └─ bounded result evidence
        ▼
Local Bourne provenance database

The Remote Worker and Compute Worker are not agents or persistent services; both are short-lived, versioned Bourne workers. Bourne does not SSH directly into compute nodes. Slurm/PBS/LSF places the Compute Worker inside the allocation and owns job lifetime after accepting the submission. The researcher's workstation / control plane may disconnect and reconcile the same execution later.

The HPC path requires no AI, MCP server, AI credential, inbound port, root access, persistent daemon, or public-internet access on the cluster. It uses the researcher's existing OpenSSH configuration and scheduler access. Agents receive typed Bourne operations—not an unrestricted remote shell.

The Bourne control plane is supported and tested on Linux and macOS. Native Windows is not yet validated or supported.

Bourne remains agent-native, not agent-dependent. The CLI and Python services work without an agent or MCP.

Quick Start

Human

Install Project Bourne v0.8.1 from PyPI:

python -m pip install "bourneprov==0.8.1"

bourne run python examples/demo.py
bourne list
bourne show @1

# Or execute an ExecutionRequest v2 document:
bourne execute --request bourne.json

Configure a site-aware SSH workflow with the installed CLI:

bourne site add imperial \
  --ssh login.example.edu \
  --scheduler slurm \
  --local-root "$PWD" \
  --remote-root /work/$USER/project

bourne discover --site imperial
bourne plan --site imperial --request bourne.json --provider constraints.json

The first plan call prints bounded candidates. A human or agent then makes the preference decision explicitly:

bourne plan --site imperial --request bourne.json \
  --provider constraints.json \
  --trust-provider-classifications \
  --candidate sha256:...

bourne execute --plan <plan-id>
bourne execution wait <execution-id>

The trust flag is an explicit review decision for semantic classifications in that declarative provider; the provider cannot grant itself that authority. Use --approve-variant-change PARAMETER or --declare-execution-only PARAMETER for narrower user decisions. If the selected candidate changes a provider-bound JSON input, Bourne preserves the original and automatically binds a separately hashed WorkloadVariant to the plan.

Slurm/PBS/LSF owns the job after acceptance. The researcher's workstation / control plane, VPN, SSH connection, MCP host, and agent may disconnect; Bourne reconnects later and reconciles the exact execution. An ambiguous connection failure never triggers blind resubmission.

Agent / MCP

The v0.8.1 agent and MCP entrypoints remain local stdio:

python -m pip install "bourneprov[mcp]==0.8.1"
bourne mcp

# Or use the public transparent launcher:
npx -y @project-bourne/mcp@0.8.1

Development

Project Bourne uses uv as its development, dependency-locking, test, and build frontend. After installing uv, synchronize the committed lockfile and run the suite with:

uv sync --locked --all-extras --dev
uv run --frozen --no-sync python -W error::ResourceWarning -m unittest discover -s tests -v
uv build --no-sources

CI uses locked/frozen variants of these commands so an out-of-date uv.lock fails instead of drifting. uv is development tooling only: it is not a bourneprov runtime dependency, is not required for pip install, is not used by the npm launcher, and is never required on HPC login or compute nodes. See CONTRIBUTING.md for the complete contributor workflow.

Why Bourne

Bourne wraps arbitrary executables without requiring changes to the scientific program. It is local-first and framework-agnostic: Python, compiled solvers, Julia, MPI programs, and other commands use the same durable experiment model.

bourne run bash -c "echo hello"
bourne run ./solver case.yaml
bourne run julia simulation.jl
bourne run mpirun -np 64 ./solver

Program stdout and stderr remain visible during execution and are preserved in the experiment record.

Runtime truth in v0.8

v0.8 keeps planning truth, scheduler truth, runtime truth, experiment truth, verification, and scientific validity separate. The execution-scoped Compute Worker records versioned process, allocation, CPU, memory, I/O, GPU, and environment evidence with explicit observed, partially_observed, unavailable, unsupported, or unknown coverage. Missing telemetry does not fail a valid workload and never becomes a fabricated zero.

IBM LSF joins Slurm and PBS with bounded queue discovery, bsub, exact-job active bjobs, recent-finished bjobs -a, durable bhist reconciliation, and bkill. Existing Apptainer/Singularity images can be frozen into a selected site-aware plan; Bourne verifies the existing runtime/image on the compute side and passes the scientific command as exact argv. It does not build, pull, install, or manage images. v0.8 does not orchestrate multi-node container launch, choose MPI-launcher/container ordering, or inject an MPI launcher. See runtime evidence and scheduler coverage.

Core architecture

Bourne Core owns deterministic execution, evidence, planning, storage, and provenance. CLI, SDK, and MCP are adapters over the same services:

             Project Bourne Core
                    │
       ┌────────────┼────────────┐
       │            │            │
      CLI          SDK          MCP
    humans                     agents

The remote worker is one-shot, user-space, non-AI, and non-daemon. It accepts only versioned operations for discovery, plan validation, staging, scheduler submission, and reconciliation. Scientific commands remain exact argv in an immutable plan; no scientific argv is interpolated into remote shell text. The remote-worker protocol remains v1. v0.8 adds worker-result protocol v3 and staged-plan protocol v4 while retaining readers for released worker-result v1/v2 and staged-plan v1/v2/v3 payloads.

Agent and MCP Integration

The canonical local stdio server is bourne mcp. The stable official MCP Registry identity is io.github.KozakHou/project-bourne, and the portable Agent Skill is at skills/project-bourne. The v0.8.1 npm package and matching Registry metadata use the same release identity.

An MCP-compatible agent can translate an explicit request such as “Run this simulation using four GPUs and preserve provenance” into ExecutionRequest v2, ask Bourne to plan it, show the deterministic resolution, and execute the immutable plan after execution intent is established. Bourne itself does not interpret unconstrained natural language and does not call another model.

The agent path is deliberately two-phase:

agent intent → ExecutionRequest v2 → bourne_plan → inspect → bourne_execute_plan

Planning never runs the workload or silently discovers infrastructure. Ambiguous targets and unknown facts remain unresolved. MCP annotations are host UX hints; Bourne Core still enforces immutable plans, exact argv, scheduler job ownership, artifact semantics, and provenance. See MCP integration and Agent guidance.

Execution Requests

An execution can now be described once in a bounded, versioned JSON request:

{
  "kind": "bourne.execution-request",
  "version": 2,
  "command": ["python", "train.py", "--case", "case1"],
  "artifacts": {
    "inputs": ["config.yaml"],
    "outputs": ["result.h5"]
  },
  "resources": {"cpus": 8, "gpus": 1, "walltime": "2h"},
  "execution": {"backend": "direct"},
  "verification": {
    "checks": [
      {"type": "output_exists", "path": "result.h5"},
      {"type": "output_min_bytes", "path": "result.h5", "min_bytes": 1024}
    ]
  }
}

Save it as bourne.json, then use the same intent for planning or execution:

bourne request validate bourne.json
bourne request show bourne.json

bourne discover
bourne plan --request bourne.json
bourne execute --request bourne.json

Create a minimal request without executing or discovering anything:

bourne request init --output bourne.json -- python train.py
bourne request schema > execution-request-v2.schema.json

Existing flag-based commands remain supported. They compile into the same ExecutionRequest → WorkloadSpec → ExecutionPlan pipeline rather than a parallel implementation:

bourne execute --backend direct --cpus 2 --output result.txt -- python script.py

For a request file, a relative working_directory is resolved from the request file's directory. Declared artifacts are then resolved from that scientific working directory. Bourne preserves both the lexical and resolved working-directory values and does not expand $HOME, evaluate shell syntax, import project code, or execute anything while parsing or planning.

Parent references follow the same intent-preserving rule. A request may use latest, @N, a unique prefix, or a full ULID. Bourne retains that requested value while separately recording the canonical parent ULID used by the compiled workload.

Summary telemetry is enabled by default and uses already captured facts: wall time, UTF-8 stdout/stderr byte counts, known artifact byte totals, requested resources, observed allocation, and scheduler queue timing when timestamps establish it. "telemetry": {"mode": "off"} disables the summary. Missing metrics remain unavailable, never zero.

The initial deterministic verification checks are output_exists, output_min_bytes, and output_sha256. They evaluate only captured declared output Artifact records. Verification is persisted separately from process status: an experiment may be completed while verification is failed or unknown. These checks establish artifact facts, not general scientific validity. See Execution requests, telemetry, and verification for the exact contract and safety limits.

Planning and Execution

Project Bourne v0.4.0 adds a durable planning layer over v0.3 inventories:

bourne discover

bourne plan --backend direct -- python examples/demo.py
bourne execute --backend direct -- python examples/demo.py

bourne execution list
bourne execution show @1

bourne plan never runs the scientific command and never performs discovery. It creates a framework-independent WorkloadSpec, compares its explicit and inferred requirements with an existing inventory, explains every candidate, and persists an immutable ExecutionPlan only when selection is unambiguous. Use explicit resource and placement constraints when needed:

bourne plan \
  --backend slurm \
  --target gpu \
  --cpus 16 \
  --gpus 4 \
  --nodes 1 \
  --memory 64G \
  --walltime 2h \
  -- ./solver case.yaml

Execute a selected Slurm plan and then inspect or wait for the resulting execution attempt:

bourne execute --plan @1
bourne execution show @1
bourne execution wait @1

While a recorded job is still active, bourne execution cancel @1 requests cancellation of that Bourne-managed job. The same planning and lifecycle model supports --backend pbs and --backend lsf.

Direct execution reuses Bourne's existing live-output, process-group, artifact, lineage, and experiment-provenance machinery. Slurm, PBS, and LSF plans use a self-contained Bourne worker staged with the plan. The worker performs preflight and records the actual allocated host and scientific experiment; the access-side controller imports its bounded JSON result transactionally. No compute-node SSH or preinstalled bourneprov package is required, although the compute allocation must provide Python 3 and visibility of the staging and working directories.

Submission is not an experiment, scheduler completion is not scientific success, and requested resources are not allocated resources. Bourne records these as separate durable facts. Cancellation accepts a Bourne execution reference—not an arbitrary scheduler job ID—and checks the submitting identity. See Workload planning and scheduler execution for the exact model, safety boundary, and current limitations.

Compute-site discovery (v0.3.0)

Bourne can take an immutable, local snapshot of the execution surface visible to your current identity:

bourne discover
bourne inventory
bourne inventory --find python
bourne inventory --json

Discovery covers the current identity and access target, allow-listed user-relevant storage paths, direct execution contexts, generic PATH executables, optional Conda/virtualenv/container/module contexts, safe system capabilities, Bourne history, and read-only Slurm/PBS/LSF target-class summaries when available. An unknown executable is recorded generically without being run. Laptops, desktop and GPU workstations, DGX-class personal machines, shared laboratory systems, and scheduler-backed HPC sites are all valid compute sites. A scheduler-free machine is complete in its own right.

Discovery is observational: an executable is not verified workload compatibility, a visible scheduler partition is not proof of submission authorization, and a storage role hint is not a retention or backup policy. Inventories remain local. Providers do not traverse other users' homes, crawl shared storage, inspect SSH credentials or container secrets, dump arbitrary environment variables, SSH into compute nodes, submit or cancel scheduler jobs, or modify environments. See Compute-site discovery for the exact topology, evidence, limits, and security semantics.

Provenance, Artifacts and Lineage

Project Bourne v0.2 adds explicit input/output fingerprints, a minimal derived_from relationship, safe execution-context observations, and artifact tracing. Run the deterministic example from an isolated directory:

cp -R examples/provenance /tmp/bourne-provenance-demo
cd /tmp/bourne-provenance-demo
export BOURNE_DB="$PWD/bourne.sqlite3"

bourne run \
  --input config_A.json \
  --output result_A.csv \
  -- python demo_simulation.py config_A.json result_A.csv

bourne run \
  --derived-from @1 \
  --input config_B.json \
  --input result_A.csv \
  --output result_B.csv \
  -- python demo_simulation.py config_B.json result_B.csv

bourne show @2
bourne show @1
bourne trace result_B.csv

Inputs are fingerprinted before execution. Outputs are fingerprinted afterward, including expected outputs that are missing after a failed or interrupted run. SHA-256 reads are streamed in chunks; Bourne does not copy or upload declared files.

A path is not artifact identity. Each capture has a stable ULID, while SHA-256 distinguishes content versions. When a historical path could identify several versions and the current file content cannot disambiguate them, bourne trace lists candidates and refuses to guess.

See Artifacts, lineage, and execution context for exact capture, trace, migration, and security semantics.

Human-friendly experiment references

Canonical experiment identities remain 26-character ULIDs. Commands that accept an experiment also understand:

01M02GDJEW...   case-insensitive unique ULID prefix
latest          most recent experiment
@1              most recent experiment
@2              second-most-recent experiment
@3              third-most-recent experiment

For example:

bourne show latest
bourne show 01M02GDJEW
bourne compare @2 @1
bourne run --derived-from @1 -- ./solver case_B.yaml

Bourne never guesses when a prefix is ambiguous. bourne list displays a 10-character prefix by default; bourne list --full-id displays canonical IDs.

Shell completion

Completion candidates include canonical experiment IDs, latest, and recent @N references. Activate completion for the current shell session with:

# Bash
source <(bourne completion bash)

# Zsh
source <(bourne completion zsh)

# Fish
bourne completion fish | source

Completion for bourne show and bourne compare queries the currently configured database, including BOURNE_DB.

What Bourne records

Every experiment records:

• execution status (completed, failed, or interrupted), exact argument vector, working directory, UTC timestamps, duration, and exit code;
• live and captured stdout/stderr;
• Git repository root, commit, branch, and dirty state when available;
• operating system, architecture, hostname, CPU, and optional NVIDIA runtime metadata;
• requested and resolved executable paths plus strictly allow-listed virtualenv/Conda context hints;
• explicitly declared input/output artifact versions and immediate lineage.

Collectors degrade gracefully. Missing Git, NVIDIA tooling, GPUs, environment hints, or executable resolution does not stop the workload. Arbitrary environment variables are not persisted, so credentials and tokens are not captured by default.

Failed and interrupted commands are saved before bourne returns their process semantics:

bourne run --output expected.csv -- python -c "raise RuntimeError('boom')"
bourne show @1

On POSIX systems, Bourne uses a dedicated process group so Ctrl+C normally terminates descendants without targeting unrelated processes.

Execution success is not verification, and deterministic artifact verification is not general scientific validity. Bourne records these states separately.

Local storage and migration

The default SQLite path is:

~/.local/share/bourne/experiments.sqlite3

Use a project-specific database with:

export BOURNE_DB=/path/to/experiments.sqlite3

Opening an older Bourne database, including released v0.1.1 through v0.7.0 databases, with v0.8.0 performs deterministic transactional migrations through schema 7. Existing experiments, artifacts, lineage, inventories, workloads, plans, executions, scheduler jobs, allocations, events, and experiment links remain readable. Migration does not invent ExecutionRequest history for v0.4 records. Unknown or newer schema versions fail explicitly; Bourne never resets an existing database. Each new discovery creates a separate immutable snapshot.

License

Project Bourne v0.5.0 and later are distributed under the Apache License 2.0. Releases through v0.4.0 remain under the MIT License terms under which they were released. See the licensing history for details.

Release validation

The release version is 0.8.1. The base runtime has zero third-party dependencies; MCP support remains an explicit optional extra.

Run the source-tree tests with:

uv sync --locked --all-extras --dev
uv run --frozen --no-sync python -W error::ResourceWarning -m unittest discover -s tests -v
uv build --no-sources

Compute-worker stdout and stderr remain live and are bounded to 8 MiB per captured stream in the result bundle; truncation is explicit runtime evidence. Ordinary local bourne run retains its existing capture behavior. Disk-spooled logs, automatic artifact discovery/archival, scientific dependency installation or source builds, generic data synchronization, unrestricted remote shell, scheduler-free disconnect-safe remote supervision, whole-allocation distributed telemetry, queue/performance prediction, arbitrary verification scripts, hosted HTTP MCP, embedded LLMs, and broad scientific-validity inference remain outside v0.8. See runtime evidence and scheduler coverage, the site-aware architecture, and VISION.

Live LSF and live Apptainer validation have not yet been performed. Runtime sampling is execution-scoped and does not automatically aggregate across a multi-node allocation. Bourne does not inject MPI launchers or automatically choose container/MPI ordering. Portable LSF memory/GPU resource syntax remains site-specific and unresolved.