What is clio-kit CLAUDE.md?

Project instructions for CLIO Kit, a collection of more than 15 MCP servers for scientific computing, high-performance computing (HPC), and research data.

Use them when setting up, developing, testing, or running CLIO Kit and its scientific-computing servers.

They give developers a shared guide for working in the collection, whose separate servers are started through one command-line launcher.

How iowarp/clio-kit configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to iowarp/clio-kit. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/iowarp/clio-kit/chore/355-remove-wrp-bin/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/iowarp/clio-kit

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/iowarp/clio-kit/claude-md/github.svg)](https://agentmods.dev/instructions/iowarp/clio-kit/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/iowarp/clio-kit/claude-md"><img src="https://agentmods.dev/badge/instructions/iowarp/clio-kit/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/iowarp/clio-kit/claude-md"><img src="https://agentmods.dev/badge/instructions/iowarp/clio-kit/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 4,847 This file is loaded in full into every session.

When invoked 4,847 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.04847	$0.04847
Opus 5.5	$0.01939	$0.01939
Sonnet 5.5	$0.00969	$0.00969
Haiku 4.5	$0.00485	$0.00485

Measured 11d ago against content hash 6e7b45fc4c33, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

clio-kit CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

CLAUDE.md · 534 lines

How it starts

The opening of the file, as written. The whole thing — 534 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

CLIO Kit is part of the IoWarp platform's tooling layer for AI agents. It is a production-grade monorepo containing 15+ MCP (Model Context Protocol) servers designed for scientific computing research, with plans to expand to additional agent capabilities (skills, plugins, extensions). The project enables AI agents and LLMs to interact with HPC resources, scientific data formats, and research datasets through a standardized protocol.

The repository uses a unified launcher with auto-discovery pattern: each MCP server is independently developed and tested, but all are launched through a single clio-kit <server-name> command.

Platform Context: CLIO Kit is the tooling layer of the IoWarp platform, providing comprehensive agent capabilities beyond just MCP servers.

Key Technologies: FastMCP 3.0, Python 3.10+, UV package manager, Pydantic, pytest, Ruff

Project Structure

clio-kit/                           # Monorepo root
├── src/clio_kit/                   # Unified launcher CLI
├── clio-kit-mcp-servers/                # 16 independent MCP servers
│   ├── hdf5/ ⭐                       # Flagship server (v2.0, 28 tools)
│   ├── pandas/                        # Data analysis operations
│   ├── slurm/                         # HPC job management
│   ├── arxiv/                         # Research paper fetching
│   ├── chronolog/                     # Distributed logging
│   ├── compression/                   # File compression
│   ├── darshan/                       # I/O performance analysis
│   ├── jarvis/                        # Data pipeline management
│   ├── lmod/                          # Environment modules
│   ├── ndp/                           # Dataset discovery
│   ├── node-hardware/                 # System hardware info
│   ├── parallel-sort/                 # Large file sorting
│   ├── paraview/                      # Scientific visualization
│   ├── parquet/                       # Parquet file handling
│   ├── plot/                          # Data visualization
│   ├── adios/                         # ADIOS2 data I/O
│   └── [each has its own pyproject.toml, dependencies, tests]
├── clio-agentic-search/             # Standalone hybrid retrieval engine (not an MCP server)
├── clio-kit-website/                # Docusaurus documentation site
├── scripts/                           # Utility scripts (generate_docs.py, etc)
├── .github/workflows/                 # CI/CD automation
└── [root config files]                # pyproject.toml, uv.lock

Read the full file on GitHub · 534 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

1mo ago Changed · -527 lines · -4,813 tokens per session 97b990ed9c5d
2mo ago First seen · 534 lines · 4,847 tokens per session scan A 6e7b45fc4c33

Subscribe to this mod's changes

clio-kit CLAUDE.md is an instructions file published in the GitHub repository iowarp/clio-kit (30 stars, last pushed 9d ago), licensed BSD-3-Clause. It adds 4,847 tokens to every session, about $0.0194 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Research Scientific ai4hpc ai4science hpc hpc-ai mcp mcp-tools

clio-kit CLAUDE.md next to 6 instructions from other repositories
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clio-kit: Instructions file for Claude Code