clio-kit

# CLIO Kit

<!-- mcp-name: io.github.iowarp/adios-mcp -->
<!-- mcp-name: io.github.iowarp/arxiv-mcp -->
<!-- mcp-name: io.github.iowarp/chronolog-mcp -->
<!-- mcp-name: io.github.iowarp/compression-mcp -->
<!-- mcp-name: io.github.iowarp/darshan-mcp -->
<!-- mcp-name: io.github.iowarp/geo-mcp -->
<!-- mcp-name: io.github.iowarp/geojson-mcp -->
<!-- mcp-name: io.github.iowarp/hdf5-mcp -->
<!-- mcp-name: io.github.iowarp/jarvis-mcp -->
<!-- mcp-name: io.github.iowarp/lmod-mcp -->
<!-- mcp-name: io.github.iowarp/ndp-mcp -->
<!-- mcp-name: io.github.iowarp/node-hardware-mcp -->
<!-- mcp-name: io.github.iowarp/pandas-mcp -->
<!-- mcp-name: io.github.iowarp/parallel-sort-mcp -->
<!-- mcp-name: io.github.iowarp/paraview-mcp -->
<!-- mcp-name: io.github.iowarp/parquet-mcp -->
<!-- mcp-name: io.github.iowarp/plot-mcp -->
<!-- mcp-name: io.github.iowarp/sac-mcp -->
<!-- mcp-name: io.github.iowarp/scientific-catalog-mcp -->
<!-- mcp-name: io.github.iowarp/seismic-mcp -->
<!-- mcp-name: io.github.iowarp/slurm-mcp -->
<!-- mcp-name: io.github.iowarp/spack-mcp -->
<!-- mcp-name: io.github.iowarp/terrain-mcp -->

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**CLIO Kit** - Part of the IoWarp platform's tooling layer for AI agents. A comprehensive collection of tools, skills, plugins, and extensions. It ships 22 Model Context Protocol (MCP) servers for scientific computing and enables AI agents to interact with HPC resources, scientific data formats, and research datasets.

[**Website**](https://docs.iowarp.ai/) | [**IOWarp**](https://iowarp.ai)

Chat with us on [**Zulip**](https://iowarp.zulipchat.com/#narrow/channel/543872-Agent-Toolkit) or [**join us**](https://iowarp.zulipchat.com/join/e4wh24du356e4y2iw6x6jeay/)

Developed by <img src="https://grc.iit.edu/img/logo.png" alt="GRC Logo" width="18" height="18"> [**Gnosis Research Center**](https://grc.iit.edu/)

---

## ❌ Without CLIO Kit

Working with scientific data and HPC resources requires manual scripting and tool-specific knowledge:

- ❌ Write custom scripts for every HDF5/Parquet file exploration
- ❌ Manually craft Slurm job submission scripts
- ❌ Switch between multiple tools for data analysis
- ❌ No AI assistance for scientific workflows
- ❌ Repetitive coding for common research tasks

## ✅ With CLIO Kit

AI agents handle scientific computing tasks through natural language:

- ✅ **"Analyze the temperature dataset in this HDF5 file"** - HDF5 MCP does it
- ✅ **"Submit this simulation to Slurm with 32 cores"** - Slurm MCP handles it
- ✅ **"Find papers on neural networks from ArXiv"** - ArXiv MCP searches
- ✅ **"Plot the results from this CSV file"** - Plot MCP visualizes
- ✅ **"Optimize memory usage for this pandas DataFrame"** - Pandas MCP optimizes
- ✅ **"Find all documents where pressure exceeds 200 kPa"** - Agentic Search retrieves

**One unified interface. 22 MCP servers. Hybrid search engine. 150+ specialized tools. Built for research.**

CLIO Kit is part of the IoWarp platform's comprehensive tooling ecosystem for AI agents. It brings AI assistance to your scientific computing workflow—whether you're analyzing terabytes of HDF5 data, managing Slurm jobs across clusters, or exploring research papers. Built by researchers, for researchers, at Illinois Institute of Technology with NSF support.

> **Part of IoWarp Platform**: CLIO Kit is the tooling layer of the IoWarp platform, providing skills, plugins, and extensions for AI agents working in scientific computing environments.

> **One simple command.** Production-ready, fully typed, BSD-3-Clause licensed, and live-tested in real HPC environments.

## 🚀 Quick Installation

### One Command for Any Server

```bash
# Install the released CLI into its own persistent tool environment
uv tool install 'clio-kit==2.4.3'
# If uv reports that its executable directory is not on PATH:
uv tool update-shell

# List all 23 available MCP servers
clio-kit mcp-servers

# Run any installed server
clio-kit mcp-server hdf5
clio-kit mcp-server pandas
clio-kit mcp-server slurm

# Agentic search — hybrid retrieval for scientific corpora
clio-kit search serve               # Start search API server
clio-kit search query --namespace local_fs --q "pressure > 200 kPa"

# AI prompts also available
clio-kit prompts                    # List all prompts
clio-kit prompt code-coverage-prompt # Use a prompt
```

`uv tool install` keeps CLIO Kit in a persistent, isolated tool environment.
Use `uvx --from 'clio-kit==2.4.3' clio-kit ...` only for a temporary, one-shot
invocation.

Released `clio-kit` wheels execute each embedded MCP server from that server's
shipped `uv.lock`. The launcher uses a source-and-lock-addressed environment
under the user cache, installs only production dependencies, and refuses to
resolve an embedded server whose lock is missing. The `--branch` launcher
option is an explicit development path and is not an immutable
release-artifact path.

The root wheel also ships machine-readable user contracts for the locked
JARVIS, SLURM, Spack, and Scientific Catalog servers. These artifacts are generated from real stdio
`tools/list` exchanges and include canonical SHA-256 digests for downstream
federation gates:

```bash
clio-kit mcp-contracts
clio-kit mcp-contract clio-kit-jarvis-user-v3.5
clio-kit mcp-contract clio-kit-slurm-user-v3
clio-kit mcp-contract clio-kit-spack-user-v2.1
clio-kit mcp-contract clio-kit-scientific-catalog-user-v1.1
```

<details>
<summary><b>Install in Cursor</b></summary>

Add to your Cursor `~/.cursor/mcp.json`:

```json
{
  "mcpServers": {
    "hdf5-mcp": {
      "command": "clio-kit",
      "args": ["mcp-server", "hdf5"]
    },
    "pandas-mcp": {
      "command": "clio-kit",
      "args": ["mcp-server", "pandas"]
    },
    "slurm-mcp": {
      "command": "clio-kit",
      "args": ["mcp-server", "slurm"]
    }
  }
}
```

See [Cursor MCP docs](https://docs.cursor.com/context/model-context-protocol) for more info.

</details>

<details>
<summary><b>Install in Claude Code</b></summary>

```bash
# Add HDF5 MCP
claude mcp add hdf5-mcp -- clio-kit mcp-server hdf5

# Add Pandas MCP
claude mcp add pandas-mcp -- clio-kit mcp-server pandas

# Add Slurm MCP
claude mcp add slurm-mcp -- clio-kit mcp-server slurm
```

See [Claude Code MCP docs](https://docs.anthropic.com/en/docs/agents-and-tools/claude-code/tutorials#set-up-model-context-protocol-mcp) for more info.

</details>

<details>
<summary><b>Install in VS Code</b></summary>

Add to your VS Code MCP config:

```json
"mcp": {
  "servers": {
    "hdf5-mcp": {
      "type": "stdio",
      "command": "clio-kit",
      "args": ["mcp-server", "hdf5"]
    },
    "pandas-mcp": {
      "type": "stdio",
      "command": "clio-kit",
      "args": ["mcp-server", "pandas"]
    }
  }
}
```

See [VS Code MCP docs](https://code.visualstudio.com/docs/copilot/chat/mcp-servers) for more info.

</details>

<details>
<summary><b>Install in Claude Desktop</b></summary>

Edit `claude_desktop_config.json`:

```json
{
  "mcpServers": {
    "hdf5-mcp": {
      "command": "clio-kit",
      "args": ["mcp-server", "hdf5"]
    },
    "arxiv-mcp": {
      "command": "clio-kit",
      "args": ["mcp-server", "arxiv"]
    }
  }
}
```

See [Claude Desktop MCP docs](https://modelcontextprotocol.io/quickstart/user) for more info.

</details>

## Available Packages

The version below is each MCP server's agent-facing contract version, not the
containing `clio-kit` wheel version. JARVIS 3.4 and SLURM 3.0 have contracts
redesigned for agent use. Spack is at 2.1, while the other
contracts retain their existing 2.x identities until a focused upgrade.

The Spack install contract makes concretization explicit: `reuse=true` passes
`spack install --reuse`, while `reuse=false` passes `spack install --fresh`.
Agents should discover first, install only when needed, then pass the exact
`spack_locate` result to JARVIS for runtime loading. A find with no installed
match is normal typed data (`count=0`, `packages=[]`); locate reports the
distinct `not_installed` semantic, while real Spack failures remain errors.

<div align="center">

| 📦 **Package** | 📌 **Ver** | 🔧 **System** | 📋 **Description** | ⚡ **Install Command** |
|:---|:---:|:---:|:---|:---|
| **`adios`** | 2.2.3 | Data I/O | Read data using ADIOS2 engine | `clio-kit mcp-server adios` |
| **`arxiv`** | 2.2.3 | Research | Fetch research papers from ArXiv | `clio-kit mcp-server arxiv` |
| **`chronolog`** | 2.0.1 | Logging | Log and retrieve data from ChronoLog | `clio-kit mcp-server chronolog` |
| **`compression`** | 2.2.3 | Utilities | File compression with gzip | `clio-kit mcp-server compression` |
| **`darshan`** | 2.2.3 | Performance | I/O performance trace analysis | `clio-kit mcp-serv