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Reported issues for CLIO Scientific Catalog

Pod holds 17 of 27 problems reported by people outside the maintainer team. Issues filed by the project's own owners, members and collaborators are excluded entirely — a maintainer's release checklist is not a warning to a prospective user.

Back to CLIO Scientific Catalog.

Most discussed

Campaign: server code health + MCP tasks semantics + scientific-catalog eviction

[clio-kit] Campaign: server code health + MCP tasks semantics + scientific-catalog eviction

Why (owner findings, 2026-08-10)

The kit's MCP servers accreted into mega-files with no size guard; the four infrastructure servers negotiate MCP 2026-07-28 but expose zero tasks semantics for long-running operations; and scientific-catalog entered the kit (2.4.0, #297) without design approval. One unified campaign — the refactor and the tasks work touch the same files and land together, not as s

Read the thread · 2026-08-11 · open · 2 comments

MCP environment cache: no eviction — 72 venvs for 11 servers (43.5 GB); needs LRU/max-per-server + uv cache prune

Storage audit on a heavy-use dev box (clio-agent, one month): ~/.cache/clio-kit held 43.5 GB — uv-cache 33.9 GB and mcp-environments 9.45 GB comprising 72 full venvs for only 11 distinct servers (jarvis ×19, spack ×16, slurm ×7, adios ×7, scientific-catalog ×7...). Each spec/version change builds a NEW env keyed by spec-hash and never deletes the old one; heavy envs are 200–434 MB each, re-installing the same pandas/numpy/rasterio/pyproj/matplotlib stack. The private uv-cache accum

Read the thread · 2026-07-20 · closed · 2 comments

jarvis MCP: interceptor/preloader target-binding lost - add_step cannot express what Darshan wraps (blocks agent I/O instrumentation; contract v3.7.1)

Verified 2026-08-19 (owner recalled the special case; the code is gone):

  • The relay jarvis contract v3.7 (jarvis-user-v3.7.json) has NO interceptor/preloader vocabulary: jarvis_add_step takes only pipeline_id/step_id/package_name/config - an interceptor cannot declare the package it wraps through the wire schema.
  • clio-kit's jarvis MCP (jarvis_handler.py append_pkg) appends every package generically; the only interceptor awareness is a passive read of the pipeline's interceptors l

Read the thread · 2026-08-19 · open · 1 comment

spack server: the agent provisioning loop — typed not-installed → lookup → HITL-approved install-as-task → redeploy

Owner design spec (2026-08-11). The spack MCP exists so that the agent can build packages. The intended product loop:

  1. A deploy attempt on a package whose runtime is absent returns a typed "package not installed" error — not a hang, not an ambiguous probe status, not a silent empty result.
  2. The agent looks the package up on the remote spack (search/info: does a recipe exist, what versions/variants, what would an install entail).
  3. The agent asks the user for approval to install

Read the thread · 2026-08-12 · open · 1 comment

Packaging

A dicsussion shoudl be had around packaging

Read the thread · 2026-08-10 · open · 1 comment

JARVIS package search never indexes declared configuration — stageable-input packages are unreachable by capability queries

Summary

jarvis_mcp/server.py::_package_search_rank ranks a package only over _PackageInventoryEntry = name + short_name + the module docstring scraped by _first_docstring_or_comment. A package's declared settings — including ConfigurationInputBinding declarations, the ONLY signal that a setting is a stageable local-file input — are not in the search corpus at all.

Live consequence (correct-shape relay deployment, 69-package inventory): the only shell package with a stageable `script

Read the thread · 2026-08-07 · closed · 1 comment

Support partial installations with optional dependencies

Add support for installing only specific MCP servers using optional dependencies:

uv pip install iowarp-agent-toolkit[hdf5,adios,parquet]

This would install only the selected servers and their dependencies instead of all 15 servers.

Then run with:

uvx iowarp-agent-toolkit mcp-server hdf5

Benefits:

  • Smaller installation footprint
  • Faster install times
  • Only install what you need

Implementation: Add [project.optional-dependencies] to root pyproject.toml

Read the thread · 2025-11-16 · open · 1 comment

Add BP5 Variable Chunking Support: Adios MCP

Problem Statement

The current read_variable_at_step tool loads entire variables into memory, causing significant issues when working with large scientific datasets:

  • Memory Exhaustion: Variables with huge elements cause out-of-memory errors
  • AI Token Limits: Large arrays overwhelm AI context windows, making analysis impossible
  • Performance Issues: Loading massive multi-dimensional datasets blocks processing
  • Scalability Problems: Time-series and spatial data

Read the thread · 2025-07-29 · open · 1 comment

Most recent

jarvis_add_step: config-level 'target' key collides with the top-level target parameter - raw TypeError instead of a typed refusal

Defect (found live on ares during the clio-relay v1.7.0 darshan acceptance run, kit 2.10.6 / jarvis-cd 1.8.1)

jarvis_add_step with an interceptor-class package requires the v3.7.2 top-level target parameter — correct. But if a caller ALSO carries target inside the step config object (the natural fallback for a client whose tool schema predates v3.7.2), the server crashes with:

append_pkg() got multiple values for keyword argument 'target'

instead of a typed refusal. The han

Read the thread · 2026-08-28 · open · 0 comments

lmod server: the third provisioning leg — module discovery + env resolution as data, same contract as spack/native

Owner direction (2026-08-11): the provisioning story has three legs, and the 2026-08-11 missions proved two of them — spack (LAMMPS: spack DB → resolved prefixes → jarvis environment.yaml snapshot applied as data) and natively-installed apps (gray-scott: absolute executable path + RPATH-baked binary, zero env injection needed). The third leg is module-managed apps via Lmod — the standard mechanism on HPC clusters for natively-installed software — and the owner planned to use the exis

Read the thread · 2026-08-12 · open · 0 comments

ndp: inner 3x30s retry loop silently burns the caller's timeout budget against a single hardcoded plain-HTTP host

Evidence (2026-08-06, clio-agent round-9 live run)

All three parallel ndp children timed out at ~181s on ndp_search_datasets (clio-agent's outer asyncio ceiling is 180s), tightly clustered — then the same call reproduced at ~1.1s 25 minutes later. Mechanism (ndp/src/ndp_mcp/server.py:219-262, NDPClient._make_request):

  • Single hardcoded plain-HTTP host http://155.101.6.191:8003 (NDP pilot), no fallback.
  • httpx.Timeout(30.0) with an internal 3-attempt exponential-backoff retry ON EV

Read the thread · 2026-08-06 · open · 0 comments

Declare MCP tool titles (spec 2025-06-18 tool.title) on every server's tools

Problem

No clio-kit server declares MCP tool display titles. title appears in plot only as a plot-content parameter (plot_mcp/server.py — "Custom title for the plot"), not as tool metadata. Clients therefore render raw identifiers (plot_line_plot, pandas_load_data), and namespacing clients double the prefix (plot_plot_timeline_series).

MCP added a dedicated display-name field in the 2025-06-18 revision: tool.title (with tool.annotations.title as the older 2025-03-26 location).

Read the thread · 2026-08-05 · open · 0 comments

plot server parses the full CSV before applying max_rows — 50MB file needs 180s+ or times out

Live evidence (clio-agent P5 demo runs, 2026-08-04): plot_plot_timeseries against a staged 50,424,246-byte EarthScope CSV (MTA1.CI.LY_.30.csv) timed out at a 30s call ceiling twice WITH max_rows: 500 — the row cap does not reduce the read/parse cost, so the server evidently loads/parses the whole file before slicing. With the ceiling raised to 180s the default-cap attempt still timed out and only a 500-row retry succeeded, so the delivered plot covers 500 of 250,000 rows.

Asks:

  1. Apply t

Read the thread · 2026-08-04 · open · 0 comments

Feature: a cheap resolve probe for locked MCP servers (print the launch plan without spawning)

Context

clio-agent is eliminating the resident launcher overhead of MCP fleets (iowarp/clio-agent#934, campaign iowarp/clio-agent#930). On Windows, clio-kit mcp-server <name> stays resident as a 7-process chain per server (trampoline → bootstrap python → clio-kit CLI → uv run → venv shim → venv python → server): ~90 MB of wrapper overhead per namespace for the life of the fleet, of which only the leaf (~110-180 MB) is the server.

clio-agent now learns the leaf argv from a live chain and

Read the thread · 2026-07-15 · open · 0 comments

Modernize remaining MCPs with agent-oriented contracts and independent server versions

Goal

Modernize the remaining clio-kit MCP servers from one-tool-per-API/CLI wrappers into compact contracts designed around how an agent reasons about a native resource.

JARVIS v3 and Slurm v3 are reference implementations, but the lesson is not simply "fewer tools." The design process is:

  1. Separate user intent from operator, compatibility, and low-level API operations.
  2. Group related verbs and views around the native resource an agent is managing.
  3. Preserve the authoritative native

Read the thread · 2026-07-12 · open · 0 comments

NDP

Please update the readme to be complaint with the expectations of the automated documentation script and the requirments of the repo

Update the main readme to add the new mcp

Read the thread · 2025-08-21 · closed · 0 comments

Data Fusion MCP

Researcb following topics Apache Arrow Apache DataFusion Apache Parquet

Next steps in to integrate it with the Parquet MCP

Read the thread · 2025-08-04 · open · outside contributor · 0 comments

The remaining reports are on the project's issue tracker.