What is hpc-runtime-doctor?

A troubleshooting guide for jobs that run on high-performance computing clusters, where many CPUs or GPUs work together under a job scheduler.

It helps check CPU, GPU, MPI, OpenMP, CUDA, modules, scratch storage, time limits, job arrays, restart files, and scheduler settings before a retry.

It helps find whether a failed, slow, or terminated materials-simulation job used the wrong resources or environment, instead of blaming the simulation itself.

hpc-runtime-doctor — Skill for Claude Code by HeshamFS

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add HeshamFS/materials-simulation-skills --skill hpc-runtime-doctor

Clone the repo

git clone --depth 1 https://github.com/HeshamFS/materials-simulation-skills

Made for: Claude Code.

Or install hpc-deployment, the plugin that ships this one along with the rest of its 2 skills.

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/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor/github.svg)](https://agentmods.dev/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor)

Your own site

<a href="https://agentmods.dev/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor"><img src="https://agentmods.dev/badge/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor/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/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor"><img src="https://agentmods.dev/badge/skills/heshamfs/materials-simulation-skills/hpc-runtime-doctor.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 99 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,429 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. 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	$0.00099	$0.02429
Opus 5	$0.00049	$0.01215
Sonnet 5	$0.00020	$0.00486
Haiku 4.5	$0.00010	$0.00243

Measured 10d ago against content hash 4855ebeb61ff, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

hpc-runtime-doctor scanned grade A with 1 finding 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 10d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/hpc_runtime_doctor.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

- No `eval`, `exec`, `os.system`, or `subprocess`; the script does not launch a scheduler

skills/hpc-deployment/hpc-runtime-doctor/SKILL.md · 182 lines

How it starts

The opening of the file, as written. The whole thing — 182 lines — stays where its author put it; the contents beside it link to each section on GitHub.

HPC Runtime Doctor

Goal

Turn cluster symptoms into a resource-layout diagnosis, environment checklist, and safe retry plan.

Requirements

Python 3.10+
No external dependencies
Works on Linux, macOS, and Windows

Inputs to Gather

Input	Description	Example
Scheduler	SLURM, PBS, LSF, local	`slurm`
Nodes/tasks/threads	Runtime layout	`2 nodes, 128 tasks, 2 threads`
GPUs	Total (whole-job) GPUs via `--gpus`, or per node via `--gpus-per-node`	`--gpus 4` or `--gpus-per-node 1`
Symptoms	Observed failure	`oom,killed,slow-gpu`
MPI/OpenMP/GPU use	Parallel modes	`mpi+openmp+gpu`
Walltime	Requested time	`12:00:00`
Scratch	Whether scratch is used	`true`

Decision Guidance

Check resource layout before changing physics settings.
Confirm module/compiler/MPI/CUDA consistency before debugging solver behavior.
Treat missing restart files and scratch cleanup as workflow failures, not physics failures.
For GPU jobs, confirm the executable was built with the requested accelerator backend.

Script Outputs

scripts/hpc_runtime_doctor.py emits:

resource_layout (includes tasks_per_node, total_cpus, total gpus, and gpus_per_node)
diagnoses
environment_checks
retry_plan
scheduler_notes
warnings (layout flags such as ranks-per-GPU oversubscription, OpenMP/thread mismatch, and uneven task placement)

In default (non-JSON) mode the script also prints the resource-layout summary, any warnings, environment checks, and retry plan, so the most actionable items are never hidden.

Workflow

--gpus is the total (whole-job) GPU count. Use --gpus-per-node (SLURM --gres=gpu:N semantics) when you know the per-node allocation; total GPUs are then gpus_per_node * nodes and it overrides --gpus.

python3 skills/hpc-deployment/hpc-runtime-doctor/scripts/hpc_runtime_doctor.py \
  --scheduler slurm \
  --nodes 2 \
  --tasks 128 \
  --cpus-per-task 2 \
  --gpus 4 \
  --symptoms oom,slow-gpu \
  --uses-mpi \
  --uses-openmp \
  --uses-gpu \
  --json

Read the full file on GitHub · 182 lines

Files

What ships with it

4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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.

10d ago First seen · 182 lines · 99 tokens per session scan A 4855ebeb61ff

Subscribe to this mod's changes

hpc-runtime-doctor is a skill published in the GitHub repository HeshamFS/materials-simulation-skills (66 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 99 tokens to every session and 2,429 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Debugging LLM Scientific agent-skills agents cli-tools computational-science materials-science

hpc-runtime-doctor

Getting it into your agent

Wrote this? Show the measurements

What it costs to keep this loaded

Grade A, and why

Runs shell commandslowCapability

How it starts

HPC Runtime Doctor

Goal

Requirements

Inputs to Gather

Decision Guidance

Script Outputs

Workflow

What ships with it

What this file has done since we first saw it

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