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Agent skill

Pbs Hpc

by argonne-lcf in argonne-lcf/ChemGraph

Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output.

Apache-2.0Auto-check passedResearch & Science

Install Pbs Hpc

skills CLI
$ npx skills add argonne-lcf/ChemGraph --skill pbs-hpc -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install argonne-lcf/ChemGraph pbs-hpc --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/argonne-lcf/ChemGraph.git skills-src && mkdir -p .claude/skills && cp -r skills-src/src/chemgraph/skills/pbs-hpc .claude/skills/pbs-hpc && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
pbs-hpc
GitHub stars
162
Token cost
~1.2k tokens
SKILL.md length
558 words
Files
5 (incl. references, assets)
Skills in repo
3
Repo updated
First seen
Licence
Apache-2.0

At a glance

Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output.

  • Works in 5 steps: Read the PBS template and write a… → Check input visibility on compute nodes.… → Submit once on the authorized submission… → …
  • ChemGraph execution on Polaris
  • SKILL.md covers Establish the environment, Prepare and track a job and ChemGraph execution boundaries
  • Calls bash

What it does

Pbs Hpc is an agent skill from argonne-lcf/ChemGraph. Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output. Use for qsub, qstat, PBS scripts, allocations, and ChemGraph execution on Polaris, Aurora, or Crux; also Polaris and Aurora environments, MPI/GPU affinity, monitoring, and Aurora /soft access troubleshooting.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including reference files and assets (for example `references/aurora.md`, `references/crux.md` and `references/polaris.md`). Compatibility notes: Submission requires PBS commands on an authorized submission host; compute execution requires an allocation and the site's application environment.

It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Agentic framework for computational chemistry and materials science workflows. The licence is Apache-2.0.

When your agent uses it

  • ChemGraph execution on Polaris
  • Also Polaris and Aurora environments
  • MPI/GPU affinity
  • Aurora /soft access troubleshooting

Example prompts

  • “/pbs-hpc”

Requirements

  • Python 3
  • Compatibility (from SKILL.md): Submission requires PBS commands on an authorized submission host; compute execution requires an allocation and the site's application environment.

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Read the PBS template and write a completed copy
  2. Check input visibility on compute nodes. Arrange staging first when the
  3. Submit once on the authorized submission host, following existing tool approvals.
  4. Inspect with qstat -f JOB_ID; distinguish queued, held, running, and terminal
  5. Inspect stdout/stderr and application result files. A job disappearing from

What it can do on your machine

Read from SKILL.md and the folder at commit e890eb3. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • bash

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • docs.alcf.anl.gov

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

  • Compatibility

    Submission requires PBS commands on an authorized submission host; compute execution requires an allocation and the site's application environment.

    From compatibility in the SKILL.md frontmatter.

Context cost

Pbs Hpc loads about 1.2k tokens when it runs, and up to ~7.9k if it reads all its reference files. Until then it costs about 83 tokens; SKILL.md has 558 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~83
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~7.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from argonne-lcf/ChemGraph at commit e890eb3, republished under its Apache-2.0 licence (© argonne-lcf). 558 words, ~1,220 tokens.

Download SKILL.mdSave it as .claude/skills/pbs-hpc/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
pbs-hpc
description
Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output. Use for qsub, qstat, PBS scripts, allocations, and ChemGraph execution on Polaris, Aurora, or Crux; also Polaris and Aurora environments, MPI/GPU affinity, monitoring, and Aurora /soft access troubleshooting.
compatibility
Submission requires PBS commands on an authorized submission host; compute execution requires an allocation and the site's application environment.
license
Apache-2.0
metadata.authors
Murat Keceli
metadata.maintainers
tdpham2

PBS and HPC workflows

Establish the environment

Identify the target system, submission host, project/account, queue, walltime, node count, required filesystems, and application environment. Obtain missing values from the user or deployment configuration. Do not copy another user's allocation, endpoint, private path, or environment.

Check whether execute runs on that host. A local shell on a laptop cannot run remote PBS commands merely because a skill or an HPC MCP server is attached. When the shell runs on the submission host, write the job files and submit with PBS commands directly. Otherwise use suitable attached HPC tools, or prepare the script and state where the user must submit it.

Read the applicable site reference before choosing launch settings: Polaris, Aurora, or Crux. Consult the linked official guides for current queue limits and site policies.

The Polaris reference includes login-node usage, modules, network proxy setup, queues, MPI/OpenMP examples, CPU/GPU affinity, MPS/MIG, and storage. Read it for Polaris environment setup as well as job submission.

The Aurora reference covers hardware, queue selection, PALS, Intel GPU hierarchy and affinity, monitoring, and group-restricted /soft access. Read it for Aurora operations and environment troubleshooting as well as job submission.

Prepare and track a job

For ASE calculations, also read the chemgraph skill's Python batch example. Write the calculation script in the workspace and run it inside PBS; no MCP server or Parsl is needed.

  1. Read the PBS template and write a completed copy into the execution filesystem. Replace every placeholder, keep PBS directives before executable statements, and quote shell paths. Choose the launch command for the target site and application.
  2. Check input visibility on compute nodes. Arrange staging first when the submitting host and workers do not share files. Validate the script syntax with bash -n when the execution environment provides Bash.
  3. Submit once on the authorized submission host, following existing tool approvals. Save submission evidence and the complete scheduler ID in the run directory.
  4. Inspect with qstat -f JOB_ID; distinguish queued, held, running, and terminal states. Explain scheduler comments rather than submitting duplicate jobs.
  5. Inspect stdout/stderr and application result files. A job disappearing from the active queue does not prove success. Use available job history and exit status, and report missing evidence explicitly. Cancel only the requested job.
Show full SKILL.md (180 more words)Show less

Run this submission sequence from the fresh host run directory after completing and inspecting the files:

bash
set -euo pipefail
bash -n job.pbs
test ! -e job.id
if ! (set -C; : > submission.started) 2>/dev/null; then
    echo "Submission already attempted; inspect PBS before retrying." >&2
    exit 1
fi
qsub job.pbs > job.id 2> qsub.stderr
test -s job.id
cat job.id

Keep the marker and stderr if qsub fails or returns no ID: acceptance can be uncertain. Inspect PBS by job name and run directory before any retry. A later agent session reads the existing job.id, checks that job with qstat -f (or qstat -xf for retained history), and inspects output files without resubmitting. An explicitly requested retry uses a fresh directory after resolving the prior job's state. Cancellation uses qdel JOB_ID only when requested.

PBS command reference: ALCF running jobs.

ChemGraph execution boundaries

ChemGraph's hpc_configs Parsl configurations for these systems use LocalProvider inside existing allocations; they do not acquire a PBS allocation automatically. Aurora and Crux require PBS_NODEFILE; Polaris has a local/testing fallback, which is not evidence of a valid allocation.

Use CHEMGRAPH_WORKER_INIT or the configured Python environment for worker setup. Check the deployment's shared filesystem assumption: Globus Compute workers may not see files written by the submitting server. A Globus endpoint has its own execution configuration and is distinct from direct qsub usage.

© argonne-lcf, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files (references, assets) in src/chemgraph/skills/pbs-hpc of argonne-lcf/ChemGraph.

  • SKILL.md
  • assets/job.pbs.template
  • references/aurora.md
  • references/crux.md
  • references/polaris.md

Open the folder on GitHubat commit e890eb3

Compare with similar skills

Pbs Hpc next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Pymol VisualizationChatMol/ChatMol373—~1.2kAutomated safety check: PassMIT

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Categories

Questions about Pbs Hpc

What does Pbs Hpc do?

Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output. Pbs Hpc is an agent skill from argonne-lcf/ChemGraph. Prepare PBS HPC jobs, choose allocation and filesystem settings, submit and monitor jobs, and diagnose job output.

When should I use Pbs Hpc?

Pbs Hpc fits situations like: chemGraph execution on Polaris; also Polaris and Aurora environments; MPI/GPU affinity; aurora /soft access troubleshooting.

How do I install Pbs Hpc in Claude Code?

Run `npx skills add argonne-lcf/ChemGraph --skill pbs-hpc -a claude-code`. Or copy the skill folder (src/chemgraph/skills/pbs-hpc in argonne-lcf/ChemGraph) into .claude/skills/pbs-hpc in your project. Claude Code loads it when a task matches its description.

How do I install Pbs Hpc in Codex?

Run `npx skills add argonne-lcf/ChemGraph --skill pbs-hpc -a codex`. Or copy the skill folder (src/chemgraph/skills/pbs-hpc in argonne-lcf/ChemGraph) into .agents/skills/pbs-hpc in your project. Codex loads it when a task matches its description.

Can I use Pbs Hpc in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add argonne-lcf/ChemGraph --skill pbs-hpc -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pbs-hpc, .gemini/skills/pbs-hpc, .github/skills/pbs-hpc and .opencode/skills/pbs-hpc in your project.

What does Pbs Hpc need to run?

Going by SKILL.md and its folder, Pbs Hpc needs the command-line tools its instructions call (bash). Our summary lists: Python 3. Compatibility (from SKILL.md): Submission requires PBS commands on an authorized submission host; compute execution requires an allocation and the site's application environment..

Does Pbs Hpc access the network?

SKILL.md names 1 domain. As links in the text: docs.alcf.anl.gov. This is read from the text; nothing was executed.

Is Pbs Hpc safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Pbs Hpc use?

Pbs Hpc is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pbs Hpc use?

About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 6.7k tokens, read only when the agent opens those files.

What are the alternatives to Pbs Hpc?

Skills that share tags, products or a category with Pbs Hpc: Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.7k stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars) and Weather (trpc-group/trpc-agent-go, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pbs Hpc?

argonne-lcf (a GitHub organization) maintains it in argonne-lcf/ChemGraph, which has 162 GitHub stars. The repository holds 3 skills in this directory. The repository was last updated on October 9, 2026.

Source: argonne-lcf/ChemGraph on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.