How do I install the Debugging Processes skill?

Run npx skillmds@latest add aiidateam/debugging-processes in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Debugging Processes skill do?

Use when diagnosing failed, stuck, or misbehaving AiiDA processes or the daemon. It is listed under Coding & Dev Tools on SkillMD.

Is Debugging Processes safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Debugging Processes?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Debugging Processes free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Debugging Processes?

aiidateam (@aiidateam) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Debugging Processes by aiidateam — Agent Skill

Name: Debugging Processes
Author: aiidateam

File contents

Debugging processes and the daemon

Inspecting a single process

verdi process status <PK>       # call stack and where execution stopped
verdi process report <PK>       # log messages emitted during execution
verdi process show <PK>         # inputs, outputs, exit code
verdi node show <PK>            # node attributes and extras

For a full provenance dump including input/output files:

verdi process dump <PK>         # dump a process and its provenance

For CalcJobs specifically, jump to the remote working directory on the HPC (requires SSH access, which may not be available for sandboxed agents):

verdi calcjob gotocomputer <PK>

Inspecting the daemon

# storage (PostgreSQL or SQLite) + daemon & broker (RabbitMQ, if configured):
verdi status
# tail daemon logs in real-time
# best with a single daemon worker, multiple workers garble output:
verdi daemon logshow
# requeue processes stuck after a daemon crash (stop the daemon first):
verdi process repair

Common failure modes

Process stuck in waiting : usually means the daemon lost track of it after a crash or restart. Run verdi process repair to requeue.
Process state inconsistent with node attributes : check whether seal() has been called; only _updatable_attributes can change on a stored ProcessNode before sealing.
presto-marked test failures : these use an in-memory SqliteTempBackend, so the bug is in the code, not in service configuration.
Daemon subprocess killed on shutdown : daemon-launched subprocesses must pass start_new_session=True or they inherit the daemon's signal handling and die with it.

Interactive inspection

verdi shell                       # interactive IPython shell with AiiDA loaded
verdi devel run-sql "SELECT ..."  # run raw SQL against the profile database (USE WITH CAUTION)

Useful patterns inside verdi shell:

from aiida.orm import QueryBuilder, Node, load_node

# Find nodes by type
qb = QueryBuilder().append(Node, filters={'node_type': {'like': 'data.core.dict.%'}})

# Inspect a specific node
node = load_node(<PK>)
node.base.attributes.all   # all stored attributes
node.base.extras.all        # all extras (mutable even after storing)
node.base.repository.list_object_names()  # files in the node's repository

Related source

Process runner: src/aiida/engine/runners.py
Daemon client: src/aiida/engine/daemon/client.py
CalcJob exec manager (file copying, job submission, retrieval): src/aiida/engine/daemon/execmanager.py
Transport tasks (submit, update, retrieve): src/aiida/engine/processes/calcjobs/tasks.py

---name: debugging-processesdescription: Use when diagnosing failed, stuck, or misbehaving AiiDA processes or the daemon.---# Debugging processes and the daemon## Inspecting a single process```bashverdi process status <PK> # call stack and where execution stoppedverdi process report <PK> # log messages emitted during executionverdi process show <PK> # inputs, outputs, exit codeverdi node show <PK> # node attributes and extras```For a full provenance dump including input/output files:```bashverdi process dump <PK> # dump a process and its provenance```For CalcJobs specifically, jump to the remote working directory on the HPC (requires SSH access, which may not be available for sandboxed agents):```bashverdi calcjob gotocomputer <PK>```## Inspecting the daemon```bash# storage (PostgreSQL or SQLite) + daemon & broker (RabbitMQ, if configured):verdi status# tail daemon logs in real-time# best with a single daemon worker, multiple workers garble output:verdi daemon logshow# requeue processes stuck after a daemon crash (stop the daemon first):verdi process repair```## Common failure modes- **Process stuck in `waiting`** : usually means the daemon lost track of it after a crash or restart. Run `verdi process repair` to requeue.- **Process state inconsistent with node attributes** : check whether `seal()` has been called; only `_updatable_attributes` can change on a stored `ProcessNode` before sealing.- **`presto`-marked test failures** : these use an in-memory `SqliteTempBackend`, so the bug is in the code, not in service configuration.- **Daemon subprocess killed on shutdown** : daemon-launched subprocesses must pass `start_new_session=True` or they inherit the daemon's signal handling and die with it.## Interactive inspection```bashverdi shell # interactive IPython shell with AiiDA loadedverdi devel run-sql "SELECT ..." # run raw SQL against the profile database (USE WITH CAUTION)```Useful patterns inside `verdi shell`:```pythonfrom aiida.orm import QueryBuilder, Node, load_node# Find nodes by typeqb = QueryBuilder().append(Node, filters={'node_type': {'like': 'data.core.dict.%'}})# Inspect a specific nodenode = load_node(<PK>)node.base.attributes.all # all stored attributesnode.base.extras.all # all extras (mutable even after storing)node.base.repository.list_object_names() # files in the node's repository```## Related source- Process runner: `src/aiida/engine/runners.py`- Daemon client: `src/aiida/engine/daemon/client.py`- CalcJob exec manager (file copying, job submission, retrieval): `src/aiida/engine/daemon/execmanager.py`- Transport tasks (submit, update, retrieve): `src/aiida/engine/processes/calcjobs/tasks.py`

Frequently asked questions

Debugging Processes