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debugging-processes

Testing & Quality
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Use when diagnosing failed, stuck, or misbehaving AiiDA processes or the daemon.

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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