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Make TS adapter spawning degrade gracefully instead of silently or fatally #996

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Make TS adapter spawning degrade gracefully instead of silently or fatally #996

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2 changes: 1 addition & 1 deletion arc/exceptions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ class ConverterError(Exception):

class DependencyError(Exception):
"""
An exception raised when converting molecular representations.
An exception raised when a required external dependency is not installed or configured.
"""
pass

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3 changes: 2 additions & 1 deletion arc/job/adapters/ts/autotst_ts.py
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Expand Up @@ -9,6 +9,7 @@
from typing import TYPE_CHECKING

from arc.common import almost_equal_coords, ARC_PATH, get_logger, read_yaml_file
from arc.exceptions import DependencyError
from arc.imports import settings
from arc.job.adapter import JobAdapter
from arc.job.adapters.common import _initialize_adapter
Expand Down Expand Up @@ -215,7 +216,7 @@ def execute_incore(self):
participates in its well, so a well with a repeated species stays atom-balanced.
"""
if not AUTOTST_PYTHON or not os.path.isfile(AUTOTST_PYTHON):
raise FileNotFoundError('AutoTST python executable was not found. '
raise DependencyError('AutoTST python executable was not found. '
'Make sure the tst_env exists and AUTOTST_PYTHON is configured. '
f'See {self.url} for more information, or use the Makefile provided with ARC.')
self._log_job_execution()
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3 changes: 2 additions & 1 deletion arc/job/adapters/ts/kinbot_test.py
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Expand Up @@ -13,6 +13,7 @@
from unittest import mock

from arc.common import ARC_TESTING_PATH, get_logger, read_yaml_file, save_yaml_file
from arc.exceptions import DependencyError
import arc.job.adapters.ts.kinbot_ts as kinbot_ts
from arc.reaction import ARCReaction
from arc.species import ARCSpecies
Expand Down Expand Up @@ -84,7 +85,7 @@ def test_missing_kinbot_python(self):
"""Test that execute_incore() raises if the kinbot_env python executable is missing."""
adapter = self.get_adapter(dir_name='tst_missing_python')
with mock.patch.object(kinbot_ts, 'KINBOT_PYTHON', None):
with self.assertRaises(FileNotFoundError):
with self.assertRaises(DependencyError):
adapter.execute_incore()

def test_intra_h_migration(self):
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3 changes: 2 additions & 1 deletion arc/job/adapters/ts/kinbot_ts.py
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Expand Up @@ -14,6 +14,7 @@
from typing import TYPE_CHECKING

from arc.common import ARC_PATH, almost_equal_coords, get_logger, read_yaml_file, save_yaml_file
from arc.exceptions import DependencyError
from arc.imports import settings
from arc.job.adapter import JobAdapter
from arc.job.adapters.common import _initialize_adapter
Expand Down Expand Up @@ -250,7 +251,7 @@ def execute_incore(self):
Execute a job incore.
"""
if not KINBOT_PYTHON or not os.path.isfile(KINBOT_PYTHON):
raise FileNotFoundError('The KinBot python executable was not found. '
raise DependencyError('The KinBot python executable was not found. '
'Make sure the kinbot_env exists and KINBOT_PYTHON is configured '
'(run devtools/install_kinbot.sh to create the environment). '
f'See {self.url} for more information.')
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53 changes: 44 additions & 9 deletions arc/scheduler.py
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Expand Up @@ -30,7 +30,8 @@
sort_two_lists_by_the_first,
torsions_to_scans,
)
from arc.exceptions import (InputError,
from arc.exceptions import (DependencyError,
InputError,
SchedulerError,
SpeciesError,
TrshError,
Expand Down Expand Up @@ -1855,10 +1856,9 @@ def spawn_ts_jobs(self):
logger.info(f'Not spawning TS search jobs for reaction {rxn} for which the multiplicity is unknown.')
else:
rxn.ts_species.tsg_spawned = True
tsg_index = 0
tsg_index, eligible_methods = 0, list()
family_known = rxn.family is not None and rxn.family in ts_adapters_by_rmg_family
for method in self.ts_adapters:
family_known = (rxn.family is not None
and rxn.family in ts_adapters_by_rmg_family)
admit_unknown_family = (not family_known
and method in ts_adapters_for_unknown_unimolecular
and rxn.is_unimolecular())
Expand All @@ -1870,12 +1870,47 @@ def spawn_ts_jobs(self):
logger.info(f'Admitting TS adapter {method!r} for reaction {rxn.label} '
f'via ts_adapters_for_unknown_unimolecular '
f'(RMG family is {rxn.family!r}).')
self.run_job(job_type='tsg',
job_adapter=method,
reactions=[rxn],
tsg=tsg_index,
)
eligible_methods.append(method)
try:
self.run_job(job_type='tsg',
job_adapter=method,
reactions=[rxn],
tsg=tsg_index,
)
except DependencyError as e:
# An optional adapter's backend (e.g. KinBot, AutoTST) is not installed;
# record it and carry on so one missing dependency can't abort the run.
logger.error(f'The {method!r} TS search adapter is not available and '
f'was skipped for reaction {rxn.label}: {e}')
if method not in rxn.ts_species.unsuccessful_methods:
rxn.ts_species.unsuccessful_methods.append(method)
# Roll back the job run_job() registered before it raised, so a
# never-run 'tsg<i>' entry isn't serialized and parsed as completed.
if f'tsg{tsg_index}' in self.running_jobs.get(rxn.ts_label, list()):
self.running_jobs[rxn.ts_label].remove(f'tsg{tsg_index}')
self.job_dict.get(rxn.ts_label, dict()).get('tsg', dict()).pop(tsg_index, None)
continue
tsg_index += 1
if not tsg_index and not rxn.ts_species.ts_guesses:
# No adapter ran and no user guess was given, and tsg_spawned is already
# latched True, so warn explicitly rather than fail silently much later.
eligible = ts_adapters_by_rmg_family.get(rxn.family) if family_known else None
if eligible_methods:
reason = (f'all of its eligible adapters {eligible_methods} are unavailable '
f'on this machine (see the errors above). Install one of them, or add '
f'an eligible adapter that is installed')
else:
reason = (f'none of the configured ts_adapters {self.ts_adapters} is eligible for it. '
+ (f'Its RMG family {rxn.family!r} admits {eligible}; the two lists do '
f'not intersect.' if eligible is not None else
f'Its RMG family {rxn.family!r} is not in ts_adapters_by_rmg_family, '
f'and it did not qualify for {ts_adapters_for_unknown_unimolecular} '
f'(is_unimolecular={rxn.is_unimolecular()}).')
+ ' Add an eligible adapter to ts_adapters')
logger.warning(f'Not spawning any TS search job for reaction {rxn.label}: {reason} '
f'(in the input file or in ~/.arc/settings.py) to compute this TS. '
f'No TS guess will be generated and this reaction will be reported '
f'as not converged.')
if all('user guess' in tsg.method for tsg in rxn.ts_species.ts_guesses):
rxn.ts_species.tsg_spawned = True
self.run_conformer_jobs(labels=[rxn.ts_label])
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