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Backport fix from PR #218 #219

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Merged
lohedges merged 1 commit into from
Sep 21, 2026
Merged

Backport fix from PR #218 #219

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78 changes: 37 additions & 41 deletions src/somd2/runner/_repex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1953,6 +1953,9 @@ def run(self):
# to handle non-integer ratios between the checkpoint and energy frequencies.
next_checkpoint = cycles_per_checkpoint

# Whether the most recent cycle saved the replica exchange state.
is_checkpoint = False

# Perform the replica exchange simulation.
for i in range(cycles):
_logger.info(f"Running dynamics for cycle {i + 1} of {cycles}")
Expand Down Expand Up @@ -2155,54 +2158,18 @@ def run(self):
# Advance the checkpoint threshold.
next_checkpoint += cycles_per_checkpoint

# Guard the repex state and transition matrix saving with a file lock.
lock = _FileLock(self._lock_file)
with lock.acquire(timeout=self._config.timeout.to("seconds")):
# Save the transition matrix.
_logger.info("Saving replica exchange transition matrix")
self._save_transition_matrix()

# Backup the dynamics cache pickle file, if it exists.
if self._repex_state.exists():
_copyfile(
self._repex_state,
self._repex_state.with_suffix(".pkl.bak"),
)

# Pickle the dynamics cache.
_logger.info("Saving replica exchange state")
self._save_sampler_stats()
with open(self._repex_state, "wb") as f:
_pickle.dump(self._dynamics_cache, f)
self._save_repex_state()

dynamics_executor.shutdown(wait=True)
checkpoint_executor.shutdown(wait=True)

# Record the end time for the production block.
prod_end = time()

lock = _FileLock(self._lock_file)
with lock.acquire(timeout=self._config.timeout.to("seconds")):
# Save the final transition matrix.
_logger.info("Saving final replica exchange transition matrix")
self._save_transition_matrix()

# Backup the dynamics cache pickle file, if it exists.
if self._repex_state.exists():
_copyfile(
self._repex_state,
self._repex_state.with_suffix(".pkl.bak"),
)

# Pickle final state of the dynamics cache.
_logger.info("Saving final replica exchange state")
if self._terminal_flip_samplers is not None:
self._dynamics_cache._terminal_flip_stats = [
[s.num_attempted, s.num_accepted]
for s in self._terminal_flip_samplers
]
with open(self._repex_state, "wb") as f:
_pickle.dump(self._dynamics_cache, f)
# Save the final state, unless the last cycle was a checkpoint cycle
# and has just done so.
if not is_checkpoint:
self._save_repex_state(final=True)

# Record the end time.
end = time()
Expand Down Expand Up @@ -3060,6 +3027,35 @@ def _merge_gcmc_stats(self):

return stats if stats else None

def _save_repex_state(self, final=False):
"""
Save the transition matrix and pickle the dynamics cache, backing up
the previous pickle, under the file lock.

Parameters
----------

final: bool
Whether this is the final save of the run, for logging.
"""
label = "final replica exchange" if final else "replica exchange"

lock = _FileLock(self._lock_file)
with lock.acquire(timeout=self._config.timeout.to("seconds")):
_logger.info(f"Saving {label} transition matrix")
self._save_transition_matrix()

if self._repex_state.exists():
_copyfile(
self._repex_state,
self._repex_state.with_suffix(".pkl.bak"),
)

_logger.info(f"Saving {label} state")
self._save_sampler_stats()
with open(self._repex_state, "wb") as f:
_pickle.dump(self._dynamics_cache, f)

def _save_sampler_stats(self):
"""
Save GCMC and terminal flip sampler statistics to the dynamics cache
Expand Down