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only print when verbosity > 0, otherwise nothing is printed (bad)
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@lmseidler
lmseidler committed Jan 16, 2025
1 parent 42fcfca commit a65637f
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added
- `GXTBConfig` class for the g-xTB method, supporting SCF cycles check
- updated the parallelization to work over the number of molecules

### Fixed
- version string is now correctly formatted and printed
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148 changes: 83 additions & 65 deletions src/mindlessgen/generator/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@
from concurrent.futures import Future, as_completed, wait
from pathlib import Path
import multiprocessing as mp
from threading import Event
from threading import Event, Thread
from queue import Queue, Empty
import warnings
from dataclasses import dataclass

Expand All @@ -30,6 +31,15 @@ class Block:
ncores: int


def printer_thread(msg_queue: Queue[str], stop_event: Event):
while not stop_event.is_set() or not msg_queue.empty():
try:
msg = msg_queue.get(timeout=0.1)
print(msg)
except Empty:
continue


def generator(config: ConfigManager) -> tuple[list[Molecule], int]:
"""
Generate a molecule.
Expand Down Expand Up @@ -84,24 +94,31 @@ def generator(config: ConfigManager) -> tuple[list[Molecule], int]:
if config.general.verbosity > 0:
print(f"\n--- Appending to existing file '{MINDLESS_MOLECULES_FILE}'. ---")

backup_verbosity: int | None = None
if num_cores > 1 and config.general.verbosity > 0:
backup_verbosity = config.general.verbosity # Save verbosity level for later
config.general.verbosity = 0 # Disable verbosity if parallel

exitcode = 0
optimized_molecules: list[Molecule] = []

# Initialize parallel blocks here
blocks = setup_blocks(num_cores, config.general.num_molecules)
blocks.sort(key=lambda x: x.ncores)

backup_verbosity: int | None = None
if len(blocks) > 1 and config.general.verbosity > 0:
backup_verbosity = config.general.verbosity # Save verbosity level for later
config.general.verbosity = 0 # Disable verbosity if parallel
# NOTE: basically no messages will be printed if generation is run in parallel

# Set up parallel blocks environment
with setup_managers(num_cores // MINCORES_PLACEHOLDER, num_cores) as (
executor,
_,
manager,
resources,
):
# Prepare a message queue and printer thread
# msg_queue = Queue()
# stop_event = manager.Event()
# printer = Thread(target=printer_thread, args=(msg_queue, stop_event))
# printer.start()

# The following creates a queue of futures which occupy a certain number of cores each
# as defined by each block
# Each future represents the generation of one molecule
Expand All @@ -110,11 +127,10 @@ def generator(config: ConfigManager) -> tuple[list[Molecule], int]:
tasks: list[Future[Molecule | None]] = []
for block in blocks:
for _ in range(block.num_molecules):
# TODO: remove objects from future call that cannot be pickled (basically everything that doesn't consist only of primitives)
tasks.append(
executor.submit(
single_molecule_generator,
len(tasks) + 1,
len(tasks),
config,
resources,
refine_engine,
Expand All @@ -126,34 +142,36 @@ def generator(config: ConfigManager) -> tuple[list[Molecule], int]:
# Collect results of all tries to create a molecule
results: list[Molecule | None] = [task.result() for task in as_completed(tasks)]

# Restore verbosity level if it was changed
if backup_verbosity is not None:
config.general.verbosity = backup_verbosity
# Stop the printer thread if necessary
# stop_event.set()
# printer.join()

for molcount, optimized_molecule in enumerate(results):
if optimized_molecule is None:
# TODO: molcount might not align with the number of the molecule that actually failed, look into this
warnings.warn(
"Molecule generation including optimization (and postprocessing) "
+ f"failed for all cycles for molecule {molcount + 1}."
)
exitcode = 1
continue

# if config.general.verbosity > 0:
# print(f"Optimized mindless molecule found in {cycles_needed} cycles.")
# print(optimized_molecule)

if config.general.write_xyz:
optimized_molecule.write_xyz_to_file()
if config.general.verbosity > 0:
print(
f"Written molecule file 'mlm_{optimized_molecule.name}.xyz'.\n"
)
with open("mindless.molecules", "a", encoding="utf8") as f:
f.write(f"mlm_{optimized_molecule.name}\n")
# Restore verbosity level if it was changed
if backup_verbosity is not None:
config.general.verbosity = backup_verbosity

for molcount, optimized_molecule in enumerate(results):
if optimized_molecule is None:
# TODO: molcount might not align with the number of the molecule that actually failed, look into this
warnings.warn(
"Molecule generation including optimization (and postprocessing) "
+ f"failed for all cycles for molecule {molcount + 1}."
)
exitcode = 1
continue

# if config.general.verbosity > 0:
# print(f"Optimized mindless molecule found in {cycles_needed} cycles.")
# print(optimized_molecule)

if config.general.write_xyz:
optimized_molecule.write_xyz_to_file()
if config.general.verbosity > 0:
print(f"Written molecule file 'mlm_{optimized_molecule.name}.xyz'.\n")
with open("mindless.molecules", "a", encoding="utf8") as f:
f.write(f"mlm_{optimized_molecule.name}\n")

optimized_molecules.append(optimized_molecule)
optimized_molecules.append(optimized_molecule)

return optimized_molecules, exitcode

Expand All @@ -173,13 +191,13 @@ def single_molecule_generator(
# Wait for enough cores (cores freed automatically upon leaving managed context)
with resources.occupy_cores(ncores):
# print a decent header for each molecule iteration
# if config.general.verbosity > 0:
# print(f"\n{'='*80}")
# print(
# f"{'='*22} Generating molecule {molcount + 1:<4} of "
# + f"{config.general.num_molecules:<4} {'='*24}"
# )
# print(f"{'='*80}")
if config.general.verbosity > 0:
print(f"\n{'='*80}")
print(
f"{'='*22} Generating molecule {molcount + 1:<4} of "
+ f"{config.general.num_molecules:<4} {'='*24}"
)
print(f"{'='*80}")

with setup_managers(ncores, ncores) as (executor, manager, resources_local):
stop_event = manager.Event()
Expand Down Expand Up @@ -220,9 +238,9 @@ def single_molecule_generator(
optimized_molecule = result
break

# if config.general.verbosity > 0:
# print(f"Optimized mindless molecule found in {cycles_needed} cycles.")
# print(optimized_molecule)
if config.general.verbosity > 0:
print(f"Optimized mindless molecule found in {cycles_needed} cycles.")
print(optimized_molecule)

return optimized_molecule

Expand All @@ -243,8 +261,8 @@ def single_molecule_step(
# if config.general.verbosity == 0:
# # print the cycle in one line, not starting a new line
# print("✔", end="", flush=True)
# elif config.general.verbosity > 0:
# print(f"Cycle {cycle + 1}:")
if config.general.verbosity > 0:
print(f"Cycle {cycle + 1}:")

# _____ _
# / ____| | |
Expand All @@ -260,17 +278,17 @@ def single_molecule_step(
except (
SystemExit
) as e: # debug functionality: raise SystemExit to stop the whole execution
# if config.general.verbosity > 0:
# print(f"Generation aborted for cycle {cycle + 1}.")
# if config.general.verbosity > 1:
# print(e)
if config.general.verbosity > 0:
print(f"Generation aborted for cycle {cycle + 1}.")
if config.general.verbosity > 1:
print(e)
stop_event.set()
return None
except RuntimeError as e:
# if config.general.verbosity > 0:
# print(f"Generation failed for cycle {cycle + 1}.")
# if config.general.verbosity > 1:
# print(e)
if config.general.verbosity > 0:
print(f"Generation failed for cycle {cycle + 1}.")
if config.general.verbosity > 1:
print(e)
return None

try:
Expand All @@ -291,10 +309,10 @@ def single_molecule_step(
verbosity=config.general.verbosity,
)
except RuntimeError as e:
# if config.general.verbosity > 0:
# print(f"Refinement failed for cycle {cycle + 1}.")
# if config.general.verbosity > 1 or config.refine.debug:
# print(e)
if config.general.verbosity > 0:
print(f"Refinement failed for cycle {cycle + 1}.")
if config.general.verbosity > 1 or config.refine.debug:
print(e)
return None
finally:
if config.refine.debug:
Expand All @@ -310,16 +328,16 @@ def single_molecule_step(
verbosity=config.general.verbosity,
)
except RuntimeError as e:
# if config.general.verbosity > 0:
# print(f"Postprocessing failed for cycle {cycle + 1}.")
# if config.general.verbosity > 1 or config.postprocess.debug:
# print(e)
if config.general.verbosity > 0:
print(f"Postprocessing failed for cycle {cycle + 1}.")
if config.general.verbosity > 1 or config.postprocess.debug:
print(e)
return None
finally:
if config.postprocess.debug:
stop_event.set() # Stop further runs if debugging of this step is enabled
# if config.general.verbosity > 1:
# print("Postprocessing successful.")
if config.general.verbosity > 1:
print("Postprocessing successful.")

if not stop_event.is_set():
stop_event.set() # Signal other processes to stop
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