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Removing changed the writing of the output directory from PosixPath t…
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…o Path in as_dict, removing lambda symbols on windows, changed filenames in test_logfile_creation
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@mb2055
mb2055 committed Nov 7, 2023
1 parent 8b40942 commit 595d86b
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Showing 4 changed files with 39 additions and 25 deletions.
4 changes: 2 additions & 2 deletions src/somd2/config/_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,13 +310,13 @@ def as_dict(self, sire_compatible=False):
this simply converts any options with a value of None to a
boolean with the value False.
"""
from pathlib import PosixPath as _PosixPath
from pathlib import Path as _Path
from sire.cas import LambdaSchedule as _LambdaSchedule

d = {}
for attr, value in self.__dict__.items():
attr_l = attr[1:]
if isinstance(value, _PosixPath):
if isinstance(value, _Path):
d[attr_l] = str(value)
else:
try:
Expand Down
17 changes: 11 additions & 6 deletions src/somd2/runner/_dynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
#####################################################################

__all__ = ["Dynamics"]

import os as _os
from pathlib import Path as _Path

from ..config import Config as _Config
Expand All @@ -29,6 +29,11 @@

from somd2 import _logger

if _os.platform == "win32":
lam_sym = "lambda"
else:
lam_sym = "λ"


class Dynamics:
"""
Expand Down Expand Up @@ -191,7 +196,7 @@ def _minimisation(self, lambda_min=None):
lambda_val.
"""
if lambda_min is None:
_logger.info(f"Minimising at λ = {self._lambda_val}")
_logger.info(f"Minimising at {lam_sym} = {self._lambda_val}")
try:
m = self._system.minimisation(
cutoff_type=self._config.cutoff_type,
Expand All @@ -206,7 +211,7 @@ def _minimisation(self, lambda_min=None):
except:
raise
else:
_logger.info(f"Minimising at λ = {lambda_min}")
_logger.info(f"Minimising at {lam_sym} = {lambda_min}")
try:
m = self._system.minimisation(
cutoff_type=self._config.cutoff_type,
Expand All @@ -229,7 +234,7 @@ def _equilibration(self):
Currently just runs dynamics without any saving
"""

_logger.info(f"Equilibrating at λ = {self._lambda_val}")
_logger.info(f"Equilibrating at {lam_sym} = {self._lambda_val}")
self._setup_dynamics(equilibration=True)
self._dyn.run(
self._config.equilibration_time,
Expand Down Expand Up @@ -282,7 +287,7 @@ def generate_lam_vals(lambda_base, increment):
else:
lam_arr = self._lambda_array + self._lambda_grad

_logger.info(f"Running dynamics at λ = {self._lambda_val}")
_logger.info(f"Running dynamics at {lam_sym} = {self._lambda_val}")

if self._config.checkpoint_frequency.value() > 0.0:
### Calc number of blocks and remainder (surely there's a better way?)###
Expand Down Expand Up @@ -343,7 +348,7 @@ def generate_lam_vals(lambda_base, increment):
df.iloc[-int(energy_per_block) :],
)
_logger.info(
f"Finished block {x+1} of {num_blocks} for λ = {self._lambda_val}"
f"Finished block {x+1} of {num_blocks} for {lam_sym} = {self._lambda_val}"
)
except:
raise
Expand Down
40 changes: 25 additions & 15 deletions src/somd2/runner/_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@

__all__ = ["Runner"]


import os as _os
from sire import stream as _stream
from sire.system import System as _System

Expand All @@ -31,6 +31,11 @@

from somd2 import _logger

if _os.platform == "win32":
lam_sym = "lambda"
else:
lam_sym = "λ"


class Runner:
"""
Expand Down Expand Up @@ -456,7 +461,7 @@ def _initialise_simulation(self, system, lambda_value, device=None):
has_space=self._has_space,
)
except:
_logger.warning(f"System creation at λ = {lambda_value} failed")
_logger.warning(f"System creation at {lam_sym} = {lambda_value} failed")
raise

def _cleanup_simulation(self):
Expand Down Expand Up @@ -521,8 +526,9 @@ def run(self):
result = job.result()
except Exception as e:
result = False

_logger.error(
f"Exception raised for λ = {lambda_value}: {e}"
f"Exception raised for {lam_sym} = {lambda_value}: {e}"
)
with self._lock:
results.append(result)
Expand Down Expand Up @@ -583,8 +589,8 @@ def _run(sim):
return df, lambda_grad, speed
except Exception as e:
_logger.warning(
f"Minimisation/dynamics at λ = {lambda_value} failed with the "
f"following exception {e}, trying again with minimsation at λ = 0."
f"Minimisation/dynamics at {lam_sym} = {lambda_value} failed with the "
f"following exception {e}, trying again with minimsation at {lam_sym} = 0."
)
try:
df = sim._run(lambda_minimisation=0.0)
Expand All @@ -593,8 +599,8 @@ def _run(sim):
return df, lambda_grad, speed
except Exception as e:
_logger.error(
f"Minimisation/dynamics at λ = {lambda_value} failed, even after "
f"minimisation at λ = 0. The following warning was raised: {e}."
f"Minimisation/dynamics at {lam_sym} = {lambda_value} failed, even after "
f"minimisation at {lam_sym} = 0. The following warning was raised: {e}."
)
raise
else:
Expand All @@ -605,7 +611,7 @@ def _run(sim):
return df, lambda_grad, speed
except Exception as e:
_logger.error(
f"Dynamics at λ = {lambda_value} failed. The following warning was "
f"Dynamics at {lam_sym} = {lambda_value} failed. The following warning was "
f"raised: {e}. This may be due to a lack of minimisation."
)

Expand All @@ -619,18 +625,20 @@ def _run(sim):
).clone()
except:
_logger.warning(
f"Unable to load checkpoint file for λ={lambda_value}, starting from scratch."
f"Unable to load checkpoint file for {lam_sym}={lambda_value}, starting from scratch."
)
else:
system = self._system.clone()
if self._config.restart:
acc_time = system.time()
if acc_time > self._config.runtime - self._config.timestep:
_logger.success(f"λ = {lambda_value} already complete. Skipping.")
_logger.success(
f"{lam_sym} = {lambda_value} already complete. Skipping."
)
return True
else:
_logger.debug(
f"Restarting λ = {lambda_value} at time {acc_time}, time remaining = {self._config.runtime - acc_time}"
f"Restarting {lam_sym} = {lambda_value} at time {acc_time}, time remaining = {self._config.runtime - acc_time}"
)
# GPU platform.
if self._is_gpu:
Expand All @@ -639,11 +647,13 @@ def _run(sim):
gpu_num = self._gpu_pool[0]
self._remove_gpu_from_pool(gpu_num)
if lambda_value is not None:
_logger.info(f"Running λ = {lambda_value} on GPU {gpu_num}")
_logger.info(
f"Running {lam_sym} = {lambda_value} on GPU {gpu_num}"
)
# Assumes that device for non-parallel GPU jobs is 0
else:
gpu_num = 0
_logger.info("Running λ = {lambda_value} on GPU 0")
_logger.info("Running {lam_sym} = {lambda_value} on GPU 0")
self._initialise_simulation(system, lambda_value, device=gpu_num)
try:
df, lambda_grad, speed = _run(self._sim)
Expand All @@ -660,7 +670,7 @@ def _run(sim):

# All other platforms.
else:
_logger.info(f"Running λ = {lambda_value}")
_logger.info(f"Running {lam_sym} = {lambda_value}")

self._initialise_simulation(system, lambda_value)
try:
Expand All @@ -685,5 +695,5 @@ def _run(sim):
filename=self._fnames[lambda_value]["energy_traj"],
)
del system
_logger.success(f"λ = {lambda_value} complete")
_logger.success(f"{lam_sym} = {lambda_value} complete")
return True
3 changes: 1 addition & 2 deletions tests/runner/test_config.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -82,10 +82,9 @@ def test_logfile_creation():
config = Config(output_directory=tmpdir, log_file="test.log")
assert config.log_file is not None
assert Path.exists(config.output_directory / config.log_file)
Path.unlink(config.output_directory / config.log_file)

# Instantiate a runner using the default config.
# (All default options, other than platform="cpu".)
runner = Runner(mols, Config(output_directory=tmpdir, log_file="test.log"))
runner = Runner(mols, Config(output_directory=tmpdir, log_file="test1.log"))
assert runner._config.log_file is not None
assert Path.exists(runner._config.output_directory / runner._config.log_file)

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