def __init__(
self,
bout_paths: Optional[BoutPaths] = None,
submitter: Optional[LocalSubmitter] = None,
run_parameters: Optional[RunParameters] = None,
restart_from: Optional[Path] = None,
) -> None:
"""
Set the input parameters.
Parameters
----------
bout_paths : BoutPaths or None
Object containing the paths
If None, default BoutPaths values will be used
submitter : AbstractSubmitter
Object containing the submitter
run_parameters : RunParameters or None
Object containing the run parameters
If None, default parameters will be used
restart_from : Path or None
The path to copy the restart files from
"""
# Set member data
self.restart_from = restart_from
# NOTE: We are not setting the default as a keyword argument
# as this would mess up the paths
self.submitter = submitter if submitter is not None else LocalSubmitter(
)
self.__bout_paths = bout_paths if bout_paths is not None else BoutPaths(
)
self.__run_parameters = (run_parameters if run_parameters is not None
else RunParameters())
self.__make = Make(self.__bout_paths.project_path)
def __init__(
self,
bout_paths: Optional[BoutPaths] = None,
submitter: Optional[AbstractSubmitter] = None,
run_parameters: Optional[RunParameters] = None,
restart_from: Optional[Path] = None,
) -> None:
"""
Set the input parameters.
Parameters
----------
bout_paths : BoutPaths or None
Object containing the paths
If None, default BoutPaths values will be used
submitter : AbstractSubmitter
Object containing the submitter
run_parameters : RunParameters or None
Object containing the run parameters
If None, default parameters will be used
restart_from : Path or None
The path to copy the restart files from
"""
# NOTE: We are not setting the default as a keyword argument
# as this would mess up the paths
# NOTE: We are deepcopying bout_paths as it may be altered by for
# example the self.restart_from setter
logging.info("Start: Making an BoutRunExecutor object")
self.__bout_paths = (
deepcopy(bout_paths) if bout_paths is not None else BoutPaths()
)
self.__run_parameters = (
run_parameters if run_parameters is not None else RunParameters()
)
self.__make = Make(self.__bout_paths.project_path)
self.submitter = submitter if submitter is not None else get_submitter()
if isinstance(self.submitter, AbstractClusterSubmitter):
self.submitter.store_dir = self.__bout_paths.bout_inp_dst_dir
self.__restart_from = None
self.restart_from = restart_from
logging.info("Done: Making an BoutRunExecutor object")
def make_make_object(yield_bout_path: Path) -> Iterator[Tuple[Make, Path]]:
"""
Set up and tear down the make-object.
In order not to make collisions with the global fixture which makes the
`conduction` program, this fixture copies the content of the `conduction`
directory to a `tmp` directory, which is removed in the teardown.
This fixture calls make_obj.run_clean() before the yield statement.
Parameters
----------
yield_bout_path : Path
Path to the BOUT++ repository. See the yield_bout_path fixture for more details
Yields
------
make_obj : MakeProject
The object to call make and make clean from
exec_file : Path
The path to the executable
See Also
--------
tests.bout_runners.conftest.get_bout_directory : Fixture returning the BOUT++ path
"""
# Setup
bout_path = yield_bout_path
project_path = bout_path.joinpath("examples", "conduction")
tmp_path = project_path.parent.joinpath("tmp_make")
copy_tree(str(project_path), str(tmp_path))
exec_file = tmp_path.joinpath("conduction")
make_obj = Make(makefile_root_path=tmp_path)
make_obj.run_clean()
yield make_obj, exec_file
# Teardown
remove_tree(str(tmp_path))
def make_project(yield_conduction_path: Path) -> Iterator[Path]:
"""
Set up and tear down the Make object.
The method calls make_obj.run_clean() before and after the yield statement
Parameters
----------
yield_conduction_path : Path
Path to the BOUT++ conduction example
See the yield_conduction_path for more details
Yields
------
project_path : Path
The path to the conduction example
"""
# Setup
project_path = yield_conduction_path
make_obj = Make(makefile_root_path=project_path)
make_obj.run_make()
yield project_path
# Teardown
make_obj.run_clean()
def __init__(
self,
db_connector: DatabaseConnector,
bout_paths: BoutPaths,
final_parameters: FinalParameters,
) -> None:
"""
Set the database to use.
Parameters
----------
db_connector : DatabaseConnector
The database connector
bout_paths : BoutPaths
Object containing the paths
final_parameters : FinalParameters
Object containing the final parameters
"""
self.__db_writer = DatabaseWriter(db_connector)
self.__db_reader = DatabaseReader(db_connector)
self.__bout_paths = bout_paths
self.__final_parameters = final_parameters
self.__make = Make(self.__bout_paths.project_path)
class Executor:
r"""
Executes the command for submitting a run.
Attributes
----------
__bout_paths : BoutPaths
Getter variable for project_path
__run_parameters : RunParameters
Object containing the run parameters
__make : Make
Object for making the project
restart_from : None or Path
Path to copy restart files from prior to the execution
submitter : AbstractSubmitter
Object containing the submitter
bout_paths : BoutPaths
Object containing the paths
run_parameters : RunParameters
Object containing the run parameters
Methods
-------
get_execute_command()
Return the execute command string
execute()
Execute a BOUT++ run
Examples
--------
The easiest way to use the Executor is to run a script from the root directory of
the project (i.e. where the `Makefile` and `data` directory are normally
situated. The script can simply call
>>> Executor().execute()
and `Executor` takes care of the rest.
A more elaborate example where all the dependency objects are built manually:
Import the dependencies
>>> from pathlib import Path
>>> from bout_runners.executor.bout_paths import BoutPaths
>>> from bout_runners.submitter.local_submitter import LocalSubmitter
Create the `bout_paths` object
>>> project_path = Path().joinpath('path', 'to', 'project')
>>> bout_inp_src_dir = Path().joinpath('path', 'to', 'source', 'BOUT.inp')
>>> bout_inp_dst_dir = Path().joinpath('path', 'to', 'destination', 'BOUT.inp')
>>> bout_paths = BoutPaths(project_path=project_path,
... bout_inp_src_dir=bout_inp_src_dir,
... bout_inp_dst_dir=bout_inp_dst_dir)
Create the executor object
>>> run_parameters = RunParameters({'global': {'nout': 0}})
>>> executor = Executor(
... bout_paths=bout_paths,
... submitter=LocalSubmitter(bout_paths.project_path),
... run_parameters=run_parameters)
Execute the run
>>> executor.execute()
"""
def __init__(
self,
bout_paths: Optional[BoutPaths] = None,
submitter: Optional[LocalSubmitter] = None,
run_parameters: Optional[RunParameters] = None,
restart_from: Optional[Path] = None,
) -> None:
"""
Set the input parameters.
Parameters
----------
bout_paths : BoutPaths or None
Object containing the paths
If None, default BoutPaths values will be used
submitter : AbstractSubmitter
Object containing the submitter
run_parameters : RunParameters or None
Object containing the run parameters
If None, default parameters will be used
restart_from : Path or None
The path to copy the restart files from
"""
# Set member data
self.restart_from = restart_from
# NOTE: We are not setting the default as a keyword argument
# as this would mess up the paths
self.submitter = submitter if submitter is not None else LocalSubmitter(
)
self.__bout_paths = bout_paths if bout_paths is not None else BoutPaths(
)
self.__run_parameters = (run_parameters if run_parameters is not None
else RunParameters())
self.__make = Make(self.__bout_paths.project_path)
@property
def bout_paths(self) -> BoutPaths:
"""
Set the properties of self.bout_paths.
Returns
-------
self.__bout_paths : BoutPaths
Object containing the paths
Notes
-----
The bout_paths is read only
"""
return self.__bout_paths
@property
def run_parameters(self):
"""
Set the properties of self.run_parameters.
Returns
-------
self.__run_parameters : RunParameters
Object containing the run parameters
Notes
-----
The run_parameters is read only
"""
return self.__run_parameters
def get_execute_command(self) -> str:
"""
Return the execute command string.
Returns
-------
command : str
The terminal command for executing the run
"""
mpi_cmd = "mpirun -np"
# NOTE: No spaces if parameters are None
command = (f"{mpi_cmd} "
f"{self.submitter.processor_split.number_of_processors} "
f"./{self.__make.exec_name} "
f"-d {self.__bout_paths.bout_inp_dst_dir} "
f"{self.__run_parameters.run_parameters_str}")
return command
def execute(self, restart: bool = False) -> AbstractSubmitter:
"""
Execute a BOUT++ run.
Parameters
----------
restart : bool
If True the 'restart' will be appended to the command string
Returns
-------
submitter : AbstractSubmitter
The submitter
"""
# Make the project if not already made
self.__make.run_make()
# Submit the command
command = self.get_execute_command()
if restart:
command += " restart"
self.submitter.submit_command(command)
return self.submitter
class BoutRunExecutor:
r"""
Executes the command for submitting a bout run.
Attributes
----------
__bout_paths : BoutPaths
Getter variable for project_path
__make : Make
Object for making the project
__run_parameters : RunParameters
Object containing the run parameters
bout_paths : BoutPaths
Object containing the paths
exec_name : str
Name of the executable
restart_from : None or Path
Path to copy restart files from prior to the execution
run_parameters : RunParameters
Object containing the run parameters
submitter : AbstractSubmitter
Object containing the submitter
Methods
-------
get_execute_command()
Return the execute command string
execute()
Execute a BOUT++ run
Examples
--------
The easiest way to use the Executor is to run a script from the root directory of
the project (i.e. where the `Makefile` and `data` directory are normally
situated. The script can simply call
>>> BoutRunExecutor().execute()
and `Executor` takes care of the rest.
A more elaborate example where all the dependency objects are built manually:
Import the dependencies
>>> from pathlib import Path
>>> from bout_runners.executor.bout_paths import BoutPaths
>>> from bout_runners.submitter.local_submitter import LocalSubmitter
Create the `bout_paths` object
>>> project_path = Path().joinpath('path', 'to', 'project')
>>> bout_inp_src_dir = Path().joinpath('path', 'to', 'source', 'BOUT.inp')
>>> bout_inp_dst_dir = Path().joinpath('path', 'to', 'destination', 'BOUT.inp')
>>> bout_paths = BoutPaths(project_path=project_path,
... bout_inp_src_dir=bout_inp_src_dir,
... bout_inp_dst_dir=bout_inp_dst_dir)
Create the executor object
>>> run_parameters = RunParameters({'global': {'nout': 0}})
>>> executor = BoutRunExecutor(
... bout_paths=bout_paths,
... submitter=LocalSubmitter(bout_paths.project_path),
... run_parameters=run_parameters)
Execute the run
>>> executor.execute()
"""
def __init__(
self,
bout_paths: Optional[BoutPaths] = None,
submitter: Optional[AbstractSubmitter] = None,
run_parameters: Optional[RunParameters] = None,
restart_from: Optional[Path] = None,
) -> None:
"""
Set the input parameters.
Parameters
----------
bout_paths : BoutPaths or None
Object containing the paths
If None, default BoutPaths values will be used
submitter : AbstractSubmitter
Object containing the submitter
run_parameters : RunParameters or None
Object containing the run parameters
If None, default parameters will be used
restart_from : Path or None
The path to copy the restart files from
"""
# NOTE: We are not setting the default as a keyword argument
# as this would mess up the paths
# NOTE: We are deepcopying bout_paths as it may be altered by for
# example the self.restart_from setter
logging.info("Start: Making an BoutRunExecutor object")
self.__bout_paths = (
deepcopy(bout_paths) if bout_paths is not None else BoutPaths()
)
self.__run_parameters = (
run_parameters if run_parameters is not None else RunParameters()
)
self.__make = Make(self.__bout_paths.project_path)
self.submitter = submitter if submitter is not None else get_submitter()
if isinstance(self.submitter, AbstractClusterSubmitter):
self.submitter.store_dir = self.__bout_paths.bout_inp_dst_dir
self.__restart_from = None
self.restart_from = restart_from
logging.info("Done: Making an BoutRunExecutor object")
@property
def restart_from(self) -> Optional[Path]:
"""
Set the properties of self.restart from and update bout_inp_dst_dir.
The bout_inp_dst_dir is updated to reflect that this is a restart run.
The new bout_inp_dst_dir will be the same as
bout_run_setup.executor.restart_from with _restart_/d* appended
/d* will be the next digit based on the number of other restart directories
Notes
-----
This will not copy the restart files as the restart files may not be ready.
Copying of files can either be done manually using
bout_runner.utils.file_operations.copy_restart_files or automatically by
using BoutRunner.__inject_copy_restart_files_node which is called from
BoutRunner.__prepare_run
See Also
--------
bout_runners.runner.bout_runner.BoutRunner.__inject_copy_restart_files_node
Search for restart files, make a restart node where needed
"""
return self.__restart_from
@restart_from.setter
def restart_from(self, restart_from: Optional[Path]) -> None:
self.__restart_from = restart_from
if restart_from is not None:
logging.debug(
"Changing bout_paths.bout_inp_dst_dir as restart_from is not None"
)
restart_dir_parent = restart_from.parent
restart_dir_name = restart_from.name
restart_dirs = list(restart_dir_parent.glob(f"{restart_dir_name}*"))
restart_number = 0
restart_numbers = list()
pattern = r"_restart_(\d)+$"
for restart_dir in restart_dirs:
match = re.search(pattern, restart_dir.name)
if match is not None:
# NOTE: The zeroth group is the matching string
restart_numbers.append(int(match.group(1)))
if len(restart_numbers) != 0:
restart_numbers.sort()
restart_number = restart_numbers[-1] + 1
prev_inp_dst_dir = self.bout_paths.bout_inp_dst_dir
stripped_restart_dir_name = re.sub(pattern, "", restart_dir_name)
new_inp_dst_dir = restart_dir_parent.joinpath(
f"{stripped_restart_dir_name}_restart_{restart_number}"
)
self.bout_paths.bout_inp_dst_dir = new_inp_dst_dir
logging.debug(
"bout_run_setup.bout_paths.bout_inp_dst_dir set from %s to %s",
prev_inp_dst_dir,
new_inp_dst_dir,
)
@property
def bout_paths(self) -> BoutPaths:
"""
Get the properties of self.bout_paths.
Returns
-------
self.__bout_paths : BoutPaths
Object containing the paths
Notes
-----
The bout_paths is read only
"""
return self.__bout_paths
@property
def exec_name(self) -> str:
"""
Set the properties of self.bout_paths.
Returns
-------
self.__bout_paths : BoutPaths
Object containing the paths
Notes
-----
The exec_name is read only
"""
return self.__make.exec_name
@property
def run_parameters(self) -> RunParameters:
"""
Get the properties of self.run_parameters.
Returns
-------
self.__run_parameters : RunParameters
Object containing the run parameters
Notes
-----
The run_parameters is read only
"""
return self.__run_parameters
def get_execute_command(self) -> str:
"""
Return the execute command string.
Returns
-------
command : str
The terminal command for executing the run
"""
mpi_cmd = "mpirun -np"
# NOTE: No spaces if parameters are None
command = (
f"{mpi_cmd} "
f"{self.submitter.processor_split.number_of_processors} "
f"{self.__bout_paths.project_path.joinpath(self.exec_name)} "
f"-d {self.__bout_paths.bout_inp_dst_dir} "
f"{self.__run_parameters.run_parameters_str}"
)
return command
def execute(self, restart: bool = False) -> None:
"""
Execute a BOUT++ run.
Parameters
----------
restart : bool
If True the 'restart' will be appended to the command string
"""
# Make the project if not already made
self.__make.run_make()
# Submit the command
command = self.get_execute_command()
if restart:
command += " restart"
self.submitter.submit_command(command)