"""
MDSuite: A Zincwarecode package.
License
-------
This program and the accompanying materials are made available under the terms
of the Eclipse Public License v2.0 which accompanies this distribution, and is
available at https://www.eclipse.org/legal/epl-v20.html
SPDX-License-Identifier: EPL-2.0
Copyright Contributors to the Zincwarecode Project.
Contact Information
-------------------
email: zincwarecode@gmail.com
github: https://github.com/zincware
web: https://zincwarecode.com/
Citation
--------
If you use this module please cite us with:
Summary
-------
"""
import logging
from typing import Tuple
import numpy as np
import tensorflow as tf
from mdsuite.database.simulation_database import Database
from mdsuite.utils.meta_functions import get_machine_properties, gpu_available
from mdsuite.utils.scale_functions import (
linear_scale_function,
linearithmic_scale_function,
polynomial_scale_function,
quadratic_scale_function,
)
log = logging.getLogger(__name__)
[docs]class MemoryManager:
"""
A class to manage memory during MDSuite operations
In most MDSuite operations the memory requirements of a complete procedure will be
greater than what is available to the average computer. Therefore, some degree of
memory management is required for smooth running. This class should be instantiated
during any operation so it can update the operation on what the current memory
capabilities are.
The class can work with several tensor_values-sets in the case an analysis requires
this much tensor_values.
Attributes
----------
data_path : list
database : Database
parallel : bool
memory_fraction : float
scale_function : dict
gpu : bool
"""
def __init__(
self,
data_path: list = None,
database: Database = None,
parallel: bool = False,
memory_fraction: float = 0.2,
scale_function: dict = None,
gpu: bool = gpu_available(),
offset: int = 0,
):
"""
Constructor for the memory manager.
Parameters
----------
data_path : list
Path to the data to be used in a calculator. This is used when
asking the database how big a dataset is.
["Na/Positions", "Ionic_Current/Ionic_Current"]
database : Database
Database class to be used for checking size parameters.
parallel : bool
If true, the memory should be computed for parallel processes.
memory_fraction : float
How much memory is the calculator allowed to use.
scale_function : dict
Scaling function to compute the memory scaling of a calculator.
gpu : bool
If true, gpu should be used.
offset : int
If data is being loaded from a non-zero point in the database the
offset is used to take this into account. For example, expanding a
transformation.
"""
if scale_function is None:
scale_function = {"linear": {"scale_factor": 10}}
self.data_path = data_path
self.parallel = parallel
self.database = database
self.memory_fraction = memory_fraction
self.offset = offset
self.machine_properties = get_machine_properties()
if gpu:
memory = 0
for item in self.machine_properties["gpu"]:
if self.machine_properties["gpu"][item]["memory"] > memory:
memory = self.machine_properties["gpu"][item]["memory"]
self.machine_properties["memory"] = memory * 1e6
tf.device("gpu")
else:
tf.device("cpu")
self.batch_size = None
self.n_batches = None
self.remainder = None
self.atom_batch_size = None
self.n_atom_batches = None
self.atom_remainder = None
self.minibatch = False
(
self.scale_function,
self.scale_function_parameters,
) = self._select_scale_function(scale_function)
@staticmethod
def _select_scale_function(input_dict: dict):
"""
select a scale function
Parameters
----------
input_dict : dict
Input dict which selects the correct function.
Returns
-------
Updates the class state
"""
def _string_to_function(argument: str):
"""
Convert a string to a function choice.
Parameters
----------
argument : str
String to use in the matching.
Returns
-------
function : Callable
"""
switcher = {
"linear": linear_scale_function,
"log-linear": linearithmic_scale_function,
"quadratic": quadratic_scale_function,
"polynomial": polynomial_scale_function,
}
try:
return switcher[argument]
except KeyError:
raise KeyError("Invalid choice")
scale_function = _string_to_function(list(input_dict.keys())[0])
scale_function_parameters = input_dict[list(input_dict.keys())[0]]
return scale_function, scale_function_parameters
[docs] def get_batch_size(self, system: bool = False) -> tuple:
"""
Calculate the batch size of an operation.
This method takes the tensor_values requirements of an operation and returns
how big each batch of tensor_values should be for such an operation.
Parameters
----------
system : bool
Tell the database what kind of tensor_values it is looking at,
atomistic, or system wide.
Returns
-------
batch_size : int
number of elements that should be loaded at one time
number_of_batches : int
number of batches which can be loaded.
remainder : int
number of elements that will be left unloaded after a loop over all
batches. This amount can then be loaded to collect unused tensor_values.
"""
if self.data_path is None:
raise ValueError("No tensor_values have been requested.")
per_configuration_memory: float = 0.0
for item in self.data_path:
n_particles, n_configs, n_bytes = self.database.get_data_size(item)
per_configuration_memory += n_bytes / n_configs
per_configuration_memory = self.scale_function(
per_configuration_memory, **self.scale_function_parameters
)
maximum_loaded_configurations = int(
np.clip(
(self.memory_fraction * self.machine_properties["memory"])
/ per_configuration_memory,
1,
n_configs - self.offset,
)
)
batch_size = self._get_optimal_batch_size(maximum_loaded_configurations)
number_of_batches, remainder = divmod((n_configs - self.offset), batch_size)
self.batch_size = batch_size
self.n_batches = number_of_batches
self.remainder = remainder
return batch_size, number_of_batches, remainder
[docs] @staticmethod
def hdf5_load_time(n: int):
"""
Describes the load time of a hdf5 database i.e. O(log N)
Parameters
----------
n : int
Amount of data to be loaded
Returns
-------
load_time : float
Load time of N data points from a hdf5 database.
"""
return np.log(n)
@staticmethod
def _get_optimal_batch_size(naive_size):
"""
Use the open/close and read speeds of the hdf5 database_path as well as the
operation being performed to get an optimal batch size.
Parameters
----------
naive_size : int
Naive batch size to be optimized
Returns
-------
batch_size : int
An optimized batch size
"""
# db_io_time = self.database.get_load_time()
return naive_size
def _compute_atomwise_minibatch(self, data_range: int):
"""
Compute the number of atoms which can be loaded in at one time.
Parameters
----------
data_range : int
Data range used in the calculator.
Returns
-------
Updates the following class attributes:
self.batch_size : int
Size of each batch.
self.n_batches : int
Number of batches to be looped over.
self.remainder :
Remainder of batches after looping.
self.n_atom_batches : int
Number of batches over atoms.
self.atom_remainder : int
Remainder atoms after even batching.
"""
per_atom_memory = 0 # memory usage per atom within ONE configuration
per_configuration_memory = 0 # per configuration memory usage
total_rows = 0
for item in self.data_path:
n_particles, n_configs, n_bytes = self.database.get_data_size(item)
per_configuration_memory += n_bytes / n_configs
per_atom_memory += per_configuration_memory / n_particles
total_rows += n_particles
# per_configuration_memory = self.scale_function(per_configuration_memory,
# **self.scale_function_parameters)
per_atom_memory = self.scale_function(
per_atom_memory, **self.scale_function_parameters
)
fractions = [1 / 2, 1 / 4, 1 / 8, 1 / 20, 1 / 100, 1 / 200, 0]
for (
fraction
) in fractions: # iterate over possible mini batch fractions to fit memory
if fraction == 0:
# All fractions failed, try atom wise mini batching - Set to one atom
# at a time in the worst case.
log.info(
"Could not find a good mini batch fraction - using single atom mini"
" batching!"
)
batch_size = int(
np.clip(
self.memory_fraction
* self.machine_properties["memory"]
/ per_atom_memory,
1,
n_configs,
)
)
self.atom_batch_size = 1 # Set the mini batch size to single atom
break
atom_batch_memory = fraction * per_atom_memory
batch_size = int(
np.clip(
self.memory_fraction
* self.machine_properties["memory"]
/ atom_batch_memory,
1,
n_configs,
)
)
if (
batch_size > data_range
): # the batch size has to be larger than the data_range
self.atom_batch_size = (
n_particles * fraction
) # Set the mini batch size to total_data_points * fraction
break
self.batch_size = batch_size
self.n_batches = int(n_configs / batch_size)
self.remainder = int(n_configs % batch_size)
self.n_atom_batches = int(n_particles / self.atom_batch_size)
self.atom_remainder = int(n_particles % self.atom_batch_size)
[docs] def get_ensemble_loop(
self, data_range: int, correlation_time: int = 1
) -> Tuple[int, bool]:
"""
Get the tensor_values range partition quantity.
Not only does tensor_values need to be batched, it then needs to be looped over
in order to calculate some property. This method will return the number of
loops possible given the tensor_values range and the correlation time
Parameters
----------
data_range : int
Data range to be used in the analysis.
correlation_time : int
Correlation time to be considered when looping over the tensor_values
Returns
-------
data_range_partitions : int
Number of time the batch can be looped over with given data_range and
correlation time.
"""
final_window = self.batch_size - data_range
if final_window < 0:
self._compute_atomwise_minibatch(data_range)
final_window = self.batch_size - data_range
self.minibatch = True
return int(np.clip(final_window / correlation_time, 1, None)), True
else:
return int(np.clip(final_window / correlation_time, 1, None)), False