"""
Module containing the Population grid class object.
Here all the functionality of a Population object is defined.
Tasks:
- TODO: add functionality to 'on-init' set arguments
- TODO: add functionality to return the initial_abundance_hash
- TODO: add functionality to return the isotope_hash
- TODO: add functionality to return the isotope_list
- TODO: add functionality to return the nuclear_mass_hash
- TODO: add functionality to return the nuclear_mass_list
- TODO: add functionality to return the source_list
- TODO: add functionality to return the ensemble_list
- TODO: consider spreading the functions over more files.
- TODO: type the private functions
- TODO: fix the correct object types for the default values of the bse_options
- TODO: uncomment and implement the HPC functionality
- TODO: think of a clean and nice way to unload and remove the custom_logging_info library from memory (and from disk)
- TODO: think of a nice way to remove the loaded grid_code/ generator from memory.
"""
import argparse
import bz2
import copy
import datetime
import json
import gc
import gzip
import importlib.util
import logging
import msgpack
import multiprocessing
import os
import py_rinterpolate
import re
import resource
import setproctitle
import strip_ansi
import sys
import time
import uuid
_count = 0
from typing import Union, Any
from collections import (
OrderedDict,
)
from collections.abc import Iterable # drop `.abc` with Python 2.7 or lower
import setproctitle
import py_rinterpolate
from colorama import init as colorama_init
colorama_init()
from binarycpython.utils.grid_options_defaults import (
grid_options_defaults_dict,
moe_di_stefano_default_options,
_MOE2017_VERBOSITY_LEVEL,
_CUSTOM_LOGGING_VERBOSITY_LEVEL,
_LOGGER_VERBOSITY_LEVEL,
)
from binarycpython.utils.custom_logging_functions import (
autogen_C_logging_code,
binary_c_log_code,
create_and_load_logging_function,
)
from binarycpython.utils.functions import (
get_defaults,
remove_file,
filter_arg_dict,
get_help_all,
return_binary_c_version_info,
verbose_print,
get_moe_di_stefano_dataset,
trem,
conv_time_units,
mem_use,
get_ANSI_colours,
check_if_in_shell,
format_number,
timedelta,
)
from binarycpython.utils.ensemble import (
binaryc_json_serializer,
ensemble_compression,
ensemble_file_type,
extract_ensemble_json_from_string,
format_ensemble_results,
)
from binarycpython.utils.dicts import (
AutoVivificationDict,
custom_sort_dict,
merge_dicts,
multiply_values_dict,
recursive_change_key_to_float,
recursive_change_key_to_string,
update_dicts,
)
# from binarycpython.utils.hpc_functions import (
# get_condor_version,
# get_slurm_version,
# create_directories_hpc,
# path_of_calling_script,
# get_python_details,
# )
from binarycpython.utils.distribution_functions import (
Moecache,
LOG_LN_CONVERTER,
fill_data,
get_max_multiplicity,
Arenou2010_binary_fraction,
raghavan2010_binary_fraction,
Moe_di_Stefano_2017_multiplicity_fractions,
normalize_dict,
)
from binarycpython import _binary_c_bindings
secs_per_day = 86400 # probably needs to go somewhere more sensible
class Population:
"""
Population Object. Contains all the necessary functions to set up, run and process a
population of systems
"""
def __init__(self, **kwargs):
"""
Initialisation function of the population class
"""
# Different sections of options
# get binary_c defaults and create a cleaned up dict
# Setting stuff will check against the defaults to see if the input is correct.
self.defaults = get_defaults()
self.cleaned_up_defaults = self._cleanup_defaults()
self.available_keys = list(self.defaults.keys())
self.special_params = [
el for el in list(self.defaults.keys()) if el.endswith("%d")
]
# make the input dictionary
self.bse_options = {} # bse_options is just empty.
# Grid options
self.grid_options = copy.deepcopy(grid_options_defaults_dict)
# Custom options
self.custom_options = {}
# grid code generation
self.indent_depth = 0
self.indent_string = " "
self.code_string = ""
# Set the options that are passed at creation of the object
self.set(**kwargs)
# Load Moe and di Stefano options
self.grid_options["Moe2017_options"] = copy.deepcopy(
moe_di_stefano_default_options
)
# Write MOE2017 options to a file. NOTE: not sure why i put this here anymore
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"), exist_ok=True
)
with open(
os.path.join(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
"moeopts.dat",
),
"w",
) as f:
f.write(json.dumps(self.grid_options["Moe2017_options"], indent=4))
f.close()
# Argline dict
self.argline_dict = {}
# Set some memory dicts
self.persistent_data_memory_dict = {}
# shared memory used for logging
self.shared_memory = {}
# variable to test if we're running in a shell
self.in_shell = check_if_in_shell()
# ANSI colours: use them if in a shell
self.ANSI_colours = get_ANSI_colours()
if self.in_shell == False:
for c in self.ANSI_colours:
self.ANSI_colours[c] = ""
# Set global (OS) process id
self.grid_options["_main_pid"] = os.getpid()
# local process ID
self.process_ID = 0
# Create location to store results. Users should write to this dictionary.
# The AutoVivificationDict allows for perls method of accessing possibly non-existant subdicts
self.grid_results = AutoVivificationDict()
# Create location where ensemble results are written to
self.grid_ensemble_results = {}
###################################################
# Argument functions
###################################################
# General flow of generating the arguments for the binary_c call:
# - user provides parameter and value via set (or manually but that is risky)
# - The parameter names of these input get compared to the parameter names in the self.defaults;
# with this, we know that its a valid parameter to give to binary_c.
# - For a single system, the bse_options will be written as a arg line
# - For a population the bse_options will get copied to a temp_bse_options dict and updated with
# all the parameters generated by the grid
# I will not create the argument line by fully writing all the defaults and overriding user
# input, that seems not necessary because by using the get_defaults() function we already
# know for sure which parameter names are valid for the binary_c version
# And because binary_c uses internal defaults, its not necessary to explicitly pass them.
# I do however suggest everyone to export the binary_c defaults to a file, so that you know
# exactly which values were the defaults.
def set(self, **kwargs) -> None:
"""
Function to set the values of the population. This is the preferred method to set values
of functions, as it provides checks on the input.
the bse_options will get populated with all the those that have a key that is present
in the self.defaults
the grid_options will get updated with all the those that have a key that is present
in the self.grid_options
If neither of above is met; the key and the value get stored in a custom_options dict.
Args:
via kwargs all the arguments are either set to binary_c parameters, grid_options or custom_options (see above)
"""
# Go over all the input
for key in kwargs:
# Filter out keys for the bse_options
if key in self.defaults.keys():
verbose_print(
"adding: {}={} to BSE_options".format(key, kwargs[key]),
self.grid_options["verbosity"],
1,
)
self.bse_options[key] = kwargs[key]
# Extra check to check if the key fits one of parameter names that end with %d
elif any(
[
True
if (key.startswith(param[:-2]) and len(param[:-2]) < len(key))
else False
for param in self.special_params
]
):
verbose_print(
"adding: {}={} to BSE_options by catching the %d".format(
key, kwargs[key]
),
self.grid_options["verbosity"],
1,
)
self.bse_options[key] = kwargs[key]
# Filter out keys for the grid_options
elif key in self.grid_options.keys():
verbose_print(
"adding: {}={} to grid_options".format(key, kwargs[key]),
self.grid_options["verbosity"],
1,
)
self.grid_options[key] = kwargs[key]
# The of the keys go into a custom_options dict
else:
verbose_print(
"<<<< Warning: Key does not match previously known parameter: \
adding: {}={} to custom_options >>>>".format(
key, kwargs[key]
),
self.grid_options["verbosity"],
0, # NOTE: setting this to be 0 prevents mistakes being overlooked.
)
self.custom_options[key] = kwargs[key]
def parse_cmdline(self) -> None:
"""
Function to handle settings values via the command line in the form x=y, w=z, etc.
Best to be called after all the .set(..) lines, and just before the .evolve() is called
If you input any known parameter (i.e. contained in grid_options, defaults/bse_options
or custom_options), this function will attempt to convert the input from string
(because everything is string) to the type of the value that option had before.
The values of the bse_options are initially all strings, but after user input they
can change to ints.
The value of any new parameter (which will go to custom_options) will be a string.
"""
# get the cmd-line args in the form x=y
cmdline_args = sys.argv[1:]
if cmdline_args:
verbose_print(
"Found cmdline args. Parsing them now",
self.grid_options["verbosity"],
1,
)
# Grab the input and split them up, while accepting only non-empty entries
# cmdline_args = args
self.grid_options["_commandline_input"] = cmdline_args
# Make dict and fill it
cmdline_dict = {}
for cmdline_arg in cmdline_args:
split = cmdline_arg.split("=")
parameter = split[0]
value = split[1]
old_value_found = False
# Find an old value
if parameter in self.grid_options:
old_value = self.grid_options[parameter]
old_value_found = True
elif parameter in self.defaults:
old_value = self.defaults[parameter]
old_value_found = True
elif parameter in self.custom_options:
old_value = self.custom_options[parameter]
old_value_found = True
# (attempt to) convert
if old_value_found:
try:
verbose_print(
"Converting type of {} from {} to {}".format(
parameter, type(value), type(old_value)
),
self.grid_options["verbosity"],
2,
)
value = type(old_value)(value)
verbose_print("Success!", self.grid_options["verbosity"], 2)
except ValueError:
verbose_print(
"Tried to convert the given parameter {}/value {} to its correct type {} (from old value {}). But that wasn't possible.".format(
parameter, value, type(old_value), old_value
),
self.grid_options["verbosity"],
0,
)
# Add to dict
cmdline_dict[parameter] = value
# unpack the dictionary into the setting function that handles where the values are set
self.set(**cmdline_dict)
def _return_argline(self, parameter_dict=None):
"""
Function to create the string for the arg line from a parameter dict
"""
if not parameter_dict:
parameter_dict = self.bse_options
argline = "binary_c "
for param_name in sorted(parameter_dict):
argline += "{} {} ".format(param_name, parameter_dict[param_name])
argline = argline.strip()
return argline
def _last_grid_variable(self):
"""
Function that returns the last grid variable
(i.e. the one with the highest grid_variable_number)
"""
number = len(self.grid_options["_grid_variables"])
for grid_variable in self.grid_options["_grid_variables"]:
if (
self.grid_options["_grid_variables"][grid_variable][
"grid_variable_number"
]
== number - 1
):
return grid_variable
def update_grid_variable(self, name: str, **kwargs) -> None:
"""
Function to update the values of a grid variable.
Args:
name:
name of the grid variable to be changed.
**kwargs:
key-value pairs to override the existing grid variable data. See add_grid_variable for these names.
"""
grid_variable = None
try:
grid_variable = self.grid_options["_grid_variables"][name]
except KeyError:
msg = "Unknown grid variable {} - please create it with the add_grid_variable() method.".format(
name
)
raise KeyError(msg)
for key, value in kwargs.items():
grid_variable[key] = value
verbose_print(
"Updated grid variable: {}".format(json.dumps(grid_variable, indent=4)),
self.grid_options["verbosity"],
1,
)
def delete_grid_variable(
self,
name: str,
) -> None:
try:
del self.grid_options["_grid_variables"][name]
verbose_print(
"Deleted grid variable: {}".format(name),
self.grid_options["verbosity"],
1,
)
except:
msg = "Failed to remove grid variable {} : please check it exists.".format(
name
)
raise ValueError(msg)
def rename_grid_variable(self, oldname: str, newname: str) -> None:
"""
Function to rename a grid variable.
note: this does NOT alter the order
of the self.grid_options["_grid_variables"] dictionary.
The order in which the grid variables are loaded into the grid is based on their
`grid_variable_number` property
Args:
oldname:
old name of the grid variable
newname:
new name of the grid variable
"""
try:
self.grid_options["_grid_variables"][newname] = self.grid_options[
"_grid_variables"
].pop(oldname)
self.grid_options["_grid_variables"][newname]["name"] = newname
verbose_print(
"Rename grid variable: {} to {}".format(oldname, newname),
self.grid_options["verbosity"],
1,
)
except:
msg = "Failed to rename grid variable {} to {}.".format(oldname, newname)
raise ValueError(msg)
def add_grid_variable(
self,
name: str,
parameter_name: str,
longname: str,
valuerange: Union[list, str],
samplerfunc: str,
probdist: str,
dphasevol: Union[str, int] = -1,
gridtype: str = "centred",
branchpoint: int = 0,
branchcode: Union[str, None] = None,
precode: Union[str, None] = None,
postcode: Union[str, None] = None,
topcode: Union[str, None] = None,
bottomcode: Union[str, None] = None,
condition: Union[str, None] = None,
) -> None:
"""
Function to add grid variables to the grid_options.
The execution of the grid generation will be through a nested for loop.
Each of the grid variables will get create a deeper for loop.
The real function that generates the numbers will get written to a new file in the TMP_DIR,
and then loaded imported and evaluated.
beware that if you insert some destructive piece of code, it will be executed anyway.
Use at own risk.
Tasks:
- TODO: Fix this complex function.
Args:
name:
name of parameter used in the grid Python code.
This is evaluated as a parameter and you can use it throughout
the rest of the function
Examples:
name = 'lnm1'
parameter_name:
name of the parameter in binary_c
This name must correspond to a Python variable of the same name,
which is automatic if parameter_name == name.
Note: if parameter_name != name, you must set a
variable in "precode" or "postcode" to define a Python variable
called parameter_name
longname:
Long name of parameter
Examples:
longname = 'Primary mass'
range:
Range of values to take. Does not get used really, the samplerfunc is used to
get the values from
Examples:
range = [math.log(m_min), math.log(m_max)]
samplerfunc:
Function returning a list or numpy array of samples spaced appropriately.
You can either use a real function, or a string representation of a function call.
Examples:
samplerfunc = "const(math.log(m_min), math.log(m_max), {})".format(resolution['M_1'])
precode:
Extra room for some code. This code will be evaluated within the loop of the
sampling function (i.e. a value for lnm1 is chosen already)
Examples:
precode = 'M_1=math.exp(lnm1);'
postcode:
Code executed after the probability is calculated.
probdist:
Function determining the probability that gets assigned to the sampled parameter
Examples:
probdist = 'Kroupa2001(M_1)*M_1'
dphasevol:
part of the parameter space that the total probability is calculated with. Put to -1
if you want to ignore any dphasevol calculations and set the value to 1
Examples:
dphasevol = 'dlnm1'
condition:
condition that has to be met in order for the grid generation to continue
Examples:
condition = 'self.grid_options['binary']==1'
gridtype:
Method on how the value range is sampled. Can be either 'edge' (steps starting at
the lower edge of the value range) or 'centred'
(steps starting at lower edge + 0.5 * stepsize).
topcode:
Code added at the very top of the block.
bottomcode:
Code added at the very bottom of the block.
"""
# check parameters
if False and dphasevol != -1.0 and gridtype == 'discrete':
print("Error making grid: you have set the phasevol to be not -1 and gridtype to discrete, but a discrete grid has no phasevol calculation. You should only set the gridtype to discrete and not set the phasevol in this case.")
sys.exit()
# Add grid_variable
grid_variable = {
"name": name,
"parameter_name": parameter_name,
"longname": longname,
"valuerange": valuerange,
# "resolution": 0,
"samplerfunc": samplerfunc,
"precode": precode,
"postcode": postcode,
"probdist": probdist,
"dphasevol": dphasevol,
"condition": condition,
"gridtype": gridtype,
"branchpoint": branchpoint,
"branchcode": branchcode,
"topcode": topcode,
"bottomcode": bottomcode,
"grid_variable_number": len(self.grid_options["_grid_variables"]),
}
# Check for gridtype input
allowed_gridtypes = [
"edge",
"right",
"right edge",
"left",
"left edge",
"centred",
"centre",
"center",
"discrete"
]
if not gridtype in allowed_gridtypes:
msg = "Unknown gridtype {gridtype}. Please choose one of: ".format(gridtype=gridtype) + ','.join(allowed_gridtypes)
raise ValueError(msg)
# Load it into the grid_options
self.grid_options["_grid_variables"][grid_variable["name"]] = grid_variable
verbose_print(
"Added grid variable: {}".format(json.dumps(grid_variable, indent=4)),
self.grid_options["verbosity"],
1,
)
###################################################
# Return functions
###################################################
def return_population_settings(self) -> dict:
"""
Function that returns all the options that have been set.
Can be combined with JSON to make a nice file.
Returns:
dictionary containing "bse_options", "grid_options", "custom_options"
"""
options = {
"bse_options": self.bse_options,
"grid_options": self.grid_options,
"custom_options": self.custom_options,
}
return options
def return_binary_c_version_info(self, parsed=False):
"""
Function that returns the version information of binary_c
"""
version_info = return_binary_c_version_info(parsed=parsed)
return version_info
def return_binary_c_defaults(self):
"""
Function that returns the defaults of the binary_c version that is used.
"""
return self.defaults
def return_all_info(
self,
include_population_settings: bool = True,
include_binary_c_defaults: bool = True,
include_binary_c_version_info: bool = True,
include_binary_c_help_all: bool = True,
) -> dict:
"""
Function that returns all the information about the population and binary_c
Args:
include_population_settings:
whether to include the population_settings (see function return_population_settings)
include_binary_c_defaults:
whether to include a dict containing the binary_c parameters and their default
values
include_binary_c_version_info:
whether to include a dict containing all the binary_c version info
(see return_binary_c_version_info)
include_binary_c_help_all:
whether to include a dict containing all the information about
the binary_c parameters (see get_help_all)
Return:
dictionary containing all, or part of, the above dictionaries
"""
#
all_info = {}
#
if include_population_settings:
population_settings = self.return_population_settings()
all_info["population_settings"] = population_settings
#
if include_binary_c_defaults:
binary_c_defaults = self.return_binary_c_defaults()
all_info["binary_c_defaults"] = binary_c_defaults
if include_binary_c_version_info:
binary_c_version_info = return_binary_c_version_info(parsed=True)
all_info["binary_c_version_info"] = binary_c_version_info
if include_binary_c_help_all:
binary_c_help_all_info = get_help_all(print_help=False)
all_info["binary_c_help_all"] = binary_c_help_all_info
return all_info
def export_all_info(
self,
use_datadir: bool = True,
outfile: Union[str, None] = None,
include_population_settings: bool = True,
include_binary_c_defaults: bool = True,
include_binary_c_version_info: bool = True,
include_binary_c_help_all: bool = True,
) -> Union[str, None]:
"""
Function that exports the all_info to a JSON file
Tasks:
- TODO: if any of the values in the dicts here is of a not-serialisable form, then we
need to change that to a string or something so, use a recursive function that
goes over the all_info dict and finds those that fit
- TODO: Fix to write things to the directory. which options do which etc
- TODO: there's flawed logic here. rewrite this part pls
- TODO: consider actually just removing the whole 'output to file' part and let the
user do this.
Args:
include_population_settings: whether to include the population_settings
(see function return_population_settings)
include_binary_c_defaults: whether to include a dict containing the binary_c parameters
and their default values
include_binary_c_version_info: whether to include a dict containing all the binary_c
version info (see return_binary_c_version_info)
include_binary_c_help_all: whether to include a dict containing all the information
about the binary_c parameters (see get_help_all)
use_datadir: Boolean whether to use the custom_options['data_dir'] to write the file to.
If the custom_options["base_filename"] is set, the output file will be called
<custom_options["base_filename"]>_settings.json. Otherwise a file called
simulation_<date+time>_settings.json will be created
outfile: if use_datadir is false, a custom filename will be used
"""
all_info = self.return_all_info(
include_population_settings=include_population_settings,
include_binary_c_defaults=include_binary_c_defaults,
include_binary_c_version_info=include_binary_c_version_info,
include_binary_c_help_all=include_binary_c_help_all,
)
# Copy dict
all_info_cleaned = copy.deepcopy(all_info)
if use_datadir:
if self.custom_options.get("data_dir", None):
if not self.custom_options.get("base_filename", None):
base_name = "simulation_{}".format(
datetime.datetime.strftime(
datetime.datetime.now(), "%Y%m%d_%H%M%S"
)
)
else:
base_name = os.path.splitext(self.custom_options["base_filename"])[
0
]
settings_name = base_name + "_settings.json"
# Check directory, make if necessary
os.makedirs(self.custom_options["data_dir"], exist_ok=True)
settings_fullname = os.path.join(
self.custom_options["data_dir"], settings_name
)
verbose_print(
"Writing settings to {}".format(settings_fullname),
self.grid_options["verbosity"],
1,
)
# if not outfile.endswith('json'):
with open(settings_fullname, "w") as file:
file.write(
json.dumps(
all_info_cleaned,
indent=4,
default=binaryc_json_serializer,
)
)
return settings_fullname
else:
msg = "Exporting all info without passing a value for `outfile` requires custom_options['data_dir'] to be present. That is not the cause. Either set the `data_dir` or pass a value for `outfile` "
raise ValueError
else:
verbose_print(
"Writing settings to {}".format(outfile),
self.grid_options["verbosity"],
1,
)
if not outfile.endswith("json"):
verbose_print(
"Error: outfile ({}) must end with .json".format(outfile),
self.grid_options["verbosity"],
0,
)
raise ValueError
with open(outfile, "w") as file:
file.write(
json.dumps(
all_info_cleaned, indent=4, default=binaryc_json_serializer
)
)
return outfile
def _boxed(self, *list, colour="yellow on black", boxchar="*", separator="\n"):
"""
Function to output a list of strings in a single box.
Args:
list = a list of strings to be output. If these contain the separator
(see below) these strings are split by it.
separator = strings are split on this, default "\n"
colour = the colour to be used, usually this is 'yellow on black'
as set in the ANSI_colours dict
boxchar = the character used to make the box, '*' by default
Note: handles tabs (\t) badly, do not use them!
"""
strlen = 0
strings = []
lengths = []
# make a list of strings
if separator:
for l in list:
strings += l.split(sep=separator)
else:
strings = list
# get lengths without ANSI codes
for string in strings:
lengths.append(len(strip_ansi.strip_ansi(string)))
# hence the max length
strlen = max(lengths)
strlen += strlen % 2
header = boxchar * (4 + strlen)
# start output
out = self.ANSI_colours[colour] + header + "\n"
# loop over strings to output, padding as required
for n, string in enumerate(strings):
if lengths[n] % 2 == 1:
string = " " + string
pad = " " * int((strlen - lengths[n]) / 2)
out = out + boxchar + " " + pad + string + pad + " " + boxchar + "\n"
# close output and return
out = out + header + "\n" + self.ANSI_colours["reset"]
return out
def _set_custom_logging(self):
"""
Function/routine to set all the custom logging so that the function memory pointer
is known to the grid.
When the memory adress is loaded and the library file is set we'll skip rebuilding the library
"""
# Only if the values are the 'default' unset values
if (
self.grid_options["custom_logging_func_memaddr"] == -1
and self.grid_options["_custom_logging_shared_library_file"] is None
):
verbose_print(
"Creating and loading custom logging functionality",
self.grid_options["verbosity"],
1,
)
# C_logging_code gets priority of C_autogen_code
if self.grid_options["C_logging_code"]:
# Generate entire shared lib code around logging lines
custom_logging_code = binary_c_log_code(
self.grid_options["C_logging_code"],
verbosity=self.grid_options["verbosity"]
- (_CUSTOM_LOGGING_VERBOSITY_LEVEL - 1),
)
# Load memory address
(
self.grid_options["custom_logging_func_memaddr"],
self.grid_options["_custom_logging_shared_library_file"],
) = create_and_load_logging_function(
custom_logging_code,
verbosity=self.grid_options["verbosity"]
- (_CUSTOM_LOGGING_VERBOSITY_LEVEL - 1),
custom_tmp_dir=self.grid_options["tmp_dir"],
)
elif self.grid_options["C_auto_logging"]:
# Generate real logging code
logging_line = autogen_C_logging_code(
self.grid_options["C_auto_logging"],
verbosity=self.grid_options["verbosity"]
- (_CUSTOM_LOGGING_VERBOSITY_LEVEL - 1),
)
# Generate entire shared lib code around logging lines
custom_logging_code = binary_c_log_code(
logging_line,
verbosity=self.grid_options["verbosity"]
- (_CUSTOM_LOGGING_VERBOSITY_LEVEL - 1),
)
# Load memory address
(
self.grid_options["custom_logging_func_memaddr"],
self.grid_options["_custom_logging_shared_library_file"],
) = create_and_load_logging_function(
custom_logging_code,
verbosity=self.grid_options["verbosity"]
- (_CUSTOM_LOGGING_VERBOSITY_LEVEL - 1),
custom_tmp_dir=self.grid_options["tmp_dir"],
)
else:
verbose_print(
"Custom logging library already loaded. Not setting them again.",
self.grid_options["verbosity"],
1,
)
###################################################
# Ensemble functions
###################################################
# Now they are stored in the _process_run_population thing.
# Needed less code since they all
###################################################
# Evolution functions
###################################################
def _pre_run_cleanup(self) -> None:
"""
Function to clean up some stuff in the grid before a run (like results, ensemble results etc)
"""
# empty results
self.grid_options["results"] = {}
self.grid_results = AutoVivificationDict()
self.grid_ensemble_results = {}
# Reset the process ID (should not have a value initially, but can't hurt if it does)
self.process_ID = 0
# Reset population ID:
self.grid_options["_population_id"] = uuid.uuid4().hex
# save number of stored log stats
self.shared_memory["n_saved_log_stats"] = multiprocessing.Value("i", 0)
# set previous logging time
_t = time.time()
self.shared_memory["prev_log_time"] = multiprocessing.Array(
"d", [_t] * self.grid_options["n_logging_stats"]
)
# set previous logging system number to 0
self.shared_memory["prev_log_system_number"] = multiprocessing.Array(
"i", [0] * self.grid_options["n_logging_stats"]
)
# arrays to store memory and max memory use per-thread
mem = 1.0 * mem_use()
self.shared_memory["memory_use_per_thread"] = multiprocessing.Array(
"d", [mem] * self.grid_options["num_cores"]
)
self.shared_memory["max_memory_use_per_thread"] = multiprocessing.Array(
"d", [mem] * self.grid_options["num_cores"]
)
def clean(self) -> None:
"""
Clean the contents of the population object so it can be reused.
Calling _pre_run_cleanup()
TODO: decide to deprecate this function
"""
self._pre_run_cleanup()
def evolve(self) -> None:
"""
Entry point function of the whole object. From here, based on the settings,
we set up a SLURM or CONDOR grid, or if no setting is given we go straight
to evolving the population.
There are no direct arguments to this function, rather it is based on the grid_options settings:
grid_options['slurm']: integer Boolean whether to use a slurm_grid evolution
grid_options['condor']: integer Boolean whether to use a condor_grid evolution
If neither of the above is set, we continue without using HPC routines
(that doesn't mean this cannot be run on a server with many cores)
Returns an dictionary containing the analytics of the run
TODO: change the way this is done. Slurm & CONDOR should probably do this differently
NOTE: SLURM and CONDOR options are not working properly yet
"""
# Just to make sure we don't have stuff from a previous run hanging around
self._pre_run_cleanup()
# Check which type:
if self.grid_options["slurm"] == 1:
# Execute Slurm subroutines
# self._slurm_grid()
raise ValueError("Slurm evolution not available at this moment")
elif self.grid_options["condor"] == 1:
# Execute condor subroutines
# self._condor_grid()
raise ValueError("Condor evolution not available at this moment")
else:
# Execute population evolution subroutines
self._evolve_population()
# Put all interesting stuff in a variable and output that afterwards, as analytics of the run.
analytics_dict = {
"population_name": self.grid_options["_population_id"],
"evolution_type": self.grid_options["evolution_type"],
"failed_count": self.grid_options["_failed_count"],
"failed_prob": self.grid_options["_failed_prob"],
"failed_systems_error_codes": self.grid_options[
"_failed_systems_error_codes"
].copy(),
"errors_exceeded": self.grid_options["_errors_exceeded"],
"errors_found": self.grid_options["_errors_found"],
"total_probability": self.grid_options["_probtot"],
"total_count": self.grid_options["_count"],
"start_timestamp": self.grid_options["_start_time_evolution"],
"end_timestamp": self.grid_options["_end_time_evolution"],
"total_mass_run": self.grid_options["_total_mass_run"],
"total_probability_weighted_mass_run": self.grid_options[
"_total_probability_weighted_mass_run"
],
"zero_prob_stars_skipped": self.grid_options["_zero_prob_stars_skipped"],
}
# Add analytics dict to the metadata too:
self.grid_ensemble_results["metadata"].update(analytics_dict)
##
# Clean up code: remove files, unset values, unload interpolators etc. This is placed in the general evolve function,
# because that makes for easier control
self._cleanup()
return analytics_dict
def _evolve_population(self):
"""
Function to evolve populations. This handles the setting up, evolving
and cleaning up of a population of stars.
Choices here are:
to evolve a population via multiprocessing or linearly on 1 core.
NOT IMPLEMENTED YET to evolve a population via a variable grid, a source file or MC
Tasks:
- TODO: include options for different ways of generating a population here. (i.e. MC or source file)
"""
##
# Prepare code/initialise grid.
# set custom logging, set up store_memaddr, build grid code. dry run grid code.
self._setup()
##
# Evolve systems: via grid_options one can choose to do this linearly, or
# multiprocessing method.
if (
self.grid_options["evolution_type"]
in self.grid_options["_evolution_type_options"]
):
if self.grid_options["evolution_type"] == "grid":
self._evolve_population_grid()
elif self.grid_options["evolution_type"] == "custom_generator":
# Use the same as the normal grid evolution but just a different generator
self._evolve_population_grid()
# elif self.grid_options["evolution_type"] == "mc":
# # TODO: add MC option
else:
print(
"Warning. you chose a wrong option for the grid evolution types.\
Please choose from the following: {}.".format(
self.grid_options["_evolution_type_options"]
)
)
# finished!
self.grid_options["_end_time_evolution"] = time.time()
# Log and print some information
dtsecs = (
self.grid_options["_end_time_evolution"]
- self.grid_options["_start_time_evolution"]
)
string1 = "Population-{} finished!\nThe total probability is {:g}.".format(
self.grid_options["_population_id"], self.grid_options["_probtot"]
)
string2 = "It took a total of {dtsecs} to run {starcount} systems on {ncores} cores\n = {totaldtsecs} of CPU time.\nMaximum memory use {memuse:.3f} MB".format(
dtsecs=timedelta(dtsecs),
starcount=self.grid_options["_total_starcount"],
ncores=self.grid_options["num_cores"],
totaldtsecs=timedelta(dtsecs * self.grid_options["num_cores"]),
memuse=sum(self.shared_memory["max_memory_use_per_thread"]),
)
verbose_print(self._boxed(string1, string2), self.grid_options["verbosity"], 0)
if self.grid_options["_errors_found"]:
# Some information afterwards
verbose_print(
self._boxed(
"During the run {} failed systems were found\nwith a total probability of {:g}\nwith the following unique error codes: {} ".format(
self.grid_options["_failed_count"],
self.grid_options["_failed_prob"],
self.grid_options["_failed_systems_error_codes"],
)
),
self.grid_options["verbosity"],
0,
)
# Some information afterwards
verbose_print(
"The full argline commands for {} these systems have been written to {}".format(
"ALL"
if not self.grid_options["_errors_exceeded"]
else "SOME (only the first ones, as there were too many to log all of them)",
os.path.join(
self.grid_options["tmp_dir"],
"failed_systems_{}_X.txt".format(
self.grid_options["_population_id"]
),
),
),
self.grid_options["verbosity"],
0,
)
else:
verbose_print(
"There were no errors found in this run.",
self.grid_options["verbosity"],
0,
)
def _get_stream_logger(self, level=logging.DEBUG):
"""Return logger with configured StreamHandler."""
stream_logger = logging.getLogger("stream_logger")
stream_logger.handlers = []
stream_logger.setLevel(level)
sh = logging.StreamHandler()
sh.setLevel(level)
fmt = "[%(asctime)s %(levelname)-8s %(processName)s] --- %(message)s"
formatter = logging.Formatter(fmt)
sh.setFormatter(formatter)
stream_logger.addHandler(sh)
return stream_logger
def _system_queue_filler(self, job_queue, num_cores):
"""
Function that is responsible for keeping the queue filled.
This will generate the systems until it is full, and then keeps trying to fill it.
Will have to play with the size of this.
"""
stream_logger = self._get_stream_logger()
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"setting up the system_queue_filler now")
# Setup of the generator
# Check again if we use custom generator or not:
if self.grid_options["evolution_type"] == "custom_generator":
generator = self.grid_options["custom_generator"]
else:
self._generate_grid_code(dry_run=False)
self._load_grid_function()
generator = self.grid_options["_system_generator"](
self, print_results=False
)
# TODO: build in method to handle with the HPC.
# Continuously fill the queue
for system_number, system_dict in enumerate(generator):
# skip systems before start_at, and apply modulo
if not (
system_number >= self.grid_options["start_at"]
and (system_number - self.grid_options["start_at"])
% self.grid_options["modulo"]
== 0
):
continue
# Put job in queue
job_queue.put((system_number, system_dict))
# Print some info
verbose_print(
"Queue produced system {}".format(system_number),
self.grid_options["verbosity"],
3,
)
# Send closing signal to workers. When they receive this they will terminate
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Signalling processes to stop") # DEBUG
for _ in range(num_cores):
job_queue.put("STOP")
def _evolve_population_grid(self):
"""
Function that handles running the population using multiprocessing.
First we set up the multiprocessing manager and the job and result queue.
Then we spawn <self.grid_options["num_cores"]> number of process instances,
and signal them to start.
While the processes are waiting for their instructions, we start the queue filler,
which goes over the grid code and puts all the tasks in a queue until its full.
The processes take these jobs, evolve the and store results.
When all the systems have been put in the queue we pass a STOP signal
that will make the processes wrap up.
We read out the information in the result queue and store them in the grid object
"""
# Set process name
setproctitle.setproctitle("binarycpython parent process")
# Set up the manager object that can share info between processes
manager = multiprocessing.Manager()
job_queue = manager.Queue(maxsize=self.grid_options["max_queue_size"])
# backwards compatibility
if "amt_cores" in self.grid_options:
self.grid_options["num_cores"] = self.grid_options["amt_cores"]
result_queue = manager.Queue(maxsize=self.grid_options["num_cores"])
# Create process instances
processes = []
for ID in range(self.grid_options["num_cores"]):
processes.append(
multiprocessing.Process(
target=self._process_run_population_grid,
args=(job_queue, result_queue, ID),
)
)
# Activate the processes
for p in processes:
p.start()
# Set up the system_queue
self._system_queue_filler(job_queue, num_cores=self.grid_options["num_cores"])
# Join the processes
for p in processes:
p.join()
# Handle the results by merging all the dictionaries. How that merging happens exactly is
# described in the merge_dicts description.
combined_output_dict = OrderedDict()
sentinel = object()
for output_dict in iter(result_queue.get, sentinel):
combined_output_dict = merge_dicts(combined_output_dict, output_dict)
if result_queue.empty():
break
# Extra ensemble result manipulation:
combined_output_dict["ensemble_results"]["ensemble"] = format_ensemble_results(
combined_output_dict["ensemble_results"].get("ensemble", {})
)
gc.collect()
# Take into account that we run this on multiple cores
combined_output_dict[
"_total_probability_weighted_mass_run"
] = combined_output_dict["_total_probability_weighted_mass_run"]
# Put the values back as object properties
self.grid_results = combined_output_dict["results"]
#################################
# Put Ensemble results
self.grid_ensemble_results = combined_output_dict[
"ensemble_results"
] # Ensemble results are also passed as output from that dictionary
# Add metadata
self.grid_ensemble_results["metadata"] = {}
self.grid_ensemble_results["metadata"]["population_id"] = self.grid_options[
"_population_id"
]
self.grid_ensemble_results["metadata"][
"total_probability_weighted_mass"
] = combined_output_dict["_total_probability_weighted_mass_run"]
self.grid_ensemble_results["metadata"][
"factored_in_probability_weighted_mass"
] = False
if self.grid_options["ensemble_factor_in_probability_weighted_mass"]:
multiply_values_dict(
self.grid_ensemble_results["ensemble"],
1
/ self.grid_ensemble_results["metadata"][
"total_probability_weighted_mass"
],
)
self.grid_ensemble_results["metadata"][
"factored_in_probability_weighted_mass"
] = True
# Add settings of the populations
all_info = self.return_all_info(
include_population_settings=True,
include_binary_c_defaults=True,
include_binary_c_version_info=True,
include_binary_c_help_all=True,
)
# self.grid_ensemble_results["metadata"]["settings"] = json.loads(
# json.dumps(all_info, default=binaryc_json_serializer)
# )
self.grid_ensemble_results['metadata']['settings'] = all_info
##############################
# Update grid options
self.grid_options["_failed_count"] = combined_output_dict["_failed_count"]
self.grid_options["_failed_prob"] = combined_output_dict["_failed_prob"]
self.grid_options["_failed_systems_error_codes"] = list(
set(combined_output_dict["_failed_systems_error_codes"])
)
self.grid_options["_errors_exceeded"] = combined_output_dict["_errors_exceeded"]
self.grid_options["_errors_found"] = combined_output_dict["_errors_found"]
self.grid_options["_probtot"] = combined_output_dict["_probtot"]
self.grid_options["_count"] = combined_output_dict["_count"]
self.grid_options["_total_mass_run"] = combined_output_dict["_total_mass_run"]
self.grid_options[
"_total_probability_weighted_mass_run"
] = combined_output_dict["_total_probability_weighted_mass_run"]
self.grid_options["_zero_prob_stars_skipped"] = combined_output_dict[
"_zero_prob_stars_skipped"
]
def _evolve_system_mp(self, full_system_dict):
"""
Function that the multiprocessing evolution method calls to evolve a system
this function is called by _process_run_population_grid
"""
binary_cmdline_string = self._return_argline(full_system_dict)
persistent_data_memaddr = -1
if self.bse_options.get("ensemble", 0) == 1:
persistent_data_memaddr = self.persistent_data_memory_dict[self.process_ID]
# print("thread {}: persistent_data_memaddr: ".format(self.process_ID), persistent_data_memaddr)
# vb2 logging
if self.grid_options["verbosity"] >= 2:
self.vb2print(full_system_dict, binary_cmdline_string)
# Get results binary_c
# print("running: {}".format(binary_cmdline_string))
out = _binary_c_bindings.run_system(
argstring=binary_cmdline_string,
custom_logging_func_memaddr=self.grid_options[
"custom_logging_func_memaddr"
],
store_memaddr=self.grid_options["_store_memaddr"],
population=1, # since this system is part of a population, we set this flag to prevent the store from being freed
persistent_data_memaddr=persistent_data_memaddr,
)
# Check for errors
_ = self._check_binary_c_error(out, full_system_dict)
# Have some user-defined function do stuff with the data.
if self.grid_options["parse_function"]:
self.custom_options["parameter_dict"] = full_system_dict
self.grid_options["parse_function"](self, out)
def _process_run_population_grid(self, job_queue, result_queue, ID):
"""
Worker process that gets items from the job_queue and runs those systems.
It keeps track of several things like failed systems, total time spent on systems etc.
Input:
job_queue: Queue object containing system dicts
result_queue: Queue where the resulting analytic dictionaries will be put in
ID: id of the worker process
"""
# set start timer
start_process_time = datetime.datetime.now()
#
self.process_ID = (
ID # Store the ID as a object property again, lets see if that works.
)
stream_logger = self._get_stream_logger()
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Setting up processor: process-{self.process_ID}")
# Set the process names
name = "binarycpython population thread {}".format(ID)
name_proc = "binarycpython population process {}".format(ID)
setproctitle.setproctitle(name_proc)
# setproctitle.setthreadtitle(name)
# Set to starting up
with open(
os.path.join(
self.grid_options["tmp_dir"],
"process_status",
"process_{}.txt".format(self.process_ID),
),
"w",
) as f:
f.write("STARTING")
f.close()
# lets try out making stores for all the grids:
self.grid_options["_store_memaddr"] = _binary_c_bindings.return_store_memaddr()
verbose_print(
"Process {} started at {}.\tUsing store memaddr {}".format(
ID,
datetime.datetime.now().isoformat(),
self.grid_options["_store_memaddr"],
),
self.grid_options["verbosity"],
3,
)
# Set the ensemble memory address
if self.bse_options.get("ensemble", 0) == 1:
# set persistent data memory address if necessary.
persistent_data_memaddr = (
_binary_c_bindings.return_persistent_data_memaddr()
)
self.persistent_data_memory_dict = {
self.process_ID: persistent_data_memaddr
}
verbose_print(
"\tUsing persistent_data memaddr: {}".format(persistent_data_memaddr),
self.grid_options["verbosity"],
3,
)
# Set up local variables
localcounter = (
0 # global counter for the whole loop. (need to be ticked every loop)
)
probability_of_systems_run = (
0 # counter for the probability of the actual systems this tread ran
)
number_of_systems_run = (
0 # counter for the actual amt of systems this thread ran
)
zero_prob_stars_skipped = 0
total_time_calling_binary_c = 0
total_mass_run = 0
total_probability_weighted_mass_run = 0
# variables for the statu bar prints
start_grid_time = time.time()
next_log_time = (
self.shared_memory["prev_log_time"][0] + self.grid_options["log_dt"]
)
next_mem_update_time = start_grid_time + self.grid_options["log_dt"]
############################################################
# Go over the queue
for system_number, system_dict in iter(job_queue.get, "STOP"):
# At the first system set the status of the thread to running
if localcounter == 0:
# Set status to running
with open(
os.path.join(
self.grid_options["tmp_dir"],
"process_status",
"process_{}.txt".format(self.process_ID),
),
"w",
) as f:
f.write("RUNNING")
f.close()
# Combine that with the other settings
full_system_dict = self.bse_options.copy()
full_system_dict.update(system_dict)
# In the first system, explicitly check all the keys that are passed to see if
# they match the keys known to binary_c.
# Won't do that every system cause that is a bit of a waste of computing time.
# TODO: check if we can rename the below var
if number_of_systems_run == 0:
# TODO: Put this someplace else and wrap in a function call
for key in full_system_dict.keys():
if not key in self.available_keys:
# Deal with special keys
if not any(
[
True
if (
key.startswith(param[:-2])
and len(param[:-2]) < len(key)
)
else False
for param in self.special_params
]
):
msg = "Error: Found a parameter unknown to binary_c: {}. Abort".format(
key
)
raise ValueError(msg)
# self._print_info(
# i + 1, self.grid_options["_total_starcount"], full_system_dict
# )
# verbose_print(
# "Process {} is handling system {}".format(ID, system_number),
# self.grid_options["verbosity"],
# 1,
# )
######################
# Print status of runs
# save the current time (used often)
now = time.time()
# update memory use stats every log_dt seconds (not every time, this is likely a bit expensive)
if now > next_mem_update_time:
m = mem_use()
self.shared_memory["memory_use_per_thread"][ID] = m
next_mem_update_time = now + self.grid_options["log_dt"]
if m > self.shared_memory["max_memory_use_per_thread"][ID]:
self.shared_memory["max_memory_use_per_thread"][ID] = m
# calculate the next logging time
next_log_time = (
self.shared_memory["prev_log_time"][0] + self.grid_options["log_dt"]
)
# Check if we need to log info again
# TODO: Check if we can put this functionality elsewhere
if now > next_log_time:
# we have exceeded the next log time : output and update timers
# Lock the threads. TODO: Do we need to release this?
lock = multiprocessing.Lock()
# Do the printing itself
self.vb1print(ID, now, system_number, system_dict)
# Set some values for next time
next_log_time = now + self.grid_options["log_dt"]
# print("PREV ",self.shared_memory["prev_log_time"])
# print("N LOG STATS",self.shared_memory["n_saved_log_stats"].value)
# shift the arrays
self.shared_memory["prev_log_time"][
-(self.grid_options["n_logging_stats"] - 1) :
] = self.shared_memory["prev_log_time"][
: (self.grid_options["n_logging_stats"] - 1)
]
self.shared_memory["prev_log_system_number"][
-(self.grid_options["n_logging_stats"] - 1) :
] = self.shared_memory["prev_log_system_number"][
: (self.grid_options["n_logging_stats"] - 1)
]
# set the current time and system number
self.shared_memory["prev_log_time"][0] = now
self.shared_memory["prev_log_system_number"][0] = system_number
# increase the number of stats
self.shared_memory["n_saved_log_stats"].value = min(
self.shared_memory["n_saved_log_stats"].value + 1,
self.grid_options["n_logging_stats"],
)
# print("FIRST (0) ",self.shared_memory["prev_log_time"][0])
# print("LAST (",self.shared_memory["n_saved_log_stats"].value-1,")",self.shared_memory["prev_log_time"][self.shared_memory["n_saved_log_stats"].value-1])
###############
# Log current system info
# In some cases, the whole run crashes. To be able to figure out which system
# that was on, we log each current system to a file (each thread has one).
# Each new system overrides the previous
if self.grid_options["log_args"]:
with open(
os.path.join(
self.grid_options["log_args_dir"],
"current_system",
"process_{}.txt".format(self.process_ID),
),
"w",
) as f:
binary_cmdline_string = self._return_argline(full_system_dict)
f.write(binary_cmdline_string)
f.close()
##############
# Running the system
start_runtime_binary_c = time.time()
# If we want to actually evolve the systems
if self.grid_options["_actually_evolve_system"]:
run_system = True
# Check option to ignore 0 probability systems
if not self.grid_options["run_zero_probability_system"]:
if full_system_dict.get("probability", 1) == 0:
run_system = False
zero_prob_stars_skipped += 1
if run_system:
# Evolve the system
self._evolve_system_mp(full_system_dict)
end_runtime_binary_c = time.time()
total_time_calling_binary_c += (
end_runtime_binary_c - start_runtime_binary_c
) # keep track of total binary_c call time
############
# Logging runtime
# Debug line: logging all the lines
if self.grid_options["log_runtime_systems"] == 1:
with open(
os.path.join(
self.grid_options["tmp_dir"],
"runtime_systems",
"process_{}.txt".format(self.process_ID),
),
"a+",
) as f:
binary_cmdline_string = self._return_argline(full_system_dict)
f.write(
"{} {} '{}'\n".format(
start_runtime_binary_c,
end_runtime_binary_c - start_runtime_binary_c,
binary_cmdline_string,
)
)
f.close()
####################
# Tallying system information
# Keep track of systems:
probability_of_systems_run += full_system_dict.get("probability", 1)
number_of_systems_run += 1
localcounter += 1
# Tally up some numbers
total_mass_system = (
full_system_dict.get("M_1", 0)
+ full_system_dict.get("M_2", 0)
+ full_system_dict.get("M_3", 0)
+ full_system_dict.get("M_4", 0)
)
total_mass_run += total_mass_system
total_probability_weighted_mass_run += (
total_mass_system * full_system_dict.get("probability", 1)
)
# Set status to finishing
with open(
os.path.join(
self.grid_options["tmp_dir"],
"process_status",
"process_{}.txt".format(self.process_ID),
),
"w",
) as f:
f.write("FINISHING")
f.close()
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Process-{self.process_ID} is finishing.")
###########################
# Handle ensemble outut
# if ensemble==1, then either directly write that data to a file, or combine everything into 1 file.
ensemble_json = {} # Make sure it exists already
if self.bse_options.get("ensemble", 0) == 1:
verbose_print(
"Process {}: is freeing ensemble output (using persistent_data memaddr {})".format(
ID, self.persistent_data_memory_dict[self.process_ID]
),
self.grid_options["verbosity"],
3,
)
ensemble_raw_output = (
_binary_c_bindings.free_persistent_data_memaddr_and_return_json_output(
self.persistent_data_memory_dict[self.process_ID]
)
)
if ensemble_raw_output is None:
verbose_print(
"Process {}: Warning! Ensemble output is empty. ".format(ID),
self.grid_options["verbosity"],
1,
)
# save the ensemble chunk to a file
if (
self.grid_options["save_ensemble_chunks"] is True
or self.grid_options["combine_ensemble_with_thread_joining"] is False
):
output_file = os.path.join(
self.custom_options["data_dir"],
"ensemble_output_{}_{}.json".format(
self.grid_options["_population_id"], self.process_ID
),
)
verbose_print(
"Writing process {} JSON ensemble chunk output to {} ".format(
ID, output_file
),
self.grid_options["verbosity"],
1,
)
ensemble_output = extract_ensemble_json_from_string(ensemble_raw_output)
self.write_ensemble(output_file, ensemble_output)
# combine ensemble chunks
if self.grid_options["combine_ensemble_with_thread_joining"] is True:
verbose_print(
"Process {}: Extracting ensemble info from raw string".format(ID),
self.grid_options["verbosity"],
1,
)
ensemble_json["ensemble"] = extract_ensemble_json_from_string(
ensemble_raw_output
) # Load this into a dict so that we can combine it later
##########################
# Clean up and return
verbose_print(
"process {} free memory and return ".format(ID),
self.grid_options["verbosity"],
1,
)
# free store memory:
_binary_c_bindings.free_store_memaddr(self.grid_options["_store_memaddr"])
# Return a set of results and errors
output_dict = {
"results": self.grid_results,
"ensemble_results": ensemble_json,
"_failed_count": self.grid_options["_failed_count"],
"_failed_prob": self.grid_options["_failed_prob"],
"_failed_systems_error_codes": self.grid_options[
"_failed_systems_error_codes"
],
"_errors_exceeded": self.grid_options["_errors_exceeded"],
"_errors_found": self.grid_options["_errors_found"],
"_probtot": probability_of_systems_run,
"_count": number_of_systems_run,
"_total_mass_run": total_mass_run,
"_total_probability_weighted_mass_run": total_probability_weighted_mass_run,
"_zero_prob_stars_skipped": zero_prob_stars_skipped,
}
end_process_time = datetime.datetime.now()
# thread end message
colour = "cyan on black"
verbose_print(
self._boxed(
"{colour}Process {ID} finished:\ngenerator started at {start}\ngenerator finished at {end}\ntotal: {timesecs}\nof which {binary_c_secs} with binary_c\nRan {nsystems} systems\nwith a total probability of {psystems:g}\n{failcolour}This thread had {nfail} failing systems{colour}\n{failcolour}with a total failed probability of {pfail}{colour}\n{zerocolour}Skipped a total of {nzero} zero-probability systems{zeroreset}\n".format(
colour=self.ANSI_colours[colour],
ID=ID,
start=start_process_time.isoformat(),
end=end_process_time.isoformat(),
timesecs=timedelta(
(end_process_time - start_process_time).total_seconds()
),
binary_c_secs=timedelta(total_time_calling_binary_c),
nsystems=number_of_systems_run,
psystems=probability_of_systems_run,
failcolour=self.ANSI_colours["red"]
if self.grid_options["_failed_count"] > 0
else "",
failreset=self.ANSI_colours[colour]
if self.grid_options["_failed_count"] > 0
else "",
nfail=self.grid_options["_failed_count"],
pfail=self.grid_options["_failed_prob"],
nzero=zero_prob_stars_skipped,
zerocolour=self.ANSI_colours["yellow"]
if zero_prob_stars_skipped > 0
else "",
zeroreset=self.ANSI_colours[colour]
if zero_prob_stars_skipped > 0
else "",
),
colour=colour,
),
self.grid_options["verbosity"],
1,
)
# Write summary
summary_dict = {
"population_id": self.grid_options["_population_id"],
"process_id": self.process_ID,
"start_process_time": start_process_time.timestamp(),
"end_process_time": end_process_time.timestamp(),
"total_time_calling_binary_c": total_time_calling_binary_c,
"number_of_systems_run": number_of_systems_run,
"probability_of_systems_run": probability_of_systems_run,
"failed_systems": self.grid_options["_failed_count"],
"failed_probability": self.grid_options["_failed_prob"],
"failed_system_error_codes": self.grid_options[
"_failed_systems_error_codes"
],
"zero_prob_stars_skipped": zero_prob_stars_skipped,
}
with open(
os.path.join(
self.grid_options["tmp_dir"],
"process_summary",
"process_{}.json".format(self.process_ID),
),
"w",
) as f:
f.write(json.dumps(summary_dict, indent=4))
f.close()
# Set status to finished
with open(
os.path.join(
self.grid_options["tmp_dir"],
"process_status",
"process_{}.txt".format(self.process_ID),
),
"w",
) as f:
f.write("FINISHED")
f.close()
verbose_print(
"process {} queue put output_dict ".format(ID),
self.grid_options["verbosity"],
1,
)
result_queue.put(output_dict)
if self.grid_options["verbosity"] >= _LOGGER_VERBOSITY_LEVEL:
stream_logger.debug(f"Process-{self.process_ID} is finished.")
# Don't do this : Clean up the interpolators if they exist
# TODO: make a cleanup function for the individual threads
# TODO: make sure this is necessary. Actually its probably not, because we have a centralised queue
verbose_print(
"process {} return ".format(ID),
self.grid_options["verbosity"],
1,
)
return
# Single system
def evolve_single(self, clean_up_custom_logging_files: bool = True) -> Any:
"""
Function to run a single system, based on the settings in the grid_options
The output of the run gets returned, unless a parse function is given to this function.
Args:
clean_up_custom_logging_files: whether the clean up all the custom_logging files.
returns:
either returns the raw binary_c output, or whatever the parse_function does
"""
### Custom logging code:
self._set_custom_logging()
# Check if there are actually arguments passed:
if self.bse_options:
# Get argument line and
argline = self._return_argline(self.bse_options)
verbose_print(
"Running {}".format(argline), self.grid_options["verbosity"], 1
)
# Run system
out = _binary_c_bindings.run_system(
argstring=argline,
custom_logging_func_memaddr=self.grid_options[
"custom_logging_func_memaddr"
],
store_memaddr=self.grid_options["_store_memaddr"],
population=0,
)
# Clean up custom logging
if clean_up_custom_logging_files:
self._clean_up_custom_logging(evol_type="single")
# Parse output and return the result
if self.grid_options["parse_function"]:
return self.grid_options["parse_function"](self, out)
# Otherwise just return the raw output
return out
else:
msg = "No actual evolution options passed to the evolve call. Aborting"
raise ValueError(msg)
############################################################
def _setup(self):
"""
Function to set up the necessary stuff for the population evolution.
The idea is to do all the stuff that is necessary for a population to run.
Since we have different methods of running a population, this setup function
will do different things depending on different settings
Tasks:
TODO: Make other kinds of populations possible. i.e, read out type of grid,
and set up accordingly
TODO: make this function more general. Have it explicitly set the system_generator
function
"""
# Make sure the subdirs of the tmp dir exist:
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "failed_systems"), exist_ok=True
)
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "current_system"), exist_ok=True
)
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "process_status"), exist_ok=True
)
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "process_summary"), exist_ok=True
)
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "runtime_systems"), exist_ok=True
)
# Check for parse function
if not self.grid_options["parse_function"]:
print("Warning: No parse function set. Make sure you intended to do this.")
# #######################
# ### Custom logging code:
self._set_custom_logging()
### ensemble: make some checks for this
## check the settings and set all the warnings.
if self.bse_options.get("ensemble", None):
if not self.bse_options.get("ensemble_defer", 0) == 1:
verbose_print(
"Error, if you want to run an ensemble in a population, the output needs to be deferred. Please set 'ensemble_defer' to 1",
self.grid_options["verbosity"],
0,
)
raise ValueError
if not any(
[key.startswith("ensemble_filter_") for key in self.bse_options]
):
verbose_print(
"Warning: Running the ensemble without any filter requires a lot of available RAM",
self.grid_options["verbosity"],
0,
)
if self.bse_options.get("ensemble_filters_off", 0) != 1:
verbose_print(
"Warning: Running the ensemble without any filter requires a lot of available RAM",
self.grid_options["verbosity"],
0,
)
if self.grid_options["combine_ensemble_with_thread_joining"] == False:
if not self.custom_options.get("data_dir", None):
verbose_print(
"Error: chosen to write the ensemble output directly to files but data_dir isn't set",
self.grid_options["verbosity"],
0,
)
raise ValueError
# Unset some value
self.grid_options["_probtot"] = 0
## Check which type of population generation
# grid type
if self.grid_options["evolution_type"] == "grid":
#######################
# Dry run and getting starcount
# Put in check
if len(self.grid_options["_grid_variables"]) == 0:
print("Error: you haven't defined any grid variables! Aborting")
raise ValueError
# Set up the grid code with a dry run option to see total probability
if self.grid_options["do_dry_run"]:
print("Doing dry run to calculate total starcount and probability")
self._generate_grid_code(dry_run=True)
# Load the grid code
self._load_grid_function()
# Do a dry run
self._dry_run()
verbose_print(
self._boxed(
"Total starcount for this run is {starcount}".format(
starcount=self.grid_options["_total_starcount"]
),
"Total probability is {probtot:g}".format(
probtot=self.grid_options["_probtot"]
),
),
self.grid_options["verbosity"],
0,
)
if self.grid_options["exit_after_dry_run"]:
sys.exit()
#######################
# Reset values and prepare the grid function
self.grid_options[
"_probtot"
] = 0 # To make sure that the values are reset. TODO: fix this in a cleaner way
self.grid_options[
"_start_time_evolution"
] = time.time() # Setting start time of grid
# # Making sure the loaded grid code isn't lingering in the main PID
# self._generate_grid_code(dry_run=False)
# #
# self._load_grid_function()
#
self.grid_options["_system_generator"] = None
# user-provided custom generator
if self.grid_options["evolution_type"] == "custom_generator":
if not isinstance(self.grid_options["custom_generator"], Iterable):
print(
"Error. provided no or wrong custom value for the system generator (custom_generator: {})".format(
self.grid_options["custom_generator"]
)
)
raise ValueError
# NOTE: In the part above i apparently have moved the load grid function call to another part. Now i wonder if that was useful, because it would be best if that is handled in this function
# TODO: place the load grid function back to the part above
# Source file
elif self.grid_options["evolution_type"] == "source_file":
# TODO: fix this function
raise ValueError("This functionality is not available yet")
# Source file
elif self.grid_options["evolution_type"] == "montecarlo":
if self.grid_options["do_dry_run"]:
# Do a dry run
self._dry_run_source_file()
print(
"Total starcount for this run will be: {}".format(
self.grid_options["_total_starcount"]
)
)
#######################
# Reset values and prepare the grid function
self.grid_options[
"_probtot"
] = 0 # To make sure that the values are reset. TODO: fix this in a cleaner way
self.grid_options[
"_start_time_evolution"
] = time.time() # Setting start time of grid
#
# TODO: fix this function
raise ValueError("This functionality is not available yet")
#######################
# Reset values and prepare the grid function
self.grid_options[
"_probtot"
] = 0 # To make sure that the values are reset. TODO: fix this in a cleaner way
self.grid_options[
"_start_time_evolution"
] = time.time() # Setting start time of grid
def _cleanup(self):
"""
Function that handles all the cleaning up after the grid has been generated and/or run
- reset values to 0
- remove grid file
- unload grid function/module
- remove dry grid file
- unload dry grid function/module
"""
# Reset values
self.grid_options["_count"] = 0
self.grid_options["_probtot"] = 0
self.grid_options["_system_generator"] = None
self.grid_options["_failed_count"] = 0
self.grid_options["_failed_prob"] = 0
self.grid_options["_errors_found"] = False
self.grid_options["_errors_exceeded"] = False
self.grid_options["_failed_systems_error_codes"] = []
self.grid_options["_total_mass_run"] = 0
self.grid_options["_total_probability_weighted_mass_run"] = 0
# Remove files
# TODO: remove files
# Unload functions
# TODO: unload functions
# Unload/free custom_logging_code
# TODO: cleanup custom logging code.
###################################################
# Grid code functions
#
# Function below are used to run populations with
# a variable grid
###################################################
def _add_code(self, *args, indent=0):
"""
Function to add code to the grid code string
add code to the code_string
indent (=0) is added once at the beginning
mindent (=0) is added for every line
don't use both!
"""
indent_block = self._indent_block(indent)
for thing in args:
self.code_string += indent_block + thing
def _indent_block(self, n=0):
"""
return an indent block, with n extra blocks in it
"""
return (self.indent_depth + n) * self.indent_string
def _increment_indent_depth(self, delta):
"""
increment the indent indent_depth by delta
"""
self.indent_depth += delta
def _generate_grid_code(self, dry_run=False):
"""
Function that generates the code from which the population will be made.
dry_run: when True, it will return the starcount at the end so that we know
what the total number of systems is.
The phasevol values are handled by generating a second array
# TODO: Add correct logging everywhere
# TODO: add part to handle separation if orbital_period is added. Idea. use default values
# for orbital parameters and possibly overwrite those or something.
# TODO: add sensible description to this function.
# TODO: Check whether all the probability and phasevol values are correct.
# TODO: import only the necessary packages/functions
# TODO: Put all the masses, eccentricities and periods in there already
# TODO: Put the certain blocks that are repeated in some sub functions
# TODO: make sure running systems with multiplicity 3+ is also possible.
Results in a generated file that contains a system_generator function.
"""
verbose_print("Generating grid code", self.grid_options["verbosity"], 1)
total_grid_variables = len(self.grid_options["_grid_variables"])
self._add_code(
# Import packages
"import math\n",
"import numpy as np\n",
"from collections import OrderedDict\n",
"from binarycpython.utils.distribution_functions import *\n",
"from binarycpython.utils.spacing_functions import *\n",
"from binarycpython.utils.useful_funcs import *\n",
"\n\n",
# Make the function
"def grid_code(self, print_results=True):\n",
)
# Increase indent_depth
self._increment_indent_depth(+1)
self._add_code(
# Write some info in the function
"# Grid code generated on {}\n".format(datetime.datetime.now().isoformat()),
"# This function generates the systems that will be evolved with binary_c\n\n"
# Set some values in the generated code:
"# Setting initial values\n",
"_total_starcount = 0\n",
"starcounts = [0 for i in range({})]\n".format(total_grid_variables + 1),
"probabilities = {}\n",
"probabilities_list = [0 for i in range({})]\n".format(
total_grid_variables + 1
),
"probabilities_sum = [0 for i in range({})]\n".format(
total_grid_variables + 1
),
"parameter_dict = {}\n",
"phasevol = 1\n",
)
# Set up the system parameters
self._add_code(
"M_1 = None\n",
"M_2 = None\n",
"M_3 = None\n",
"M_4 = None\n",
"orbital_period = None\n",
"orbital_period_triple = None\n",
"orbital_period_quadruple = None\n",
"eccentricity = None\n",
"eccentricity2 = None\n",
"eccentricity3 = None\n",
"\n",
# Prepare the probability
"# setting probability lists\n",
)
for grid_variable_el in sorted(
self.grid_options["_grid_variables"].items(),
key=lambda x: x[1]["grid_variable_number"],
):
# Make probabilities dict
grid_variable = grid_variable_el[1]
self._add_code('probabilities["{}"] = 0\n'.format(grid_variable["name"]))
#################################################################################
# Start of code generation
#################################################################################
self._add_code("\n")
# turn vb to True to have debugging output
vb = False
# Generate code
print("Generating grid code")
for loopnr, grid_variable_el in enumerate(
sorted(
self.grid_options["_grid_variables"].items(),
key=lambda x: x[1]["grid_variable_number"],
)
):
verbose_print(
"Constructing/adding: {}".format(grid_variable_el[0]),
self.grid_options["verbosity"],
2,
)
grid_variable = grid_variable_el[1]
####################
# top code
if grid_variable["topcode"]:
self._add_code(grid_variable["topcode"])
#########################
# Setting up the for loop
# Add comment for for loop
self._add_code(
"# for loop for variable {name} gridtype {gridtype}".format(
name=grid_variable["name"],
gridtype=grid_variable["gridtype"],
) + "\n",
"sampled_values_{} = {}".format(
grid_variable["name"], grid_variable["samplerfunc"]
)
+ "\n")
if False:
self._add_code(
"print('samples','{name}',':',np.exp(sampled_values_{name}))\n".format(
name=grid_variable["name"],
)
)
if vb:
self._add_code(
"print('sample {name} from',sampled_values_{name})".format(
name=grid_variable["name"]
)
+ "\n"
)
# calculate number of values and starting location
#
# if we're sampling a continuous variable, we
# have one fewer grid point than the length of the
# sampled_values list
if (
grid_variable["gridtype"] == "centred"
or grid_variable["gridtype"] == "centre"
or grid_variable["gridtype"] == "center"
or grid_variable["gridtype"] == "edge"
or grid_variable["gridtype"] == "left edge"
or grid_variable["gridtype"] == "left"
or grid_variable["gridtype"] == "right"
or grid_variable["gridtype"] == "right edge"
):
offset = -1
elif grid_variable["gridtype"] == "discrete":
# discrete variables sample all the points
offset = 0
start = 0
# for loop over the variable
if vb:
self._add_code(
"print(\"var {name} values \",sampled_values_{name},\" len \",len(sampled_values_{name})+{offset},\" gridtype {gridtype} offset {offset}\\n\")\n".format(
name=grid_variable["name"],
offset=offset,
gridtype=grid_variable['gridtype'],
)
)
self._add_code(
"for {name}_sample_number in range({start},len(sampled_values_{name})+{offset}):".format(
name=grid_variable["name"],
offset=offset,
start=start
)
+ "\n"
)
self._increment_indent_depth(+1)
# {}_this_index is this grid point's index
# {}_prev_index and {}_next_index are the previous and next grid points,
# (which can be None if there is no previous or next, or if
# previous and next should not be used: this is deliberate)
#
if grid_variable["gridtype"] == "discrete":
# discrete grids only care about this,
# both prev and next should be None to
# force errors where they are used
self._add_code(
"{name}_this_index = {name}_sample_number ".format(
name=grid_variable["name"],
),
)
self._add_code(
"\n",
"{name}_prev_index = None if {name}_this_index == 0 else ({name}_this_index - 1) ".format(
name=grid_variable["name"],
),
"\n",
)
self._add_code(
"\n",
"{name}_next_index = None if {name}_this_index >= (len(sampled_values_{name})+{offset} - 1) else ({name}_this_index + 1)".format(
name=grid_variable["name"],
offset=offset
),
"\n",
)
elif (grid_variable["gridtype"] == "centred"
or grid_variable["gridtype"] == "centre"
or grid_variable["gridtype"] == "center"
or grid_variable["gridtype"] == "edge"
or grid_variable["gridtype"] == "left"
or grid_variable["gridtype"] == "left edge"):
# left and centred grids
self._add_code("if {}_sample_number == 0:\n".format(grid_variable["name"]))
self._add_code("{}_this_index = 0;\n".format(grid_variable["name"]), indent=1)
self._add_code("else:\n")
self._add_code("{name}_this_index = {name}_sample_number ".format(name=grid_variable["name"]),indent=1)
self._add_code("\n")
self._add_code("{name}_prev_index = ({name}_this_index - 1) if {name}_this_index > 0 else None ".format(name=grid_variable["name"]))
self._add_code("\n")
self._add_code("{name}_next_index = {name}_this_index + 1".format(name=grid_variable["name"]))
self._add_code("\n")
elif(grid_variable["gridtype"] == "right" or
grid_variable["gridtype"] == "right edge"):
# right edged grid
self._add_code("if {name}_sample_number == 0:\n".format(name=grid_variable["name"]))
self._add_code("{name}_this_index = 1;\n".format(name=grid_variable["name"]),indent=1)
self._add_code("else:\n")
self._add_code("{name}_this_index = {name}_sample_number + 1 ".format(name=grid_variable["name"],),indent=1)
self._add_code("\n")
self._add_code("{name}_prev_index = {name}_this_index - 1".format(name=grid_variable["name"]))
self._add_code("\n")
self._add_code("{name}_next_index = ({name}_this_index + 1) if {name}_this_index < len(sampled_values_{name}) else None".format(name=grid_variable["name"]))
self._add_code("\n")
# calculate phase volume
if(grid_variable["dphasevol"] == -1):
# no phase volume required so set it to 1.0
self._add_code("dphasevol_{name} = 1.0 # 666\n".format(name=grid_variable["name"]))
elif(grid_variable["gridtype"] == "right" or
grid_variable["gridtype"] == "right edge"):
# right edges always have this and prev defined
self._add_code(
"dphasevol_{name} = (sampled_values_{name}[{name}_this_index] - sampled_values_{name}[{name}_prev_index])".format(name=grid_variable["name"])
+ "\n"
)
elif grid_variable["gridtype"] == "discrete":
# discrete might have next defined, use it if we can,
# otherwise use prev
self._add_code(
"dphasevol_{name} = (sampled_values_{name}[{name}_next_index] - sampled_values_{name}[{name}_this_index]) if {name}_next_index else (sampled_values_{name}[{name}_this_index] - sampled_values_{name}[{name}_prev_index])".format(name=grid_variable["name"])
+ "\n"
)
else:
# left and centred always have this and next defined
self._add_code(
"dphasevol_{name} = (sampled_values_{name}[{name}_next_index] - sampled_values_{name}[{name}_this_index])".format(name=grid_variable["name"])
+ "\n"
)
##############
# Add phasevol check:
self._add_code("if dphasevol_{name} <= 0:\n".format(name=grid_variable["name"]))
# TODO: We might actually want to add the starcount and probability to the totals regardless.
# n that case we need another local variable which will prevent it from being run but will track those parameters
# Add phasevol check action:
self._add_code(
'print("Grid generator: dphasevol_{name} <= 0! (this=",{name}_this_index,"=",sampled_values_{name}[{name}_this_index],", next=",{name}_next_index,"=",sampled_values_{name}[{name}_next_index],") Skipping current sample.")'.format(name=grid_variable["name"])
+ "\n",
"continue\n",
indent=1,
)
if vb:
self._add_code(
"print('sample {name} from ',sampled_values_{name},' at this=',{name}_this_index,', next=',{name}_next_index)".format(name=grid_variable["name"])
+ "\n"
)
# select sampled point location based on gridtype (left, centre or right)
if (
grid_variable["gridtype"] == "edge"
or grid_variable["gridtype"] == "left"
or grid_variable["gridtype"] == "left edge"
or grid_variable["gridtype"] == "right"
or grid_variable["gridtype"] == "right edge"
or grid_variable['gridtype'] == 'discrete'
):
self._add_code(
"{name} = sampled_values_{name}[{name}_this_index]".format(
name=grid_variable["name"])
+ "\n"
)
elif (
grid_variable["gridtype"] == "centred"
or grid_variable["gridtype"] == "centre"
or grid_variable["gridtype"] == "center"
):
self._add_code(
"{name} = 0.5 * (sampled_values_{name}[{name}_next_index] + sampled_values_{name}[{name}_this_index])".format(name=grid_variable["name"])
+ "\n"
)
else:
msg = "Unknown gridtype value {type}.".format(type=grid_variable['gridtype'])
raise ValueError(msg)
if vb:
self._add_code(
"print('hence {name} = ',{name})\n".format(
name=grid_variable["name"]
)
)
#################################################################################
# Check condition and generate for loop
# If the grid variable has a condition, write the check and the action
if grid_variable["condition"]:
self._add_code(
# Add comment
"# Condition for {name}\n".format(name=grid_variable["name"]),
# Add condition check
"if not {condition}:\n".format(condition=grid_variable["condition"]),
indent=0,
)
# Add condition failed action:
if self.grid_options["verbosity"] >= 3:
self._add_code(
'print("Grid generator: Condition for {name} not met!")'.format(
name=grid_variable["name"]
)
+ "\n",
"continue" + "\n",
indent=1,
)
else:
self._add_code(
"continue" + "\n",
indent=1,
)
# Add some whitespace
self._add_code("\n")
# Add some whitespace
self._add_code("\n")
#########################
# Setting up pre-code and value in some cases
# Add pre-code
if grid_variable["precode"]:
self._add_code(
"{precode}".format(
precode=grid_variable["precode"].replace(
"\n", "\n" + self._indent_block(0)
)
)
+ "\n"
)
# Set phasevol
self._add_code(
"phasevol *= dphasevol_{name}\n".format(
name=grid_variable["name"],
)
)
#######################
# Probabilities
# Calculate probability
self._add_code(
"\n",
"# Setting probabilities\n",
"d{name} = dphasevol_{name} * ({probdist})".format(
name=grid_variable["name"],
probdist=grid_variable["probdist"],
)
+ "\n",
# Save probability sum
"probabilities_sum[{n}] += d{name}".format(
n=grid_variable["grid_variable_number"],
name=grid_variable["name"]
)
+ "\n",
)
if grid_variable["grid_variable_number"] == 0:
self._add_code(
"probabilities_list[0] = d{name}".format(name=grid_variable["name"]) + "\n"
)
else:
self._add_code(
"probabilities_list[{this}] = probabilities_list[{prev}] * d{name}".format(
this=grid_variable["grid_variable_number"],
prev=grid_variable["grid_variable_number"] - 1,
name=grid_variable["name"],
)
+ "\n"
)
##############
# postcode
if grid_variable["postcode"]:
self._add_code(
"{postcode}".format(
postcode=grid_variable["postcode"].replace(
"\n", "\n" + self._indent_block(0)
)
)
+ "\n"
)
#######################
# Increment starcount for this parameter
self._add_code(
"\n",
"# Increment starcount for {name}\n".format(name=grid_variable["name"]),
"starcounts[{n}] += 1".format(
n=grid_variable["grid_variable_number"],
)
+ "\n",
# Add value to dict
'parameter_dict["{name}"] = {name}'.format(
name=grid_variable["parameter_name"]
)
+ "\n",
"\n",
)
self._increment_indent_depth(-1)
# The final parts of the code, where things are returned, are within the deepest loop,
# but in some cases code from a higher loop needs to go under it again
# SO I think its better to put an if statement here that checks
# whether this is the last loop.
if loopnr == len(self.grid_options["_grid_variables"]) - 1:
self._write_gridcode_system_call(
grid_variable,
dry_run,
grid_variable["branchpoint"],
grid_variable["branchcode"],
)
# increment indent_depth
self._increment_indent_depth(+1)
####################
# bottom code
if grid_variable["bottomcode"]:
self._add_code(grid_variable["bottomcode"])
self._increment_indent_depth(-1)
self._add_code("\n")
# Write parts to write below the part that yield the results.
# this has to go in a reverse order:
# Here comes the stuff that is put after the deepest nested part that calls returns stuff.
# Here we will have a
reverse_sorted_grid_variables = sorted(
self.grid_options["_grid_variables"].items(),
key=lambda x: x[1]["grid_variable_number"],
reverse=True,
)
for loopnr, grid_variable_el in enumerate(reverse_sorted_grid_variables):
grid_variable = grid_variable_el[1]
self._increment_indent_depth(+1)
self._add_code(
"#" * 40 + "\n",
"# Code below is for finalising the handling of this iteration of the parameter {name}\n".format(
name=grid_variable["name"]
),
)
# Set phasevol
# TODO: fix. this isn't supposed to be the value that we give it here. discuss
self._add_code("phasevol /= dphasevol_{name}\n\n".format(name=grid_variable["name"]))
self._increment_indent_depth(-2)
# Check the branchpoint part here. The branchpoint makes sure that we can construct
# a grid with several multiplicities and still can make the system calls for each
# multiplicity without reconstructing the grid each time
if grid_variable["branchpoint"] > 0:
self._increment_indent_depth(+1)
self._add_code(
# Add comment
"# Condition for branchpoint at {}".format(
reverse_sorted_grid_variables[loopnr + 1][1]["name"]
)
+ "\n",
# # Add condition check
# "if not {}:".format(grid_variable["condition"])
# + "\n"
# Add branchpoint
"if multiplicity=={}:".format(grid_variable["branchpoint"]) + "\n",
)
self._write_gridcode_system_call(
reverse_sorted_grid_variables[loopnr + 1][1],
dry_run,
grid_variable["branchpoint"],
grid_variable["branchcode"],
)
self._increment_indent_depth(-1)
self._add_code("\n")
###############################
# Finalising print statements
#
self._increment_indent_depth(+1)
self._add_code("\n", "#" * 40 + "\n", "if print_results:\n")
self._add_code(
"print('Grid has handled {starcount} stars with a total probability of {probtot:g}'.format(starcount=_total_starcount,probtot=self.grid_options['_probtot']))\n",
indent=1,
)
################
# Finalising return statement for dry run.
#
if dry_run:
self._add_code("return _total_starcount\n")
self._increment_indent_depth(-1)
#################################################################################
# Stop of code generation. Here the code is saved and written
# Save the grid code to the grid_options
verbose_print(
"Saving grid code to grid_options", self.grid_options["verbosity"], 1
)
self.grid_options["code_string"] = self.code_string
# Write to file
gridcode_filename = os.path.join(
self.grid_options["tmp_dir"],
"binary_c_grid_{id}.py".format(id=self.grid_options["_population_id"]),
)
self.grid_options["gridcode_filename"] = gridcode_filename
verbose_print(
"{blue}Writing grid code to {file} [dry_run = {dry}]{reset}".format(
blue=self.ANSI_colours["blue"],
file=gridcode_filename,
dry=dry_run,
reset=self.ANSI_colours["reset"],
),
self.grid_options["verbosity"],
1,
)
with open(gridcode_filename, "w") as file:
file.write(self.code_string)
# perhaps create symlink
if self.grid_options["symlink latest gridcode"]:
global _count
symlink = os.path.join(
self.grid_options["tmp_dir"], "binary_c_grid-latest" + str(_count)
)
_count += 1
if os.path.exists(symlink):
os.unlink(symlink)
try:
os.symlink(gridcode_filename, symlink)
verbose_print(
"{blue}Symlinked grid code to {symlink} {reset}".format(
blue=self.ANSI_colours["blue"],
symlink=symlink,
reset=self.ANSI_colours["reset"]
),
self.grid_options["verbosity"],
1,
)
except OSError:
print("symlink failed")
def _write_gridcode_system_call(
self, grid_variable, dry_run, branchpoint, branchcode
):
#################################################################################
# Here are the calls to the queuing or other solution. this part is for every system
# Add comment
self._increment_indent_depth(+1)
self._add_code("#" * 40 + "\n")
if branchcode:
self._add_code("# Branch code\nif {branchcode}:\n".format(branchcode=branchcode))
if branchpoint:
self._add_code(
"# Code below will get evaluated for every system at this level of multiplicity (last one of that being {name})\n".format(
name=grid_variable["name"]
)
)
else:
self._add_code(
"# Code below will get evaluated for every generated system\n"
)
# Factor in the custom weight input
self._add_code(
"\n",
"# Weigh the probability by a custom weighting factor\n",
'probability = self.grid_options["weight"] * probabilities_list[{n}]'.format(
n=grid_variable["grid_variable_number"]
)
+ "\n",
# Take into account the multiplicity fraction:
"\n",
"# Factor the multiplicity fraction into the probability\n",
"probability = probability * self._calculate_multiplicity_fraction(parameter_dict)"
+ "\n",
# Add division by number of repeats
"\n",
"# Divide the probability by the number of repeats\n",
'probability = probability / self.grid_options["repeat"]' + "\n",
# Now we yield the system self.grid_options["repeat"] times.
"\n",
"# Loop over the repeats\n",
'for _ in range(self.grid_options["repeat"]):' + "\n",
)
self._add_code(
"_total_starcount += 1\n",
# set probability and phasevol values into the system dict
'parameter_dict["{p}"] = {p}'.format(p="probability") + "\n",
'parameter_dict["{v}"] = {v}'.format(v="phasevol") + "\n",
# Increment total probability
"self._increment_probtot(probability)\n",
indent=1,
)
if not dry_run:
# Handling of what is returned, or what is not.
self._add_code("yield(parameter_dict)\n", indent=1)
# If its a dry run, dont do anything with it
else:
self._add_code("pass\n", indent=1)
self._add_code("#" * 40 + "\n")
self._increment_indent_depth(-1)
return self.code_string
def _load_grid_function(self):
"""
Function that loads the script containing the grid code.
TODO: Update this description
Test function to run grid stuff. mostly to test the import
"""
# Code to load the
verbose_print(
message="Loading grid code function from {file}".format(
file=self.grid_options["gridcode_filename"]
),
verbosity=self.grid_options["verbosity"],
minimal_verbosity=1,
)
spec = importlib.util.spec_from_file_location(
"binary_c_python_grid",
os.path.join(self.grid_options["gridcode_filename"]),
)
grid_file = importlib.util.module_from_spec(spec)
spec.loader.exec_module(grid_file)
generator = grid_file.grid_code
self.grid_options["_system_generator"] = generator
verbose_print("Grid code loaded", self.grid_options["verbosity"], 1)
def _dry_run(self):
"""
Function to dry run the grid and know how many stars it will run
Requires the grid to be built as a dry run grid
"""
verbose_print("Dry run of the grid", self.grid_options["verbosity"], 1)
system_generator = self.grid_options["_system_generator"]
total_starcount = system_generator(self)
self.grid_options["_total_starcount"] = total_starcount
def _print_info(self, run_number, total_systems, full_system_dict):
"""
Function to print info about the current system and the progress of the grid.
# color info tricks from https://ozzmaker.com/add-colour-to-text-in-python/
https://stackoverflow.com/questions/287871/how-to-print-colored-text-in-terminal-in-python
"""
# Define frequency
if self.grid_options["verbosity"] == 1:
print_freq = 1
else:
print_freq = 10
# Calculate amount of time left
# calculate amount of time passed
# time_passed = time.time() - self.grid_options["_start_time_evolution"]
if run_number % print_freq == 0:
binary_cmdline_string = self._return_argline(full_system_dict)
info_string = "{color_part_1} \
{text_part_1}{end_part_1}{color_part_2} \
{text_part_2}{end_part_2}".format(
color_part_1="\033[1;32;41m",
text_part_1="{}/{}".format(run_number, total_systems),
end_part_1="\033[0m",
color_part_2="\033[1;32;42m",
text_part_2="{}".format(binary_cmdline_string),
end_part_2="\033[0m",
)
print(info_string)
###################################################
# Monte Carlo functions
#
# Functions below are used to run populations with
# Monte Carlo
###################################################
###################################################
# Population from file functions
#
# Functions below are used to run populations from
# a file containing binary_c calls
###################################################
def _dry_run_source_file(self):
"""
Function to go through the source_file and count the number of lines and the total probability
"""
system_generator = self.grid_options["_system_generator"]
total_starcount = 0
total_probability = 0
contains_probability = False
for line in system_generator:
total_starcount += 1
total_starcount = system_generator(self)
self.grid_options["_total_starcount"] = total_starcount
def _load_source_file(self, check=False):
"""
Function that loads the source_file that contains a binary_c calls
"""
if not os.path.isfile(self.grid_options["source_file_filename"]):
verbose_print("Source file doesnt exist", self.grid_options["verbosity"], 0)
verbose_print(
message="Loading source file from {}".format(
self.grid_options["gridcode_filename"]
),
verbosity=self.grid_options["verbosity"],
minimal_verbosity=1,
)
# We can choose to perform a check on the source file, which checks if the lines start with 'binary_c'
if check:
source_file_check_filehandle = open(
self.grid_options["source_file_filename"], "r"
)
for line in source_file_check_filehandle:
if not line.startswith("binary_c"):
failed = True
break
if failed:
verbose_print(
"Error, sourcefile contains lines that do not start with binary_c",
self.grid_options["verbosity"],
0,
)
raise ValueError
source_file_filehandle = open(self.grid_options["source_file_filename"], "r")
self.grid_options["_system_generator"] = source_file_filehandle
verbose_print("Source file loaded", self.grid_options["verbosity"], 1)
def _dict_from_line_source_file(self, line):
"""
Function that creates a dict from a binary_c arg line
"""
if line.startswith("binary_c "):
line = line.replace("binary_c ", "")
split_line = line.split()
arg_dict = {}
for i in range(0, len(split_line), 2):
if "." in split_line[i + 1]:
arg_dict[split_line[i]] = float(split_line[i + 1])
else:
arg_dict[split_line[i]] = int(split_line[i + 1])
return arg_dict
###################################################
# SLURM functions
#
# subroutines to run SLURM grids
###################################################
# def _slurm_grid(self):
# """
# Main function that manages the SLURM setup.
# Has three stages:
# - setup
# - evolve
# - join
# Which stage is used is determined by the value of grid_options['slurm_command']:
# <empty>: the function will know its the user that executed the script and
# it will set up the necessary condor stuff
# 'evolve': evolve_population is called to evolve the population of stars
# 'join': We will attempt to join the output
# """
# # Check version
# # TODO: Put in function
# slurm_version = get_slurm_version()
# if not slurm_version:
# verbose_print(
# "SLURM: Error: No installation of slurm found",
# self.grid_options["verbosity"],
# 0,
# )
# else:
# major_version = int(slurm_version.split(".")[0])
# minor_version = int(slurm_version.split(".")[1])
# if major_version > 17:
# verbose_print(
# "SLURM: Found version {} which is new enough".format(slurm_version),
# self.grid_options["verbosity"],
# 1,
# )
# else:
# verbose_print(
# "SLURM: Found version {} which is too old (we require 17+)".format(
# slurm_version
# ),
# self.grid_options["verbosity"],
# 0,
# )
# verbose_print(
# "SLURM: Running slurm grid. command={}".format(
# self.grid_options["slurm_command"]
# ),
# self.grid_options["verbosity"],
# 1,
# )
# if not self.grid_options["slurm_command"]:
# # Setting up
# verbose_print(
# "SLURM: Main controller script. Setting up",
# self.grid_options["verbosity"],
# 1,
# )
# # Set up working directories:
# verbose_print(
# "SLURM: creating working directories", self.grid_options["verbosity"], 1
# )
# create_directories_hpc(self.grid_options["slurm_dir"])
# # Create command
# python_details = get_python_details()
# scriptname = path_of_calling_script()
# command = "{} {}".format(python_details["executable"], scriptname)
# command += '{}'.format(
# " ".join(
# [
# "{}".format(self.grid_options["_commandline_input"]),
# "offset=$jobarrayindex",
# "modulo={}".format(self.grid_options["slurm_njobs"]),
# "vb={}".format(self.grid_options["verbosity"]),
# "slurm_jobid=$jobid",
# "slurm_jobarrayindex=$jobarrayindex",
# "slurm_jobname='binary_grid_'$jobid'.'$jobarrayindex",
# "slurm_njobs={}".format(self.grid_options["slurm_njobs"]),
# "slurm_dir={}".format(self.grid_options["slurm_dir"]),
# "rungrid=1",
# "slurm_command=evolve",
# ]
# ).strip()
# )
# # Construct dict with settings for the script while checking the settings at the same time
# # Check settings:
# # TODO: check settings
# # Create SLURM_DIR script:
# slurm_script_options = {}
# slurm_script_options["n"] = self.grid_options["slurm_njobs"]
# slurm_script_options["njobs"] = self.grid_options["slurm_njobs"]
# slurm_script_options["dir"] = self.grid_options["slurm_dir"]
# slurm_script_options["memory"] = self.grid_options["slurm_memory"]
# slurm_script_options["working_dir"] = self.grid_options[
# "slurm_dir"
# ] # TODO: check this
# slurm_script_options["command"] = command
# # slurm_script_options['streams'] = self.grid_options['streams']
# # Construct the script
# slurm_script_contents = ""
# slurm_script_contents += "#!/bin/bash\n"
# slurm_script_contents += "# Slurm file for binary_grid and slurm\n"
# slurm_script_contents += "#SBATCH --error={}/stderr/%A.%a\n".format(
# self.grid_options["slurm_dir"]
# )
# slurm_script_contents += "#SBATCH --output={}/stdout/%A.%a\n".format(
# self.grid_options["slurm_dir"]
# )
# slurm_script_contents += "#SBATCH --job-name={}\n".format(
# self.grid_options["slurm_jobname"]
# )
# slurm_script_contents += "#SBATCH --partition={}\n".format(
# self.grid_options["slurm_partition"]
# )
# slurm_script_contents += "#SBATCH --time={}\n".format(
# self.grid_options["slurm_time"]
# )
# slurm_script_contents += "#SBATCH --mem={}\n".format(
# self.grid_options["slurm_memory"]
# )
# slurm_script_contents += "#SBATCH --ntasks={}\n".format(
# self.grid_options["slurm_ntasks"]
# )
# slurm_script_contents += "#SBATCH --array={}\n".format(
# self.grid_options["slurm_array"]
# )
# slurm_script_contents += "\n"
# if self.grid_options["slurm_extra_settings"]:
# slurm_script_contents += "# Extra settings by user:"
# slurm_script_contents += "\n".join(
# [
# "--{}={}".format(
# key, self.grid_options["slurm_extra_settings"][key]
# )
# for key in self.grid_options["slurm_extra_settings"]
# ]
# )
# slurm_script_contents += '# set status to "running"\n'
# slurm_script_contents += (
# 'echo "running" > {}/status/$jobid.$jobarrayindex\n\n'.format(
# self.grid_options["slurm_dir"]
# )
# )
# slurm_script_contents += "# run grid of stars\n"
# slurm_script_contents += "{}\n\n".format(command)
# slurm_script_contents += '# set status to "finished"\n'
# slurm_script_contents += (
# 'echo "finished" > {}/status/$jobid.$jobarrayindex\n'.format(
# self.grid_options["slurm_dir"]
# )
# )
# slurm_script_contents += "\n"
# if self.grid_options["slurm_postpone_join"]:
# slurm_script_contents += "{} rungrid=0 results_hash_dumpfile={}/results/$jobid.all slurm_command=join\n".format(
# command, self.grid_options["slurm_dir"]
# )
# # Write script to file
# slurm_script_filename = os.path.join(
# self.grid_options["slurm_dir"], "slurm_script"
# )
# with open(slurm_script_filename, "w") as slurm_script_file:
# slurm_script_file.write(slurm_script_contents)
# # Execute or postpone
# if self.grid_options["slurm_postpone_sbatch"]:
# # Execute or postpone the real call to sbatch
# sbatch_command = "sbatch {}".format(slurm_script_filename)
# verbose_print(
# "running slurm script {}".format(slurm_script_filename),
# self.grid_options["verbosity"],
# 0,
# )
# # subprocess.Popen(sbatch_command, close_fds=True)
# # subprocess.Popen(sbatch_command, creationflags=subprocess.DETACHED_PROCESS)
# verbose_print("Submitted scripts.", self.grid_options["verbosity"], 0)
# else:
# verbose_print(
# "Slurm script is in {} but hasnt been executed".format(
# slurm_script_filename
# ),
# self.grid_options["verbosity"],
# 0,
# )
# verbose_print("all done!", self.grid_options["verbosity"], 0)
# sys.exit()
# elif self.grid_options["slurm_command"] == "evolve":
# # Part to evolve the population.
# # TODO: decide how many CPUs
# verbose_print(
# "SLURM: Evolving population", self.grid_options["verbosity"], 1
# )
# #
# self.evolve_population()
# elif self.grid_options["slurm_command"] == "join":
# # Joining the output.
# verbose_print("SLURM: Joining results", self.grid_options["verbosity"], 1)
###################################################
# CONDOR functions
#
# subroutines to run CONDOR grids
###################################################
# def _condor_grid(self):
# """
# Main function that manages the CONDOR setup.
# Has three stages:
# - setup
# - evolve
# - join
# Which stage is used is determined by the value of grid_options['condor_command']:
# <empty>: the function will know its the user that executed the script and
# it will set up the necessary condor stuff
# 'evolve': evolve_population is called to evolve the population of stars
# 'join': We will attempt to join the output
# """
# # TODO: Put in function
# condor_version = get_condor_version()
# if not condor_version:
# verbose_print(
# "CONDOR: Error: No installation of condor found",
# self.grid_options["verbosity"],
# 0,
# )
# else:
# major_version = int(condor_version.split(".")[0])
# minor_version = int(condor_version.split(".")[1])
# if (major_version == 8) and (minor_version > 4):
# verbose_print(
# "CONDOR: Found version {} which is new enough".format(
# condor_version
# ),
# self.grid_options["verbosity"],
# 0,
# )
# elif major_version > 9:
# verbose_print(
# "CONDOR: Found version {} which is new enough".format(
# condor_version
# ),
# self.grid_options["verbosity"],
# 0,
# )
# else:
# verbose_print(
# "CONDOR: Found version {} which is too old (we require 8.3/8.4+)".format(
# condor_version
# ),
# self.grid_options["verbosity"],
# 0,
# )
# verbose_print(
# "Running Condor grid. command={}".format(
# self.grid_options["condor_command"]
# ),
# self.grid_options["verbosity"],
# 1,
# )
# if not self.grid_options["condor_command"]:
# # Setting up
# verbose_print(
# "CONDOR: Main controller script. Setting up",
# self.grid_options["verbosity"],
# 1,
# )
# # Set up working directories:
# verbose_print(
# "CONDOR: creating working directories",
# self.grid_options["verbosity"],
# 1,
# )
# create_directories_hpc(self.grid_options["condor_dir"])
# # Create command
# current_workingdir = os.getcwd()
# python_details = get_python_details()
# scriptname = path_of_calling_script()
# # command = "".join([
# # "{}".python_details['executable'],
# # "{}".scriptname,
# # "offset=$jobarrayindex",
# # "modulo={}".format(self.grid_options['condor_njobs']),
# # "vb={}".format(self.grid_options['verbosity'])
# # "results_hash_dumpfile=$self->{_grid_options}{slurm_dir}/results/$jobid.$jobarrayindex",
# # 'slurm_jobid='.$jobid,
# # 'slurm_jobarrayindex='.$jobarrayindex,
# # 'slurm_jobname=binary_grid_'.$jobid.'.'.$jobarrayindex,
# # "slurm_njobs=$njobs",
# # "slurm_dir=$self->{_grid_options}{slurm_dir}",
# # );
# # Create directory with info for the condor script. By creating this directory we also check whether all the values are set correctly
# # TODO: create the condor script.
# condor_script_options = {}
# # condor_script_options['n'] =
# condor_script_options["njobs"] = self.grid_options["condor_njobs"]
# condor_script_options["dir"] = self.grid_options["condor_dir"]
# condor_script_options["memory"] = self.grid_options["condor_memory"]
# condor_script_options["working_dir"] = self.grid_options[
# "condor_working_dir"
# ]
# condor_script_options["command"] = self.grid_options["command"]
# condor_script_options["streams"] = self.grid_options["streams"]
# # TODO: condor works with running an executable.
# # Create script contents
# condor_script_contents = ""
# condor_script_contents += """
# #################################################
# #
# # Condor script to run a binary_grid via python
# #
# #################################################
# """
# condor_script_contents += "Executable\t= {}".format(executable)
# condor_script_contents += "arguments\t= {}".format(arguments)
# condor_script_contents += "environment\t= {}".format(environment)
# condor_script_contents += "universe\t= {}".format(
# self.grid_options["condor_universe"]
# )
# condor_script_contents += "\n"
# condor_script_contents += "output\t= {}/stdout/$id\n".format(
# self.grid_options["condor_dir"]
# )
# condor_script_contents += "error\t={}/sterr/$id".format(
# self.grid_options["condor_dir"]
# )
# condor_script_contents += "log\t={}\n".format(
# self.grid_options["condor_dir"]
# )
# condor_script_contents += "initialdir\t={}\n".format(current_workingdir)
# condor_script_contents += "remote_initialdir\t={}\n".format(
# current_workingdir
# )
# condor_script_contents += "\n"
# condor_script_contents += "steam_output\t={}".format(stream)
# condor_script_contents += "steam_error\t={}".format(stream)
# condor_script_contents += "+WantCheckpoint = False"
# condor_script_contents += "\n"
# condor_script_contents += "request_memory\t={}".format(
# self.grid_options["condor_memory"]
# )
# condor_script_contents += "ImageSize\t={}".format(
# self.grid_options["condor_memory"]
# )
# condor_script_contents += "\n"
# if self.grid_options["condor_extra_settings"]:
# slurm_script_contents += "# Extra settings by user:"
# slurm_script_contents += "\n".join(
# [
# "{}\t={}".format(
# key, self.grid_options["condor_extra_settings"][key]
# )
# for key in self.grid_options["condor_extra_settings"]
# ]
# )
# condor_script_contents += "\n"
# # request_memory = $_[0]{memory}
# # ImageSize = $_[0]{memory}
# # Requirements = (1) \&\& (".
# # $self->{_grid_options}{condor_requirements}.")\n";
# #
# # file name: my_program.condor
# # Condor submit description file for my_program
# # Executable = my_program
# # Universe = vanilla
# # Error = logs/err.$(cluster)
# # Output = logs/out.$(cluster)
# # Log = logs/log.$(cluster)
# # should_transfer_files = YES
# # when_to_transfer_output = ON_EXIT
# # transfer_input_files = files/in1,files/in2
# # Arguments = files/in1 files/in2 files/out1
# # Queue
# # Write script contents to file
# if self.grid_options["condor_postpone_join"]:
# condor_script_contents += "{} rungrid=0 results_hash_dumpfile={}/results/$jobid.all condor_command=join\n".format(
# command, self.grid_options["condor_dir"]
# )
# condor_script_filename = os.path.join(
# self.grid_options["condor_dir"], "condor_script"
# )
# with open(condor_script_filename, "w") as condor_script_file:
# condor_script_file.write(condor_script_contents)
# if self.grid_options["condor_postpone_sbatch"]:
# # Execute or postpone the real call to sbatch
# submit_command = "condor_submit {}".format(condor_script_filename)
# verbose_print(
# "running condor script {}".format(condor_script_filename),
# self.grid_options["verbosity"],
# 0,
# )
# # subprocess.Popen(sbatch_command, close_fds=True)
# # subprocess.Popen(sbatch_command, creationflags=subprocess.DETACHED_PROCESS)
# verbose_print("Submitted scripts.", self.grid_options["verbosity"], 0)
# else:
# verbose_print(
# "Condor script is in {} but hasnt been executed".format(
# condor_script_filename
# ),
# self.grid_options["verbosity"],
# 0,
# )
# verbose_print("all done!", self.grid_options["verbosity"], 0)
# sys.exit()
# elif self.grid_options["condor_command"] == "evolve":
# # TODO: write this function
# # Part to evolve the population.
# # TODO: decide how many CPUs
# verbose_print(
# "CONDOR: Evolving population", self.grid_options["verbosity"], 1
# )
# #
# self.evolve_population()
# elif self.grid_options["condor_command"] == "join":
# # TODO: write this function
# # Joining the output.
# verbose_print("CONDOR: Joining results", self.grid_options["verbosity"], 1)
# pass
###################################################
# Unordered functions
#
# Functions that aren't ordered yet
###################################################
def write_ensemble(self, output_file, data=None, sort_keys=True, indent=4):
"""
write_ensemble : Write ensemble results to a file.
Args:
output_file : the output filename.
If the filename has an extension that we recognise,
e.g. .gz or .bz2, we compress the output appropriately.
The filename should contain .json or .msgpack, the two
currently-supported formats.
Usually you'll want to output to JSON, but we can
also output to msgpack.
data : the data dictionary to be converted and written to the file.
If not set, this defaults to self.grid_ensemble_results.
sort_keys : if True, and output is to JSON, the keys will be sorted.
(default: True, passed to json.dumps)
indent : number of space characters used in the JSON indent. (Default: 4,
passed to json.dumps)
"""
# TODO: consider writing this in a formatted structure
# get the file type
file_type = ensemble_file_type(output_file)
# choose compression algorithm based on file extension
compression = ensemble_compression(output_file)
# default to using grid_ensemble_results if no data is given
if data is None:
data = self.grid_ensemble_results
if not file_type:
print(
"Unable to determine file type from ensemble filename {} : it should be .json or .msgpack."
).format(output_file)
sys.exit()
elif file_type is "JSON":
# JSON output
if compression == "gzip":
# gzip
f = gzip.open(output_file, "wt")
elif compression == "bzip2":
# bzip2
f = bz2.open(output_file, "wt")
else:
# raw output (not compressed)
f = open(output_file, "wt")
f.write(json.dumps(data, sort_keys=sort_keys, indent=indent))
elif file_type is "msgpack":
# msgpack output
if compression == "gzip":
f = gzip.open(output_file, "wb")
elif compression == "bzip2":
f = bz2.open(output_file, "wb")
else:
f = open(output_file, "wb")
msgpack.dump(data, f)
f.close()
print(
"Thread {thread}: Wrote ensemble results to file: {colour}{file}{reset} (file type {file_type}, compression {compression})".format(
thread=self.process_ID,
file=output_file,
colour=self.ANSI_colours["green"],
reset=self.ANSI_colours["reset"],
file_type=file_type,
compression=compression,
)
)
############################################################
def write_binary_c_calls_to_file(
self,
output_dir: Union[str, None] = None,
output_filename: Union[str, None] = None,
include_defaults: bool = False,
) -> None:
"""
Function that loops over the grid code and writes the generated parameters to a file.
In the form of a command line call
Only useful when you have a variable grid as system_generator. MC wouldn't be that useful
Also, make sure that in this export there are the basic parameters
like m1,m2,sep, orb-per, ecc, probability etc.
On default this will write to the datadir, if it exists
Tasks:
- TODO: test this function
- TODO: make sure the binary_c_python .. output file has a unique name
Args:
output_dir: (optional, default = None) directory where to write the file to. If custom_options['data_dir'] is present, then that one will be used first, and then the output_dir
output_filename: (optional, default = None) filename of the output. If not set it will be called "binary_c_calls.txt"
include_defaults: (optional, default = None) whether to include the defaults of binary_c in the lines that are written. Beware that this will result in very long lines, and it might be better to just export the binary_c defaults and keep them in a separate file.
Returns:
filename: filename that was used to write the calls to
"""
# Check if there is no compiled grid yet. If not, lets try to build it first.
if not self.grid_options["_system_generator"]:
## check the settings:
if self.bse_options.get("ensemble", None):
if self.bse_options["ensemble"] == 1:
if not self.bse_options.get("ensemble_defer", 0) == 1:
verbose_print(
"Error, if you want to run an ensemble in a population, the output needs to be deferred",
self.grid_options["verbosity"],
0,
)
raise ValueError
# Put in check
if len(self.grid_options["_grid_variables"]) == 0:
print("Error: you haven't defined any grid variables! Aborting")
raise ValueError
#
self._generate_grid_code(dry_run=False)
#
self._load_grid_function()
# then if the _system_generator is present, we go through it
if self.grid_options["_system_generator"]:
# Check if there is an output dir configured
if self.custom_options.get("data_dir", None):
binary_c_calls_output_dir = self.custom_options["data_dir"]
# otherwise check if there's one passed to the function
else:
if not output_dir:
print(
"Error. No data_dir configured and you gave no output_dir. Aborting"
)
raise ValueError
binary_c_calls_output_dir = output_dir
# check if there's a filename passed to the function
if output_filename:
binary_c_calls_filename = output_filename
# otherwise use default value
else:
binary_c_calls_filename = "binary_c_calls.txt"
binary_c_calls_full_filename = os.path.join(
binary_c_calls_output_dir, binary_c_calls_filename
)
print("Writing binary_c calls to {}".format(binary_c_calls_full_filename))
# Write to file
with open(binary_c_calls_full_filename, "w") as file:
# Get defaults and clean them, then overwrite them with the set values.
if include_defaults:
# TODO: make sure that the defaults here are cleaned up properly
cleaned_up_defaults = self.cleaned_up_defaults
full_system_dict = cleaned_up_defaults.copy()
full_system_dict.update(self.bse_options.copy())
else:
full_system_dict = self.bse_options.copy()
for system in self.grid_options["_system_generator"](self):
# update values with current system values
full_system_dict.update(system)
binary_cmdline_string = self._return_argline(full_system_dict)
file.write(binary_cmdline_string + "\n")
else:
print("Error. No grid function found!")
raise ValueError
return binary_c_calls_full_filename
def _cleanup_defaults(self):
"""
Function to clean up the default values:
from a dictionary, removes the entries that have the following values:
- "NULL"
- ""
- "Function"
Uses the function from utils.functions
TODO: Rethink this functionality. seems a bit double, could also be just outside of the class
"""
binary_c_defaults = self.return_binary_c_defaults().copy()
cleaned_dict = filter_arg_dict(binary_c_defaults)
return cleaned_dict
def _clean_up_custom_logging(self, evol_type):
"""
Function to clean up the custom logging.
Has two types:
'single':
- removes the compiled shared library
(which name is stored in grid_options['_custom_logging_shared_library_file'])
- TODO: unloads/frees the memory allocated to that shared library
(which is stored in grid_options['custom_logging_func_memaddr'])
- sets both to None
'multiple':
- TODO: make this and design this
"""
if evol_type == "single":
verbose_print(
"Cleaning up the custom logging stuff. type: single",
self.grid_options["verbosity"],
1,
)
# TODO: Explicitly unload the library
# Reset the memory adress location
self.grid_options["custom_logging_func_memaddr"] = -1
# remove shared library files
if self.grid_options["_custom_logging_shared_library_file"]:
remove_file(
self.grid_options["_custom_logging_shared_library_file"],
self.grid_options["verbosity"],
)
self.grid_options["_custom_logging_shared_library_file"] = None
if evol_type == "population":
verbose_print(
"Cleaning up the custom logging stuffs. type: population",
self.grid_options["verbosity"],
1,
)
# TODO: make sure that these also work. not fully sure if necessary tho.
# whether its a single file, or a dict of files/mem addresses
if evol_type == "MC":
pass
def _increment_probtot(self, prob):
"""
Function to add to the total probability. For now not used
"""
self.grid_options["_probtot"] += prob
def _increment_count(self):
"""
Function to add to the total number of stars. For now not used
"""
self.grid_options["_count"] += 1
def _set_loggers(self):
"""
Function to set the loggers for the execution of the grid
"""
# Set log file
binary_c_logfile = self.grid_options["log_file"]
# Create directory
os.makedirs(os.path.dirname(binary_c_logfile), exist_ok=True)
# Set up logger
self.logger = logging.getLogger("binary_c_python_logger")
self.logger.setLevel(self.grid_options["verbosity"])
# Reset handlers
self.logger.handlers = []
# Set formatting of output
log_formatter = logging.Formatter(
"%(asctime)s - %(name)s - %(levelname)s - %(message)s"
)
# Make and add file handlers
# make handler for output to file
handler_file = logging.FileHandler(filename=os.path.join(binary_c_logfile))
handler_file.setFormatter(log_formatter)
handler_file.setLevel(logging.INFO)
# Make handler for output to stdout
handler_stdout = logging.StreamHandler(sys.stdout)
handler_stdout.setFormatter(log_formatter)
handler_stdout.setLevel(logging.INFO)
# Add the loggers
self.logger.addHandler(handler_file)
self.logger.addHandler(handler_stdout)
def _check_binary_c_error(self, binary_c_output, system_dict):
"""
Function to check whether binary_c throws an error and handle accordingly.
"""
if binary_c_output:
if (binary_c_output.splitlines()[0].startswith("SYSTEM_ERROR")) or (
binary_c_output.splitlines()[-1].startswith("SYSTEM_ERROR")
):
verbose_print(
"FAILING SYSTEM FOUND",
self.grid_options["verbosity"],
0,
)
# Keep track of the amount of failed systems and their error codes
self.grid_options["_failed_prob"] += system_dict.get("probability", 1)
self.grid_options["_failed_count"] += 1
self.grid_options["_errors_found"] = True
# Try catching the error code and keep track of the unique ones.
try:
error_code = int(
binary_c_output.splitlines()[0]
.split("with error code")[-1]
.split(":")[0]
.strip()
)
if (
not error_code
in self.grid_options["_failed_systems_error_codes"]
):
self.grid_options["_failed_systems_error_codes"].append(
error_code
)
except ValueError:
verbose_print(
"Failed to extract the error-code",
self.grid_options["verbosity"],
1,
)
# Check if we have exceeded the number of errors
if (
self.grid_options["_failed_count"]
> self.grid_options["failed_systems_threshold"]
):
if not self.grid_options["_errors_exceeded"]:
verbose_print(
self._boxed(
"Process {} exceeded the maximum ({}) number of failing systems. Stopped logging them to files now".format(
self.process_ID,
self.grid_options["failed_systems_threshold"],
)
),
self.grid_options["verbosity"],
1,
)
self.grid_options["_errors_exceeded"] = True
# If not, write the failing systems to files unique to each process
else:
# Write arg lines to file
argstring = self._return_argline(system_dict)
with open(
os.path.join(
self.grid_options["tmp_dir"],
"failed_systems",
"process_{}.txt".format(self.process_ID),
),
"a+",
) as f:
f.write(argstring + "\n")
f.close()
else:
verbose_print(
"binary_c output nothing - this is strange. If there is ensemble output being generated then this is fine.",
self.grid_options["verbosity"],
3,
)
def set_moe_di_stefano_settings(self, options=None):
"""
Function to set user input configurations for the Moe & di Stefano methods
If nothing is passed then we just use the default options
"""
if not options:
options = {}
# Take the option dictionary that was given and override.
options = update_dicts(self.grid_options["Moe2017_options"], options)
self.grid_options["Moe2017_options"] = copy.deepcopy(options)
# Write options to a file
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
exist_ok=True,
)
with open(
os.path.join(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
"moeopts.dat",
),
"w",
) as f:
f.write(json.dumps(self.grid_options["Moe2017_options"], indent=4))
f.close()
def _load_moe_di_stefano_data(self):
"""
Function to load the moe & di stefano data
"""
# Only if the grid is loaded and Moecache contains information
if not self.grid_options["_loaded_Moe2017_data"]: # and not Moecache:
if self.grid_options["_Moe2017_JSON_data"]:
# Use the existing (perhaps modified) JSON data
json_data = self.grid_options["_Moe2017_JSON_data"]
else:
# Load the JSON data from a file
json_data = get_moe_di_stefano_dataset(
self.grid_options["Moe2017_options"],
verbosity=self.grid_options["verbosity"],
)
# entry of log10M1 is a list containing 1 dict.
# We can take the dict out of the list
if isinstance(json_data["log10M1"], list):
json_data["log10M1"] = json_data["log10M1"][0]
# save this data in case we want to modify it later
self.grid_options["_Moe2017_JSON_data"] = json_data
# Get all the masses
logmasses = sorted(json_data["log10M1"].keys())
if not logmasses:
msg = "The table does not contain masses."
verbose_print(
"\tMoe_di_Stefano_2017: {}".format(msg),
self.grid_options["verbosity"],
0,
)
raise ValueError(msg)
# Write to file
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
exist_ok=True,
)
with open(
os.path.join(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
"moe.log",
),
"w",
) as logfile:
logfile.write("log₁₀Masses(M☉) {}\n".format(logmasses))
# Get all the periods and see if they are all consistently present
logperiods = []
for logmass in logmasses:
if not logperiods:
logperiods = sorted(json_data["log10M1"][logmass]["logP"].keys())
dlog10P = float(logperiods[1]) - float(logperiods[0])
current_logperiods = sorted(json_data["log10M1"][logmass]["logP"])
if not (logperiods == current_logperiods):
msg = (
"Period values are not consistent throughout the dataset\logperiods = "
+ " ".join(str(x) for x in logperiods)
+ "\nCurrent periods = "
+ " ".join(str(x) for x in current_logperiods)
)
verbose_print(
"\tMoe_di_Stefano_2017: {}".format(msg),
self.grid_options["verbosity"],
0,
)
raise ValueError(msg)
############################################################
# log10period binwidth : of course this assumes a fixed
# binwidth, so we check for this too.
for i in range(len(current_logperiods) - 1):
if not dlog10P == (
float(current_logperiods[i + 1]) - float(current_logperiods[i])
):
msg = "Period spacing is not consistent throughout the dataset"
verbose_print(
"\tMoe_di_Stefano_2017: {}".format(msg),
self.grid_options["verbosity"],
0,
)
raise ValueError(msg)
# save the logperiods list in the cache:
# this is used in the renormalization integration
Moecache["logperiods"] = logperiods
# Write to file
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
exist_ok=True,
)
with open(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano", "moe.log"),
"a",
) as logfile:
logfile.write("log₁₀Periods(days) {}\n".format(logperiods))
# Fill the global dict
for logmass in logmasses:
# Create the multiplicity table
if not Moecache.get("multiplicity_table", None):
Moecache["multiplicity_table"] = []
# multiplicity as a function of primary mass
Moecache["multiplicity_table"].append(
[
float(logmass),
json_data["log10M1"][logmass]["f_multi"],
json_data["log10M1"][logmass]["single star fraction"],
json_data["log10M1"][logmass]["binary star fraction"],
json_data["log10M1"][logmass]["triple/quad star fraction"],
]
)
############################################################
# a small log10period which we can shift just outside the
# table to force integration out there to zero
epslog10P = 1e-8 * dlog10P
############################################################
# loop over either binary or triple-outer periods
first = 1
# Go over the periods
for logperiod in logperiods:
############################################################
# distributions of binary and triple star fractions
# as a function of mass, period.
#
# Note: these should be per unit log10P, hence we
# divide by dlog10P
if first:
first = 0
# Create the multiplicity table
if not Moecache.get("period_distributions", None):
Moecache["period_distributions"] = []
############################################################
# lower bound the period distributions to zero probability
Moecache["period_distributions"].append(
[
float(logmass),
float(logperiod) - 0.5 * dlog10P - epslog10P,
0.0,
0.0,
]
)
Moecache["period_distributions"].append(
[
float(logmass),
float(logperiod) - 0.5 * dlog10P,
json_data["log10M1"][logmass]["logP"][logperiod][
"normed_bin_frac_p_dist"
]
/ dlog10P,
json_data["log10M1"][logmass]["logP"][logperiod][
"normed_tripquad_frac_p_dist"
]
/ dlog10P,
]
)
Moecache["period_distributions"].append(
[
float(logmass),
float(logperiod),
json_data["log10M1"][logmass]["logP"][logperiod][
"normed_bin_frac_p_dist"
]
/ dlog10P,
json_data["log10M1"][logmass]["logP"][logperiod][
"normed_tripquad_frac_p_dist"
]
/ dlog10P,
]
)
############################################################
# distributions as a function of mass, period, q
#
# First, get a list of the qs given by Moe
#
qs = sorted(json_data["log10M1"][logmass]["logP"][logperiod]["q"])
# Fill the data and 'normalise'
qdata = fill_data(
qs, json_data["log10M1"][logmass]["logP"][logperiod]["q"]
)
# Create the multiplicity table
if not Moecache.get("q_distributions", None):
Moecache["q_distributions"] = []
for q in qs:
Moecache["q_distributions"].append(
[float(logmass), float(logperiod), float(q), qdata[q]]
)
############################################################
# eccentricity distributions as a function of mass, period, ecc
eccs = sorted(json_data["log10M1"][logmass]["logP"][logperiod]["e"])
# Fill the data and 'normalise'
ecc_data = fill_data(
eccs, json_data["log10M1"][logmass]["logP"][logperiod]["e"]
)
# Create the multiplicity table
if not Moecache.get("ecc_distributions", None):
Moecache["ecc_distributions"] = []
for ecc in eccs:
Moecache["ecc_distributions"].append(
[
float(logmass),
float(logperiod),
float(ecc),
ecc_data[ecc],
]
)
############################################################
# upper bound the period distributions to zero probability
Moecache["period_distributions"].append(
[
float(logmass),
float(logperiods[-1]) + 0.5 * dlog10P, # TODO: why this shift?
json_data["log10M1"][logmass]["logP"][logperiods[-1]][
"normed_bin_frac_p_dist"
]
/ dlog10P,
json_data["log10M1"][logmass]["logP"][logperiods[-1]][
"normed_tripquad_frac_p_dist"
]
/ dlog10P,
]
)
Moecache["period_distributions"].append(
[
float(logmass),
float(logperiods[-1]) + 0.5 * dlog10P + epslog10P,
0.0,
0.0,
]
)
verbose_print(
"\tMoe_di_Stefano_2017: Length period_distributions table: {}".format(
len(Moecache["period_distributions"])
),
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
verbose_print(
"\tMoe_di_Stefano_2017: Length multiplicity table: {}".format(
len(Moecache["multiplicity_table"])
),
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
verbose_print(
"\tMoe_di_Stefano_2017: Length q table: {}".format(
len(Moecache["q_distributions"])
),
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
verbose_print(
"\tMoe_di_Stefano_2017: Length ecc table: {}".format(
len(Moecache["ecc_distributions"])
),
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
# Write to log file
os.makedirs(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
exist_ok=True,
)
with open(
os.path.join(
os.path.join(self.grid_options["tmp_dir"], "moe_distefano"),
"moecache.json",
),
"w",
) as cache_filehandle:
cache_filehandle.write(json.dumps(Moecache, indent=4))
# Signal that the data has been loaded
self.grid_options["_loaded_Moe2017_data"] = True
def _set_moe_di_stefano_distributions(self):
"""
Function to set the Moe & di Stefano distribution
"""
############################################################
# first, the multiplicity, this is 1,2,3,4, ...
# for singles, binaries, triples, quadruples, ...
max_multiplicity = get_max_multiplicity(
self.grid_options["Moe2017_options"]["multiplicity_modulator"]
)
verbose_print(
"\tMoe_di_Stefano_2017: Max multiplicity = {}".format(max_multiplicity),
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
######
# Setting up the grid variables
# Multiplicity
self.add_grid_variable(
name="multiplicity",
parameter_name="multiplicity",
longname="multiplicity",
valuerange=[1, max_multiplicity],
samplerfunc="const_int(1, {n}, {n})".format(n=max_multiplicity),
precode='self.grid_options["multiplicity"] = multiplicity; self.bse_options["multiplicity"] = multiplicity; options={}'.format(
self.grid_options["Moe2017_options"]
),
condition="({}[int(multiplicity)-1] > 0)".format(
str(self.grid_options["Moe2017_options"]["multiplicity_modulator"])
),
gridtype="discrete",
probdist=1,
)
############################################################
# always require M1, for all systems
#
# log-spaced m1 with given resolution
self.add_grid_variable(
name="lnm1",
parameter_name="M_1",
longname="Primary mass",
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"]["M"][0]
or "const(np.log({}), np.log({}), {})".format(
self.grid_options["Moe2017_options"]["ranges"]["M"][0],
self.grid_options["Moe2017_options"]["ranges"]["M"][1],
self.grid_options["Moe2017_options"]["resolutions"]["M"][0],
),
valuerange=[
"np.log({})".format(
self.grid_options["Moe2017_options"]["ranges"]["M"][0]
),
"np.log({})".format(
self.grid_options["Moe2017_options"]["ranges"]["M"][1]
),
],
gridtype="centred",
dphasevol="dlnm1",
precode='M_1 = np.exp(lnm1); options["M_1"]=M_1',
probdist="Moe_di_Stefano_2017_pdf({{{}, {}, {}}}, verbosity=self.grid_options['verbosity'])['total_probdens'] if multiplicity == 1 else 1".format(
str(dict(self.grid_options["Moe2017_options"]))[1:-1],
"'multiplicity': multiplicity",
"'M_1': M_1",
),
)
# Go to higher multiplicities
if max_multiplicity >= 2:
# binaries: period
self.add_grid_variable(
name="log10per",
parameter_name="orbital_period",
longname="log10(Orbital_Period)",
probdist=1.0,
condition='(self.grid_options["multiplicity"] >= 2)',
branchpoint=1
if max_multiplicity > 1
else 0, # Signal here to put a branchpoint if we have a max multiplicity higher than 1.
gridtype="centred",
dphasevol="({} * dlog10per)".format(LOG_LN_CONVERTER),
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
],
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"][
"logP"
][0]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
self.grid_options["Moe2017_options"]["resolutions"]["logP"][0],
),
precode="""orbital_period = 10.0**log10per
qmin={}/M_1
qmax=maximum_mass_ratio_for_RLOF(M_1, orbital_period)
""".format(
self.grid_options["Moe2017_options"]["Mmin"]
),
) # TODO: change the maximum_mass_ratio_for_RLOF
# binaries: mass ratio
self.add_grid_variable(
name="q",
parameter_name="M_2",
longname="Mass ratio",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "options['Mmin']/M_1",
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "qmax",
],
probdist=1,
gridtype="centred",
dphasevol="dq",
precode="""
M_2 = q * M_1
sep = calc_sep_from_period(M_1, M_2, orbital_period)
""",
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"]["M"][1]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", [None, None])[0]
else "{}/M_1".format(self.grid_options["Moe2017_options"]["Mmin"]),
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", [None, None])[1]
else "qmax",
self.grid_options["Moe2017_options"]["resolutions"]["M"][1],
),
)
# (optional) binaries: eccentricity
if self.grid_options["Moe2017_options"]["resolutions"]["ecc"][0] > 0:
self.add_grid_variable(
name="ecc",
parameter_name="eccentricity",
longname="Eccentricity",
probdist=1,
gridtype="centred",
dphasevol="decc",
precode="eccentricity=ecc",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][1],
],
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"][
"ecc"
][0]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][1],
self.grid_options["Moe2017_options"]["resolutions"]["ecc"][0],
),
)
# Now for triples and quadruples
if max_multiplicity >= 3:
# Triple: period
self.add_grid_variable(
name="log10per2",
parameter_name="orbital_period_triple",
longname="log10(Orbital_Period2)",
probdist=1.0,
condition='(self.grid_options["multiplicity"] >= 3)',
branchpoint=2
if max_multiplicity > 2
else 0, # Signal here to put a branchpoint if we have a max multiplicity higher than 1.
gridtype="centred",
dphasevol="({} * dlog10per2)".format(LOG_LN_CONVERTER),
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
],
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"][
"logP"
][1]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
self.grid_options["Moe2017_options"]["resolutions"]["logP"][1],
),
precode="""orbital_period_triple = 10.0**log10per2
q2min={}/(M_1+M_2)
q2max=maximum_mass_ratio_for_RLOF(M_1+M_2, orbital_period_triple)
""".format(
self.grid_options["Moe2017_options"]["Mmin"]
),
)
# Triples: mass ratio
# Note, the mass ratio is M_outer/M_inner
self.add_grid_variable(
name="q2",
parameter_name="M_3",
longname="Mass ratio outer/inner",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "options['Mmin']/(M_1+M_2)",
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "q2max",
],
probdist=1,
gridtype="centred",
dphasevol="dq2",
precode="""
M_3 = q2 * (M_1 + M_2)
sep2 = calc_sep_from_period((M_1+M_2), M_3, orbital_period_triple)
eccentricity2=0
""",
samplerfunc=self.grid_options["Moe2017_options"]["samplerfuncs"][
"M"
][2]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "options['Mmin']/(M_1+M_2)",
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "q2max",
self.grid_options["Moe2017_options"]["resolutions"]["M"][2],
),
)
# (optional) triples: eccentricity
if self.grid_options["Moe2017_options"]["resolutions"]["ecc"][1] > 0:
self.add_grid_variable(
name="ecc2",
parameter_name="eccentricity2",
longname="Eccentricity of the triple",
probdist=1,
gridtype="centred",
dphasevol="decc2",
precode="eccentricity2=ecc2",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][1],
],
samplerfunc=self.grid_options["Moe2017_options"][
"samplerfuncs"
]["ecc"][1]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][1],
self.grid_options["Moe2017_options"]["resolutions"]["ecc"][
1
],
),
)
if max_multiplicity == 4:
# Quadruple: period
self.add_grid_variable(
name="log10per3",
parameter_name="orbital_period_quadruple",
longname="log10(Orbital_Period3)",
probdist=1.0,
condition='(self.grid_options["multiplicity"] >= 4)',
branchpoint=3
if max_multiplicity > 3
else 0, # Signal here to put a branchpoint if we have a max multiplicity higher than 1.
gridtype="centred",
dphasevol="({} * dlog10per3)".format(LOG_LN_CONVERTER),
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
],
samplerfunc=self.grid_options["Moe2017_options"][
"samplerfuncs"
]["logP"][2]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["logP"][0],
self.grid_options["Moe2017_options"]["ranges"]["logP"][1],
self.grid_options["Moe2017_options"]["resolutions"]["logP"][
2
],
),
precode="""orbital_period_quadruple = 10.0**log10per3
q3min={}/(M_3)
q3max=maximum_mass_ratio_for_RLOF(M_3, orbital_period_quadruple)
""".format(
self.grid_options["Moe2017_options"]["Mmin"]
),
)
# Quadruple: mass ratio : M_outer / M_inner
self.add_grid_variable(
name="q3",
parameter_name="M_4",
longname="Mass ratio outer low/outer high",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "options['Mmin']/(M_3)",
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "q3max",
],
probdist=1,
gridtype="centred",
dphasevol="dq3",
precode="""
M_4 = q3 * M_3
sep3 = calc_sep_from_period((M_3), M_4, orbital_period_quadruple)
eccentricity3=0
""",
samplerfunc=self.grid_options["Moe2017_options"][
"samplerfuncs"
]["M"][3]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["q"][0]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "options['Mmin']/(M_3)",
self.grid_options["Moe2017_options"]["ranges"]["q"][1]
if self.grid_options["Moe2017_options"]
.get("ranges", {})
.get("q", None)
else "q3max",
self.grid_options["Moe2017_options"]["resolutions"]["M"][2],
),
)
# (optional) triples: eccentricity
if (
self.grid_options["Moe2017_options"]["resolutions"]["ecc"][2]
> 0
):
self.add_grid_variable(
name="ecc3",
parameter_name="eccentricity3",
longname="Eccentricity of the triple+quadruple/outer binary",
probdist=1,
gridtype="centred",
dphasevol="decc3",
precode="eccentricity3=ecc3",
valuerange=[
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
1
],
],
samplerfunc=self.grid_options["Moe2017_options"][
"samplerfuncs"
]["ecc"][2]
or "const({}, {}, {})".format(
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
0
], # Just fail if not defined.
self.grid_options["Moe2017_options"]["ranges"]["ecc"][
1
],
self.grid_options["Moe2017_options"]["resolutions"][
"ecc"
][2],
),
)
# Now we are at the last part.
# Here we should combine all the information that we calculate and update the options
# dictionary. This will then be passed to the Moe_di_Stefano_2017_pdf to calculate
# the real probability. The trick we use is to strip the options_dict as a string
# and add some keys to it:
updated_options = "{{{}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}}}".format(
str(dict(self.grid_options["Moe2017_options"]))[1:-1],
'"multiplicity": multiplicity',
'"M_1": M_1',
'"M_2": M_2',
'"M_3": M_3',
'"M_4": M_4',
'"P": orbital_period',
'"P2": orbital_period_triple',
'"P3": orbital_period_quadruple',
'"ecc": eccentricity',
'"ecc2": eccentricity2',
'"ecc3": eccentricity3',
)
probdist_addition = "Moe_di_Stefano_2017_pdf({}, verbosity=self.grid_options['verbosity'])['total_probdens']".format(
updated_options
)
# and finally the probability calculator
self.grid_options["_grid_variables"][self._last_grid_variable()][
"probdist"
] = probdist_addition
verbose_print(
"\tMoe_di_Stefano_2017: Added final call to the pdf function",
self.grid_options["verbosity"],
_MOE2017_VERBOSITY_LEVEL,
)
# Signal that the MOE2017 grid has been set
self.grid_options["_set_Moe2017_grid"] = True
################################################################################################
def Moe_di_Stefano_2017(self, options=None):
"""
Function to handle setting the user input settings,
set up the data and load that into interpolators and
then set the distribution functions
Takes a dictionary as its only argument
"""
default_options = {
"apply settings": True,
"setup grid": True,
"load data": True,
"clean cache": False,
"clean load flag": False,
"clean all": False,
}
if not options:
options = {}
options = update_dicts(default_options, options)
# clean cache?
if options["clean all"] or options["clean cache"]:
Moecache.clear()
if options["clean all"] or options["clean load flag"]:
self.grid_options["_loaded_Moe2017_data"] = False
# Set the user input
if options["apply settings"]:
self.set_moe_di_stefano_settings(options=options)
# Load the data
if options["load data"]:
self._load_moe_di_stefano_data()
# construct the grid here
if options["setup grid"]:
self._set_moe_di_stefano_distributions()
def _clean_interpolators(self):
"""
Function to clean up the interpolators after a run
We look in the Moecache global variable for items that are interpolators.
Should be called by the general cleanup function AND the thread cleanup function
"""
interpolator_keys = []
for key in Moecache.keys():
if isinstance(Moecache[key], py_rinterpolate.Rinterpolate):
interpolator_keys.append(key)
for key in interpolator_keys:
Moecache[key].destroy()
del Moecache[key]
gc.collect()
##### Unsorted functions
def _calculate_multiplicity_fraction(self, system_dict):
"""
Function to calculate multiplicity fraction
Makes use of the self.bse_options['multiplicity'] value. If its not set, it will raise an error
grid_options['multiplicity_fraction_function'] will be checked for the choice
TODO: add option to put a manual binary fraction in here (solve via negative numbers being the functions)
"""
# Just return 1 if no option has been chosen
if self.grid_options["multiplicity_fraction_function"] in [0, "None"]:
verbose_print(
"_calculate_multiplicity_fraction: Chosen not to use any multiplicity fraction.",
self.grid_options["verbosity"],
3,
)
return 1
# Raise an error if the multiplicity is not set
if not system_dict.get("multiplicity", None):
msg = "Multiplicity value has not been set. When using a specific multiplicity fraction function please set the multiplicity"
raise ValueError(msg)
# Go over the chosen options
if self.grid_options["multiplicity_fraction_function"] in [1, "Arenou2010"]:
# Arenou 2010 will be used
verbose_print(
"_calculate_multiplicity_fraction: Using Arenou 2010 to calculate multiplicity fractions",
self.grid_options["verbosity"],
3,
)
binary_fraction = Arenou2010_binary_fraction(system_dict["M_1"])
multiplicity_fraction_dict = {
1: 1 - binary_fraction,
2: binary_fraction,
3: 0,
4: 0,
}
elif self.grid_options["multiplicity_fraction_function"] in [2, "Raghavan2010"]:
# Raghavan 2010 will be used
verbose_print(
"_calculate_multiplicity_fraction: Using Raghavan (2010) to calculate multiplicity fractions",
self.grid_options["verbosity"],
3,
)
binary_fraction = raghavan2010_binary_fraction(system_dict["M_1"])
multiplicity_fraction_dict = {
1: 1 - binary_fraction,
2: binary_fraction,
3: 0,
4: 0,
}
elif self.grid_options["multiplicity_fraction_function"] in [3, "Moe2017"]:
# We need to check several things now here:
# First, are the options for the MOE2017 grid set? On start it is filled with the default settings
if not self.grid_options["Moe2017_options"]:
msg = "The MOE2017 options do not seem to be set properly. The value is {}".format(
self.grid_options["Moe2017_options"]
)
raise ValueError(msg)
# Second: is the Moecache filled.
if not Moecache:
verbose_print(
"_calculate_multiplicity_fraction: Moecache is empty. It needs to be filled with the data for the interpolators. Loading the data now",
self.grid_options["verbosity"],
3,
)
# Load the data
self._load_moe_di_stefano_data()
# record the prev value
prev_M1_value_ms = self.grid_options["Moe2017_options"].get("M_1", None)
# Set value of M1 of the current system
self.grid_options["Moe2017_options"]["M_1"] = system_dict["M_1"]
# Calculate the multiplicity fraction
multiplicity_fraction_list = Moe_di_Stefano_2017_multiplicity_fractions(
self.grid_options["Moe2017_options"], self.grid_options["verbosity"]
)
# Turn into dict
multiplicity_fraction_dict = {
el + 1: multiplicity_fraction_list[el]
for el in range(len(multiplicity_fraction_list))
}
# Set the prev value back
self.grid_options["Moe2017_options"]["M_1"] = prev_M1_value_ms
# we don't know what to do next
else:
msg = "Chosen value for the multiplicity fraction function is not known."
raise ValueError(msg)
# To make sure we normalize the dictionary
multiplicity_fraction_dict = normalize_dict(
multiplicity_fraction_dict, verbosity=self.grid_options["verbosity"]
)
verbose_print(
"Multiplicity: {} multiplicity_fraction: {}".format(
system_dict["multiplicity"],
multiplicity_fraction_dict[system_dict["multiplicity"]],
),
self.grid_options["verbosity"],
3,
)
return multiplicity_fraction_dict[system_dict["multiplicity"]]
######################
# Status logging
def vb1print(self, ID, now, system_number, system_dict):
"""
Verbosity-level 1 printing, to keep an eye on a grid.
Arguments:
ID: thread ID for debugging (int)
now: the time now as a UNIX-style epoch in seconds (float)
system_number: the system number
TODO: add information about the number of cores. the TPR shows the dt/dn but i want to see the number per core too
"""
# calculate estimated time of arrive (eta and eta_secs), time per run (tpr)
localtime = time.localtime(now)
# calculate stats
n = self.shared_memory["n_saved_log_stats"].value
if n < 2:
# simple 1-system calculation: inaccurate
# but best for small n
dt = now - self.shared_memory["prev_log_time"][0]
dn = system_number - self.shared_memory["prev_log_system_number"][0]
else:
# average over n_saved_log_stats
dt = (
self.shared_memory["prev_log_time"][0]
- self.shared_memory["prev_log_time"][n - 1]
)
dn = (
self.shared_memory["prev_log_system_number"][0]
- self.shared_memory["prev_log_system_number"][n - 1]
)
eta, units, tpr, eta_secs = trem(
dt, system_number, dn, self.grid_options["_total_starcount"]
)
# compensate for multithreading and modulo
tpr *= self.grid_options["num_cores"] * self.grid_options["modulo"]
if eta_secs < secs_per_day:
fintime = time.localtime(now + eta_secs)
etf = "{hours:02d}:{minutes:02d}:{seconds:02d}".format(
hours=fintime.tm_hour, minutes=fintime.tm_min, seconds=fintime.tm_sec
)
else:
d = int(eta_secs / secs_per_day)
if d == 1:
etf = "Tomorrow"
else:
etf = "In {} days".format(d)
# modulo information
if self.grid_options["modulo"] == 1:
modulo = "" # usual case
else:
modulo = "%" + str(self.grid_options["modulo"])
# add up memory use from each thread
total_mem_use = sum(self.shared_memory["memory_use_per_thread"])
# make a string to describe the system e.g. M1, M2, etc.
system_string = ""
# use the multiplicity if given
if "multiplicity" in system_dict:
nmult = int(system_dict["multiplicity"])
else:
nmult = 4
# masses
for i in range(nmult):
i1 = str(i + 1)
if "M_" + i1 in system_dict:
system_string += (
"M{}=".format(i1) + format_number(system_dict["M_" + i1]) + " "
)
# separation and orbital period
if "separation" in system_dict:
system_string += "a=" + format_number(system_dict["separation"])
if "orbital_period" in system_dict:
system_string += "P=" + format_number(system_dict["orbital_period"])
# do the print
verbose_print(
"{opening_colour}{system_number}/{total_starcount}{modulo} {pc_colour}{pc_complete:5.1f}% complete {time_colour}{hours:02d}:{minutes:02d}:{seconds:02d} {ETA_colour}ETA={ETA:7.1f}{units} tpr={tpr:2.2e} {ETF_colour}ETF={ETF} {mem_use_colour}mem:{mem_use:.1f}MB {system_string_colour}{system_string}{closing_colour}".format(
opening_colour=self.ANSI_colours["reset"]
+ self.ANSI_colours["yellow on black"],
system_number=system_number,
total_starcount=self.grid_options["_total_starcount"],
modulo=modulo,
pc_colour=self.ANSI_colours["blue on black"],
pc_complete=(100.0 * system_number)
/ (1.0 * self.grid_options["_total_starcount"])
if self.grid_options["_total_starcount"]
else -1,
time_colour=self.ANSI_colours["green on black"],
hours=localtime.tm_hour,
minutes=localtime.tm_min,
seconds=localtime.tm_sec,
ETA_colour=self.ANSI_colours["red on black"],
ETA=eta,
units=units,
tpr=tpr,
ETF_colour=self.ANSI_colours["blue"],
ETF=etf,
mem_use_colour=self.ANSI_colours["magenta"],
mem_use=total_mem_use,
system_string_colour=self.ANSI_colours["yellow"],
system_string=system_string,
closing_colour=self.ANSI_colours["reset"],
),
self.grid_options["verbosity"],
1,
)
def vb2print(self, system_dict, cmdline_string):
print(
"Running this system now on thread {ID}\n{blue}{cmdline}{reset}\n".format(
ID=self.process_ID,
blue=self.ANSI_colours["blue"],
cmdline=cmdline_string,
reset=self.ANSI_colours["reset"],
)
)