Source code for brian2.codegen.runtime.cython_rt.cython_rt

import os
import sys

import numpy

from brian2.core.base import BrianObjectException
from brian2.core.variables import (DynamicArrayVariable, ArrayVariable,
                                   AuxiliaryVariable, Subexpression)
from brian2.core.functions import Function
from brian2.core.preferences import prefs, BrianPreference
from brian2.utils.logger import get_logger
from brian2.utils.stringtools import get_identifiers

from ...codeobject import constant_or_scalar, check_compiler_kwds
from ..numpy_rt import NumpyCodeObject
from ...templates import Templater
from ...generators.cython_generator import (CythonCodeGenerator, get_cpp_dtype,
from ...targets import codegen_targets
from ...cpp_prefs import get_compiler_and_args
from .extension_manager import cython_extension_manager

__all__ = ['CythonCodeObject']

logger = get_logger(__name__)

# Preferences
    'Cython runtime codegen preferences',
    multiprocess_safe = BrianPreference(
        Whether to use a lock file to prevent simultaneous write access
        to cython .pyx and .so files.
    cache_dir = BrianPreference(
        validator=lambda x: x is None or isinstance(x, str),
        Location of the cache directory for Cython files. By default,
        will be stored in a ``brian_extensions`` subdirectory
        where Cython inline stores its temporary files
        (the result of ``get_cython_cache_dir()``).
    delete_source_files = BrianPreference(
        Whether to delete source files after compiling. The Cython
        source files can take a significant amount of disk space, and
        are not used anymore when the compiled library file exists.
        They are therefore deleted by default, but keeping them around
        can be useful for debugging.

[docs]class CythonCodeObject(NumpyCodeObject): ''' Execute code using Cython. ''' templater = Templater('brian2.codegen.runtime.cython_rt', '.pyx', env_globals={'cpp_dtype': get_cpp_dtype, 'numpy_dtype': get_numpy_dtype, 'dtype': numpy.dtype, 'constant_or_scalar': constant_or_scalar}) generator_class = CythonCodeGenerator class_name = 'cython' def __init__(self, owner, code, variables, variable_indices, template_name, template_source, compiler_kwds, name='cython_code_object*'): check_compiler_kwds(compiler_kwds, ['libraries', 'include_dirs', 'library_dirs', 'runtime_library_dirs', 'sources'], 'Cython') super(CythonCodeObject, self).__init__(owner, code, variables, variable_indices, template_name, template_source, compiler_kwds={}, # do not pass the actual args name=name) self.compiler, self.extra_compile_args = get_compiler_and_args() self.define_macros = list(prefs['codegen.cpp.define_macros']) self.extra_link_args = list(prefs['codegen.cpp.extra_link_args']) self.headers = [] # not actually used self.include_dirs = (list(prefs['codegen.cpp.include_dirs']) + compiler_kwds.get('include_dirs', [])) self.include_dirs = list(prefs['codegen.cpp.include_dirs']) if sys.platform == 'win32': self.include_dirs += [os.path.join(sys.prefix, 'Library', 'include')] else: self.include_dirs += [os.path.join(sys.prefix, 'include')] self.library_dirs = (list(prefs['codegen.cpp.library_dirs']) + compiler_kwds.get('library_dirs', [])) if sys.platform == 'win32': self.library_dirs += [os.path.join(sys.prefix, 'Library', 'lib')] else: self.library_dirs += [os.path.join(sys.prefix, 'lib')] self.runtime_library_dirs = (list(prefs['codegen.cpp.runtime_library_dirs']), compiler_kwds.get('runtime_library_dirs', [])) self.libraries = (list(prefs['codegen.cpp.libraries']) + compiler_kwds.get('libraries', [])) self.sources = compiler_kwds.get('sources', [])
[docs] @classmethod def is_available(cls): try: compiler, extra_compile_args = get_compiler_and_args() code = ''' #cython: language_level=3 def main(): cdef int x x = 0''' compiled = cython_extension_manager.create_extension(code, compiler=compiler, extra_compile_args=extra_compile_args, extra_link_args=prefs['codegen.cpp.extra_link_args'], include_dirs=prefs['codegen.cpp.include_dirs'], library_dirs=prefs['codegen.cpp.library_dirs']) compiled.main() return True except Exception as ex: logger.warn(('Cannot use Cython, a test compilation ' 'failed: %s (%s)' % (str(ex), ex.__class__.__name__)), 'failed_compile_test') return False
[docs] def compile_block(self, block): code = getattr(self.code, block, '').strip() if not code or 'EMPTY_CODE_BLOCK' in code: return None return cython_extension_manager.create_extension( code, define_macros=self.define_macros, libraries=self.libraries, extra_compile_args=self.extra_compile_args, extra_link_args=self.extra_link_args, include_dirs=self.include_dirs, library_dirs=self.library_dirs, compiler=self.compiler,'_'+self.template_name, sources=self.sources )
[docs] def run_block(self, block): compiled_code = self.compiled_code[block] if compiled_code: try: return compiled_code.main(self.namespace) except Exception as exc: message = ('An exception occured during the execution of the {} ' 'block of code object {}.\n').format(block, raise BrianObjectException(message, self.owner) from exc
def _insert_func_namespace(self, func): impl = func.implementations[self] func_namespace = impl.get_namespace(self.owner) if func_namespace is not None: self.namespace.update(func_namespace) if impl.dependencies is not None: for dep in impl.dependencies.values(): self._insert_func_namespace(dep)
[docs] def variables_to_namespace(self): # Variables can refer to values that are either constant (e.g. dt) # or change every timestep (e.g. t). We add the values of the # constant variables here and add the names of non-constant variables # to a list # A list containing tuples of name and a function giving the value self.nonconstant_values = [] for name, var in self.variables.items(): if isinstance(var, Function): self._insert_func_namespace(var) if isinstance(var, (AuxiliaryVariable, Subexpression)): continue try: value = var.get_value() except (TypeError, AttributeError): # A dummy Variable without value or a function self.namespace[name] = var continue if isinstance(var, ArrayVariable): self.namespace[self.device.get_array_name(var, self.variables)] = value self.namespace['_num'+name] = var.get_len() if var.scalar and var.constant: self.namespace[name] = value.item() else: self.namespace[name] = value if isinstance(var, DynamicArrayVariable): dyn_array_name = self.generator_class.get_array_name(var, access_data=False) self.namespace[dyn_array_name] = self.device.get_value(var, access_data=False) # Also provide the Variable object itself in the namespace (can be # necessary for resize operations, for example) self.namespace['_var_'+name] = var # Get all identifiers in the code -- note that this is not a smart # function, it will get identifiers from strings, comments, etc. This # is not a problem here, since we only use this list to filter out # things. If we include something incorrectly, this only means that we # will pass something into the namespace unnecessarily. all_identifiers = get_identifiers( # Filter out all unneeded objects self.namespace = {k: v for k, v in self.namespace.items() if k in all_identifiers} # There is one type of objects that we have to inject into the # namespace with their current value at each time step: dynamic # arrays that change in size during runs, where the size change is not # initiated by the template itself for name, var in self.variables.items(): if (isinstance(var, DynamicArrayVariable) and var.needs_reference_update): array_name = self.device.get_array_name(var, self.variables) if array_name in self.namespace: self.nonconstant_values.append((array_name, var.get_value)) if '_num'+name in self.namespace: self.nonconstant_values.append(('_num'+name, var.get_len))
[docs] def update_namespace(self): # update the values of the non-constant values in the namespace for name, func in self.nonconstant_values: self.namespace[name] = func()