def _init_and_compile_C(
self,
derivatives,
helpers=None,
inputs=None,
max_delay=0.0,
callbacks=None,
chunksize=1,
):
"""
Initialise DDE system and compile to C.
"""
logging.info("Setting up the DDE system...")
if platform == "darwin":
# assert clang is used on macOS
os.environ["CC"] = "clang"
callbacks = callbacks or ()
self.dde_system = jitcdde_input(
f_sym=derivatives,
input=inputs,
helpers=helpers,
n=len(derivatives),
max_delay=max_delay,
callback_functions=callbacks,
)
logging.info("Compiling to C...")
self.dde_system.compile_C(
simplify=False,
do_cse=False,
extra_compile_args=self.extra_compile_args,
omp=False,
chunk_size=chunksize,
verbose=False,
)
def _run_mass(self, node, duration, dt):
coupling_variables = {k: 0.0 for k in node.required_couplings}
noise = ZeroInput(num_iid=node.num_noise_variables).as_cubic_splines(duration, dt)
system = jitcdde_input(node._derivatives(coupling_variables), input=noise)
system.constant_past(np.array(node.initial_state))
system.adjust_diff()
times = np.arange(dt, duration + dt, dt)
return np.vstack([system.integrate(time) for time in times])
def _init_and_compile_C(
self,
derivatives,
helpers=None,
inputs=None,
max_delay=0.0,
callbacks=None,
chunksize=1,
use_open_mp=False,
):
"""
Initialise DDE system and compiled to C.
"""
logging.info("Setting up the DDE system...")
if platform == "darwin":
# assert clang is used on macOS
os.environ["CC"] = "clang"
callbacks = callbacks or ()
self.dde_system = jitcdde_input(
f_sym=derivatives,
input=inputs,
helpers=helpers,
n=len(derivatives),
max_delay=max_delay,
callback_functions=callbacks,
)
if use_open_mp:
logging.info("Using OpenMP parallelisation...")
compiler_args = ["-fopenmp"]
if platform == "darwin":
logging.warning(
"MacOS detected. For openMP parallelisation the llvm and "
"libomp must be installed. If not, install them please "
"with `brew install llvm libomp` and follow steps for "
"prepending system path with llvm path.")
linker_args = ["-lomp", "-L/usr/local/opt/llvm/lib"]
else:
linker_args = ["-lgomp"]
omp_flags = (compiler_args, linker_args)
else:
omp_flags = False
logging.info("Compiling to C...")
self.dde_system.compile_C(
simplify=False,
do_cse=False,
extra_compile_args=self.extra_compile_args,
omp=omp_flags,
chunk_size=chunksize,
verbose=False,
)
def test_input(self):
combos = [
combo for l in range(1, n) for combo in combinations(range(n), l)
]
for combo in np.random.choice(combos, 3, replace=False):
combo = [3, 5]
substitutions = {y(i): input(i) for i in combo}
f_input = [expression.subs(substitutions) for expression in f]
DDE = jitcdde_input(f, self.result)
DDE.set_integration_parameters(**test_parameters)
DDE.compile_C(extra_compile_args=compile_args)
DDE.add_past_points(get_past_points())
value = DDE.integrate(T)
assert_allclose(value, y_10_ref)
def _init_load_compiled(
self,
compiled_dir,
derivatives,
helpers=None,
inputs=None,
max_delay=0.0,
callbacks=None,
):
"""
Initialise DDE system and load from compiled.
"""
logging.info("Setting up the DDE system...")
compiled_filename = os.path.join(compiled_dir, f"{self.label}.so")
assert os.path.exists(compiled_filename)
self.dde_system = jitcdde_input(
f_sym=derivatives,
input=inputs,
helpers=helpers,
n=len(derivatives),
max_delay=max_delay,
callback_functions=callbacks,
module_location=compiled_filename,
)
