def timeit_verbose(
stmt,
setup="pass",
total_duration=2,
globals=None,
norm=None,
name=None,
print_time=False,
max_length_name=33,
):
result = timeit(
stmt, setup=setup, total_duration=total_duration, globals=globals
)
if norm is None:
norm = result
norm_given = False
else:
norm_given = True
if name is None:
name = stmt.split("(")[0]
fmt_name = f"{{:{max_length_name}s}}"
name = fmt_name.format(name)
if print_time:
raw_time = f" = {result:7.3g} s"
else:
raw_time = ""
print(f"{name}: {result/norm:5.3g} * norm{raw_time}")
if not norm_given and not print_time:
print(f"norm = {norm:5.3g} s")
return result
def bench(call, norm=None):
ret = result = timeit(call, globals=loc)
if norm is None:
norm = result
result /= norm
print(f"{call.split('(')[0]:33s}: {result:.2f}")
return ret
stiffness = Stiffness()
x = np.array([0.0, 1.0, 0.0])
y = np.array([0.0, 0.0, 1.0])
m = np.zeros(21)
stiffness.compute(x, y, m)
m_3d = np.zeros(21)
stiffness.compute_3d(x, y, m_3d)
assert np.allclose(m, m_3d)
timeit = partial(timeit, globals=locals(), total_duration=8)
# time = timeit("stiffness.compute(x, y, m)", globals=locals())
# print(f"{time * 1e6:.2f} µs")
time = timeit("stiffness.compute_3d(x, y, m)")
print(f"{time * 1e6:.2f} µs")
try:
from __pythran__.bench_e8c958181e03f6fe586ca36dbe63fe01 import __for_method__Stiffness__compute_3d
except ImportError:
from __pythran__.bench_16ca22d6c4f7271d975a6bac0b0cfb62 import __for_method__Stiffness__compute_3d
s = stiffness
time = timeit(
"__for_method__Stiffness__compute_3d(s.gq3d, s.grads3d, x, y, m)")
print(f"{time * 1e6:.2f} µs")
grads = stiffness.grads3d
gq = stiffness.gq3d
def lorenz(u, t):
x, y, z = u
return 10.0 * (y - x), x * (28.0 - z) - y, x * y - 2.66 * z
lorenz_pythran = jit(native=True, xsimd=True)(lorenz)
lorenz_numba = numba.jit(lorenz)
u0 = (1.0, 0.0, 0.0)
lorenz_pythran(u0, 0)
lorenz_numba(u0, 0)
wait_for_all_extensions()
# tspan = (0.0, 100.0)
t = np.linspace(0, 100, 1001)
sol = odeint(lorenz, u0, t)
norm = timeit("odeint(lorenz, u0, t, rtol = 1e-8, atol=1e-8)", globals=locals())
timeit(
"odeint(lorenz_pythran, u0, t, rtol = 1e-8, atol=1e-8)",
globals=locals(),
norm=norm,
)
timeit(
"odeint(lorenz_numba, u0, t, rtol = 1e-8, atol=1e-8)",
globals=locals(),
norm=norm,
)
x_init = np.zeros(n_sleds)
y_init = np.random.rand(n_sleds)
v_init = np.zeros(n_sleds)
u_init = np.zeros(n_sleds) + 3.5
solver(board, x_init, y_init, u_init, v_init, 0.01, n_time)
# end code functions (don't remove this line)
bench_pythran = jit(bench)
# Numba does not support this code...
# bench_numba = jit(backend="numba")(bench)
from transonic import wait_for_all_extensions
# warmup (compilation of the Pythran extension)
bench_pythran(1, 1)
wait_for_all_extensions()
if __name__ == "__main__":
from transonic.util import timeit_verbose as timeit
n_sleds = 10
n_time = 200
g = locals()
norm = timeit("bench(n_sleds, n_time)", globals=g)
timeit("bench_pythran(n_sleds, n_time)", globals=g, norm=norm)
# timeit("bench_numba(n_sleds, n_time)", globals=g, norm=norm)
velocities = np.zeros_like(positions)
accelerations = np.zeros_like(positions)
time_step = 1.0
advance_positions_nosimd(positions, velocities, accelerations, time_step)
advance_positions_simd(positions, velocities, accelerations, time_step)
advance_positions_loops(positions, velocities, accelerations, time_step)
advance_positions_nosimd_ra(positions, velocities, accelerations, time_step)
advance_positions_simd_ra(positions, velocities, accelerations, time_step)
advance_positions_loops_ra(positions, velocities, accelerations, time_step)
wait_for_all_extensions()
norm = timeit(
"advance_positions(positions, velocities, accelerations, time_step)",
globals=locals(),
)
timeit(
"advance_positions_simd(positions, velocities, accelerations, time_step)",
globals=locals(),
norm=norm,
)
timeit(
"advance_positions_nosimd(positions, velocities, accelerations, time_step)",
globals=locals(),
norm=norm,
)
timeit(
"advance_positions_loops(positions, velocities, accelerations, time_step)",
globals=locals(),
norm=norm,
shape = 1024, dim
print("shape=", shape)
masses = np.zeros(shape[0])
positions = np.zeros(shape)
velocities = np.zeros_like(positions)
accelerations = np.zeros_like(positions)
x = 0.0
for ip in range(shape[0]):
positions[ip, 0] = x
x += 1.0
glo = globals()
norm = timeit("compute(accelerations, masses, positions)", globals=glo)
timeit("compute_opt(accelerations, masses, positions)", globals=glo, norm=norm)
timeit("compute_opt1(accelerations, masses, positions)",
globals=glo,
norm=norm)
timeit("compute_opt2(accelerations, masses, positions)",
globals=glo,
norm=norm)
"""
Oh, `pythran -P` gives:
```
coef = (1.0 / (np.square(math.sqrt(builtins.sum(np.square(vector)))) * math.sqrt(builtins.sum(np.square(vector)))))
```
I guess the C++ compiler is smart enough to simplify that, but it's a bit strange...
"""
def bench(functions, arr, columns):
print(backend_default.capitalize())
for func in functions:
result = timeit("func(arr, columns)", globals=locals())
print(f"{func.__name__:20s} {result:.3e} s")
print()
shape = 256, 4
positions = np.zeros(shape)
velocities = np.zeros_like(positions)
accelerations = np.zeros_like(positions)
time_step = 1.0
advance_positions_nosimd(positions, velocities, accelerations, time_step)
advance_positions_simd(positions, velocities, accelerations, time_step)
advance_positions_loops(positions, velocities, accelerations, time_step)
wait_for_all_extensions()
glo = globals()
norm = timeit(
"advance_positions(positions, velocities, accelerations, time_step)",
globals=glo)
timeit(
"advance_positions_nosimd(positions, velocities, accelerations, time_step)",
norm=norm,
globals=glo)
timeit(
"advance_positions_simd(positions, velocities, accelerations, time_step)",
norm=norm,
globals=glo)
timeit(
"advance_positions_loops(positions, velocities, accelerations, time_step)",
norm=norm,
globals=glo)
def bench_one(name_module="cmorph", func=None, total_duration=2):
if func is not None:
raise NotImplementedError
functions = [(mod, func_) for (mod, func_) in statements.keys()
if mod == name_module]
if not functions:
raise ValueError(f"bad name_module: {name_module}")
name_function = functions[0][1]
print(f"module: {name_module}")
stmt = statements[(name_module, name_function)]
print(stmt)
path_setup = Path("setup_codes") / f"{name_module}_{name_function}.py"
if not path_setup.exists():
raise RuntimeError
with open(path_setup) as file:
setup = file.read()
if (name_module, name_function) in import_from_skimage:
setup_from_skimage = setup.replace(
f"from future.{name_module} import {name_function}",
import_from_skimage[(name_module, name_function)],
)
time = timeit(stmt, setup_from_skimage, total_duration=total_duration)
print(f"{'from skimage':18s} {time:.2e} s")
setup_pyx = setup.replace(f"from future.{name_module} import",
f"from pyx.{name_module} import")
code = f"""
from transonic.util import timeit
setup = '''{setup}'''
stmt = '''{stmt}'''
print(timeit(stmt, setup, total_duration={total_duration}))
"""
time_old = timeit(stmt, setup_pyx, total_duration=total_duration)
print(f"cython pyx skimage {time_old:.2e} s (= norm)")
with open("tmp.py", "w") as file:
file.write(code)
for backend in ("cython", "pythran", "numba"):
time = float(getoutput(f"TRANSONIC_BACKEND='{backend}' python tmp.py"))
print(f"{backend:18s} {time:.2e} s (= {time/time_old:.2f} * norm)")
# print(getoutput("TRANSONIC_NO_REPLACE=1 python tmp.py"))
if (name_module, name_function) not in import_from_skimage:
return
setup_from_skimage = setup.replace(
f"from future.{name_module} import {name_function}",
import_from_skimage[(name_module, name_function)],
)
time = timeit(stmt, setup_from_skimage, total_duration=total_duration)
print(f"{'from skimage':18s} {time:.2e} s (= {time/time_old:.2f} * norm)")
a11 = -y[0] + y[2]
a12 = y[0] - y[1]
a21 = x[0] - x[2]
a22 = -x[0] + x[1]
for f in range(6):
for p in range(3):
grads[f, p, 0] = a11 * gq[f, p, 0] + a12 * gq[f, p, 1]
grads[f, p, 1] = a21 * gq[f, p, 0] + a22 * gq[f, p, 1]
result = np.zeros(21)
compute(x, y, grads, result)
timeit = partial(timeit, globals=locals(), total_duration=8)
time = timeit("compute(x, y, grads, result)") * 1e6
print(f"Pythran: {time:.2f} µs")
from pathlib import Path
import sys
path_tmp_julia = Path("tmp_result_julia.txt")
if not path_tmp_julia.exists():
sys.exit()
with open(path_tmp_julia) as file:
txt = file.read()
time_julia = float(txt.split("\n")[1].split(" ")[-2])
print(f"Julia: {time_julia:.2f} µs\nratio Pythran/Julia: {time/time_julia:.2f}")
n_sleds = 10
n_time = 1000
x_init = np.zeros(n_sleds)
y_init = np.random.rand(n_sleds)
v_init = np.zeros(n_sleds)
u_init = np.zeros(n_sleds) + 3.5
solver(board, x_init, y_init, v_init, u_init, 0.01, n_time, n_sleds)
bench_pythran = jit(bench)
bench_numba = jit(backend="numba")(bench)
if __name__ == "__main__":
from transonic.util import timeit_verbose as timeit
g = locals()
norm = timeit("bench()", globals=g)
timeit("bench_pythran()", globals=g, norm=norm)
timeit("bench_numba()", globals=g, norm=norm)
"""
bench : 1.000 * norm
norm = 8.35e-01 s
bench_pythran : 0.007 * norm
bench_numba : 0.009 * norm
(~140 speedup!)
"""
def test_timeit():
a = 1
b = 2
timeit("a + b", total_duration=0.001, globals=locals())
@boost
def get_num_threads():
nthreads = -1
# omp parallel
if 1:
# omp single
nthreads = omp.get_num_threads()
return nthreads
shape = 1024, dim
print("shape=", shape)
nthreads = get_num_threads()
print(nthreads)
masses = np.zeros(shape[0])
positions = np.zeros(shape)
velocities = np.zeros_like(positions)
accelerations = np.zeros([nthreads, shape[0], dim])
x = 0.0
for ip in range(shape[0]):
positions[ip, 0] = x
x += 1.0
glo = globals()
norm = timeit("compute(accelerations, masses, positions)", globals=glo)
# timeit("compute_opt(accelerations, masses, positions)", globals=glo, norm=norm)
@boost
def integrand_transonic_boost(x: float):
return np.exp(10.0 * x * np.cos(x))
integrand_numba = numba.njit(integrand)
integrand_numba_cfunc = numba.cfunc("float64(float64)")(integrand)
ll_callable = LowLevelCallable(integrand_capsule, signature="double (double)")
methods = {
"no acceleration": "integrand",
"numba": "integrand_numba",
"numba cfunc": "integrand_numba_cfunc.ctypes",
"transonic_jit": "integrand_transonic_jit",
"transonic_boost": "integrand_transonic_boost",
"pythran capsule": "ll_callable",
}
norm = None
for name, key in methods.items():
print(name)
result = timeit(
f"quad({key}, 0, 10, epsabs=1.49e-08, epsrel=1.49e-08)",
globals=locals(),
total_duration=8,
norm=norm,
)
print(f"{result * 1e6:.2f} μs")
if norm is None:
norm = result
np.int32,
)
images = images.flatten()
# Erosion goes smallest to largest; dilation goes largest to smallest.
index_sorted = np.argsort(images).astype(np.int32)
index_sorted = index_sorted[::-1]
# Make a linked list of pixels sorted by value. -1 is the list terminator.
prev = np.full(len(images), -1, np.int32)
next_ = np.full(len(images), -1, np.int32)
prev[index_sorted[1:]] = index_sorted[:-1]
next_[index_sorted[:-1]] = index_sorted[1:]
# Cython inner-loop compares the rank of pixel values.
value_rank, value_map = rank_order(images)
start = index_sorted[0]
ranks = np.array(value_rank)
strides = nb_strides
current_idx = np.int64(start)
time = timeit(
"reconstruction_loop(ranks, prev, next_, strides, current_idx, image_stride)",
globals=locals(),
total_duration=10,
)
print(f"# {time:.2e} s")
