Note
Click here to download the full example code
Benchmark inference for a linear regression#
This short code compares the execution of a couple of runtime for inference including onnxruntime. This benchmark leverages the example Benchmark Linear Regression. This simple model is useful to measure unsignificant cost for large models.
Linear Regression#
import warnings
from time import perf_counter as time
from multiprocessing import cpu_count
import numpy
from numpy.random import rand
from numpy.testing import assert_almost_equal
import matplotlib.pyplot as plt
import pandas
from onnxruntime import InferenceSession
from onnxruntime.capi._pybind_state import ( # pylint: disable=E0611
SessionIOBinding, OrtDevice as C_OrtDevice)
from sklearn import config_context
from sklearn.linear_model import LinearRegression
from sklearn.utils._testing import ignore_warnings
from skl2onnx import to_onnx
from skl2onnx.common.data_types import FloatTensorType
from mlprodict.onnxrt import OnnxInference
Available optimisation on this machine.
from mlprodict.testing.experimental_c_impl.experimental_c import code_optimisation
print(code_optimisation())
Out:
AVX-omp=8
Implementations to benchmark#
def fcts_model(X, y, n_jobs):
"LinearRegression."
model = LinearRegression(n_jobs=n_jobs)
model.fit(X, y)
initial_types = [('X', FloatTensorType([None, X.shape[1]]))]
onx = to_onnx(model, initial_types=initial_types,
black_op={'LinearRegressor'})
sess = InferenceSession(onx.SerializeToString(),
providers=['CPUExecutionProvider'])
outputs = [o.name for o in sess.get_outputs()]
oinf = OnnxInference(onx, runtime="python")
bind = SessionIOBinding(sess._sess)
# ort_device = C_OrtDevice.cpu()
ort_device = C_OrtDevice(
C_OrtDevice.cpu(), C_OrtDevice.default_memory(), 0)
def predict_skl_predict(X, model=model):
return model.predict(X)
def predict_onnxrt_predict(X, sess=sess):
return sess.run(outputs[:1], {'X': X})[0]
def predict_onnx_inference(X, oinf=oinf):
return oinf.run({'X': X})["variable"]
def predict_onnxrt_predict_bind(X, sess=sess, bind=bind,
ort_device=ort_device):
if X.__array_interface__['strides'] is not None:
raise RuntimeError("onnxruntime only supports contiguous arrays.")
bind.bind_input('X', ort_device, X.dtype, X.shape,
X.__array_interface__['data'][0])
bind.bind_output('variable', ort_device)
sess._sess.run_with_iobinding(bind, None)
ortvalues = bind.get_outputs()
return ortvalues[0].numpy()
return {'predict': {
'skl': predict_skl_predict,
'ort': predict_onnxrt_predict,
'numpy': predict_onnx_inference,
'ort-bind': predict_onnxrt_predict_bind
}}
Benchmarks#
def allow_configuration(**kwargs):
return True
def bench(n_obs, n_features, n_jobss,
methods, repeat=10, verbose=False):
res = []
for nfeat in n_features:
ntrain = 50000
X_train = numpy.empty((ntrain, nfeat)).astype(numpy.float32)
X_train[:, :] = rand(ntrain, nfeat)[:, :]
eps = rand(ntrain) - 0.5
y_train = X_train.sum(axis=1) + eps
for n_jobs in n_jobss:
fcts = fcts_model(X_train, y_train, n_jobs)
for n in n_obs:
for method in methods:
if not allow_configuration(n=n, nfeat=nfeat,
n_jobs=n_jobs, method=method):
continue
obs = dict(n_obs=n, nfeat=nfeat, method=method,
n_jobs=n_jobs)
# creates different inputs to avoid caching in any ways
Xs = []
for r in range(repeat):
x = numpy.empty((n, nfeat))
x[:, :] = rand(n, nfeat)[:, :]
Xs.append(x.astype(numpy.float32))
for name, fct in fcts[method].items():
if name == 'skl':
# measures the baseline
with config_context(assume_finite=True):
st = time()
repeated = 0
for X in Xs:
p1 = fct(X)
repeated += 1
if time() - st >= 1:
break # stops if longer than a second
end = time()
obs["time_skl"] = (end - st) / repeated
else:
st = time()
r2 = 0
for X in Xs:
p2 = fct(X)
r2 += 1
if r2 >= repeated:
break
end = time()
obs["time_" + name] = (end - st) / r2
# final
res.append(obs)
if verbose and (len(res) % 1 == 0 or n >= 10000):
print("bench", len(res), ":", obs)
# checks that both produce the same outputs
if n <= 10000:
if len(p1.shape) == 1 and len(p2.shape) == 2:
p2 = p2.ravel()
try:
assert_almost_equal(
p1.ravel(), p2.ravel(), decimal=5)
except AssertionError as e:
warnings.warn(str(e))
return res
Graphs#
def plot_rf_models(dfr):
def autolabel(ax, rects):
for rect in rects:
height = rect.get_height()
ax.annotate('%1.1fx' % height,
xy=(rect.get_x() + rect.get_width() / 2, height),
xytext=(0, 3), # 3 points vertical offset
textcoords="offset points",
ha='center', va='bottom',
fontsize=8)
engines = [_.split('_')[-1] for _ in dfr.columns if _.startswith("time_")]
engines = [_ for _ in engines if _ != 'skl']
for engine in engines:
dfr["speedup_%s" % engine] = dfr["time_skl"] / dfr["time_%s" % engine]
print(dfr.tail().T)
ncols = 2
fig, axs = plt.subplots(len(engines), ncols, figsize=(
14, 4 * len(engines)), sharey=True)
row = 0
for row, engine in enumerate(engines):
pos = 0
name = "LinearRegression - %s" % engine
for nf in sorted(set(dfr.nfeat)):
for n_jobs in sorted(set(dfr.n_jobs)):
sub = dfr[(dfr.nfeat == nf) & (dfr.n_jobs == n_jobs)]
ax = axs[row, pos]
labels = sub.n_obs
means = sub["speedup_%s" % engine]
x = numpy.arange(len(labels))
width = 0.90
rects1 = ax.bar(x, means, width, label='Speedup')
if pos == 0:
# ax.set_yscale('log')
ax.set_ylim([0.1, max(dfr["speedup_%s" % engine])])
if pos == 0:
ax.set_ylabel('Speedup')
ax.set_title('%s\n%d features\n%d jobs' % (name, nf, n_jobs))
if row == len(engines) - 1:
ax.set_xlabel('batch size')
ax.set_xticks(x)
ax.set_xticklabels(labels)
autolabel(ax, rects1)
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(8)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(8)
pos += 1
fig.tight_layout()
return fig, ax
Run benchs#
@ignore_warnings(category=FutureWarning)
def run_bench(repeat=200, verbose=False):
n_obs = [1, 10, 100, 1000, 10000]
methods = ['predict']
n_features = [10, 50]
n_jobss = [cpu_count()]
start = time()
results = bench(n_obs, n_features, n_jobss,
methods, repeat=repeat, verbose=verbose)
end = time()
results_df = pandas.DataFrame(results)
print("Total time = %0.3f sec cpu=%d\n" % (end - start, cpu_count()))
# plot the results
return results_df
name = "plot_linear_regression"
df = run_bench(verbose=True)
# df.to_csv("%s.csv" % name, index=False)
# df.to_excel("%s.xlsx" % name, index=False)
Out:
bench 1 : {'n_obs': 1, 'nfeat': 10, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00019629011861979962, 'time_ort': 7.187484763562679e-05, 'time_numpy': 0.00021339278668165208, 'time_ort-bind': 0.00012074844911694527}
bench 2 : {'n_obs': 10, 'nfeat': 10, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00019765404984354974, 'time_ort': 6.660716608166694e-05, 'time_numpy': 0.0002124141436070204, 'time_ort-bind': 0.00011531755328178406}
bench 3 : {'n_obs': 100, 'nfeat': 10, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00020135670900344848, 'time_ort': 7.430048659443855e-05, 'time_numpy': 0.00021634395234286784, 'time_ort-bind': 0.0001237885095179081}
bench 4 : {'n_obs': 1000, 'nfeat': 10, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00023233114741742612, 'time_ort': 0.0001496531069278717, 'time_numpy': 0.00024192248471081258, 'time_ort-bind': 0.00019717955961823464}
bench 5 : {'n_obs': 10000, 'nfeat': 10, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.0003627436421811581, 'time_ort': 0.0005987856443971395, 'time_numpy': 0.0003520121984183788, 'time_ort-bind': 0.0005523492209613323}
bench 6 : {'n_obs': 1, 'nfeat': 50, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00019654535688459873, 'time_ort': 6.68653566390276e-05, 'time_numpy': 0.00021199935115873814, 'time_ort-bind': 0.00011487235315144062}
bench 7 : {'n_obs': 10, 'nfeat': 50, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.0001974244974553585, 'time_ort': 6.847204640507698e-05, 'time_numpy': 0.00021117310971021652, 'time_ort-bind': 0.00011733057908713818}
bench 8 : {'n_obs': 100, 'nfeat': 50, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.00020291158929467202, 'time_ort': 9.965761564671994e-05, 'time_numpy': 0.00021780339069664477, 'time_ort-bind': 0.00014766947366297246}
bench 9 : {'n_obs': 1000, 'nfeat': 50, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.0002491867635399103, 'time_ort': 0.00040781771764159203, 'time_numpy': 0.00027243767865002154, 'time_ort-bind': 0.00045684645883738997}
bench 10 : {'n_obs': 10000, 'nfeat': 50, 'method': 'predict', 'n_jobs': 8, 'time_skl': 0.0006037381943315267, 'time_ort': 0.0014695286098867655, 'time_numpy': 0.0007756333518773317, 'time_ort-bind': 0.0013975599594414235}
Total time = 7.905 sec cpu=8
Results#
df
Graph#
fig, ax = plot_rf_models(df)
fig.savefig("%s.png" % name)
# plt.show()
Out:
5 6 7 8 9
n_obs 1 10 100 1000 10000
nfeat 50 50 50 50 50
method predict predict predict predict predict
n_jobs 8 8 8 8 8
time_skl 0.000197 0.000197 0.000203 0.000249 0.000604
time_ort 0.000067 0.000068 0.0001 0.000408 0.00147
time_numpy 0.000212 0.000211 0.000218 0.000272 0.000776
time_ort-bind 0.000115 0.000117 0.000148 0.000457 0.001398
speedup_ort 2.93942 2.883286 2.036087 0.611025 0.410838
speedup_numpy 0.927104 0.934894 0.931627 0.914656 0.778381
speedup_ort-bind 1.710989 1.682635 1.374093 0.54545 0.431994
Total running time of the script: ( 0 minutes 10.867 seconds)