Note
Click here to download the full example code
SerializeToString and ParseFromString#
Startup#
This section creates an ONNX graph if there is not one.
import numpy
import onnx
from pyquickhelper.pycode.profiling import profile, profile2graph
from cpyquickhelper.numbers.speed_measure import measure_time
import matplotlib.pyplot as plt
import pandas
from tqdm import tqdm
from onnx.checker import check_model
from mlprodict.testing.experimental_c_impl.experimental_c import code_optimisation
from mlprodict.plotting.text_plot import onnx_simple_text_plot
from mlprodict.npy.xop import loadop
try:
from mlprodict.onnx_tools._onnx_check_model import check_model as check_model_py
except ImportError:
check_model_py = None
Available optimisation on this machine.
print(code_optimisation())
AVX-omp=8
Build an ONNX graph of different size#
def build_model(n_nodes, size, opv=15):
OnnxAdd, OnnxIdentity = loadop('Add', 'Identity')
x = 'X'
for n in range(n_nodes):
y = OnnxAdd(x, numpy.random.randn(size).astype(numpy.float32),
op_version=opv)
x = y
final = OnnxIdentity(x, op_version=opv, output_names=['Y'])
x = numpy.zeros((10, 10), dtype=numpy.float32)
return final.to_onnx({'X': x}, {'Y': x}, target_opset=opv)
model = build_model(2, 5)
print(onnx_simple_text_plot(model))
opset: domain='' version=15
input: name='X' type=dtype('float32') shape=[10, 10]
init: name='init' type=dtype('float32') shape=(5,)
init: name='init_1' type=dtype('float32') shape=(5,)
Add(X, init) -> out_add_0
Add(out_add_0, init_1) -> Y
output: name='Y' type=dtype('float32') shape=[10, 10]
Measure the time of serialization functions#
def parse(buffer):
proto = onnx.ModelProto()
proto.ParseFromString(buffer)
return proto
data = []
nodes = [5, 10, 20]
for size in tqdm([10, 100, 1000, 10000, 100000, 200000, 300000]):
for n_nodes in nodes:
repeat = 20 if size < 100000 else 5
onx = build_model(n_nodes, size)
serialized = onx.SerializeToString()
onnx_size = len(serialized)
obs = measure_time(lambda: onx.SerializeToString(),
div_by_number=True, repeat=repeat)
obs['size'] = size
obs['n_nodes'] = n_nodes
obs['onnx_size'] = onnx_size
obs['task'] = "SerializeToString"
data.append(obs)
parsed = parse(serialized)
obs = measure_time(lambda: parse(serialized),
div_by_number=True, repeat=repeat)
obs['size'] = size
obs['n_nodes'] = n_nodes
obs['onnx_size'] = onnx_size
obs['task'] = "ParseFromString"
data.append(obs)
obs = measure_time(lambda: check_model(onx, full_check=False),
div_by_number=True, repeat=repeat)
obs['size'] = size
obs['n_nodes'] = n_nodes
obs['onnx_size'] = onnx_size
obs['task'] = "check_model"
data.append(obs)
if check_model_py is None:
continue
obs = measure_time(lambda: check_model_py(onx),
div_by_number=True, repeat=repeat)
obs['size'] = size
obs['n_nodes'] = n_nodes
obs['onnx_size'] = onnx_size
obs['task'] = "check_model_py"
data.append(obs)
0%| | 0/7 [00:00<?, ?it/s]
14%|#4 | 1/7 [00:13<01:18, 13.14s/it]
29%|##8 | 2/7 [00:26<01:05, 13.19s/it]
43%|####2 | 3/7 [00:39<00:53, 13.36s/it]
57%|#####7 | 4/7 [00:56<00:44, 14.73s/it]
71%|#######1 | 5/7 [01:10<00:28, 14.33s/it]
86%|########5 | 6/7 [01:33<00:17, 17.43s/it]
100%|##########| 7/7 [02:07<00:00, 22.63s/it]
100%|##########| 7/7 [02:07<00:00, 18.17s/it]
time
df = pandas.DataFrame(data).sort_values(
['task', 'onnx_size', 'size', 'n_nodes'])
df[['task', 'onnx_size', 'size', 'n_nodes', 'average']]
Summary#
df.to_excel("time.xlsx", index=False)
piv = df.pivot(index='onnx_size', columns='task', values='average')
piv
Graph#
fig, ax = plt.subplots(1, 1)
piv.plot(title="Time processing of serialization functions\n"
"lower better", ax=ax)
ax.set_xlabel("onnx size")
ax.set_ylabel("s")
Text(33.972222222222214, 0.5, 's')
Conclusion#
This graph shows that implementing check_model in python is much slower
than the C++ version. However, protobuf prevents from sharing
ModelProto from Python to C++ (see Python Updates)
unless the python package is compiled with a specific setting
(problably slower). A profiling shows that the code spends quite some time
in function getattr().
ps = profile(lambda: check_model_py(onx))[0]
root, nodes = profile2graph(ps, clean_text=lambda x: x.split('/')[-1])
text = root.to_text()
print(text)
# plt.show()
__getattr__ -- 160 160 -- 0.00099 0.00280 -- _onnx_check_model.py:68:__getattr__ (__getattr__)
<method 'endswith' of 'str' objects> -- 160 160 -- 0.00020 0.00020 -- ~:0:<method 'endswith' of 'str' objects> (<method 'endswith' of 'str' objects>) +++
<built-in method builtins.getattr> -- 160 160 -- 0.00067 0.00067 -- ~:0:<built-in method builtins.getattr> (<built-in method builtins.getattr>) +++
<built-in method builtins.hasattr> -- 160 160 -- 0.00094 0.00094 -- ~:0:<built-in method builtins.hasattr> (<built-in method builtins.hasattr>) +++
__init__ -- 2 2 -- 0.00002 0.00002 -- _onnx_check_model.py:312:__init__ (__init__)
get_ir_version -- 21 21 -- 0.00004 0.00004 -- _onnx_check_model.py:326:get_ir_version (get_ir_version)
get_opset_imports -- 21 21 -- 0.00001 0.00001 -- _onnx_check_model.py:334:get_opset_imports (get_opset_imports)
set_opset_imports -- 2 2 -- 0.00000 0.00000 -- _onnx_check_model.py:338:set_opset_imports (set_opset_imports)
__init__ -- 2 3 -- 0.00001 0.00001 -- _onnx_check_model.py:377:__init__ (__init__)
copy -- 1 1 -- 0.00000 0.00001 -- _onnx_check_model.py:398:copy (copy)
__init__ -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:377:__init__ (__init__) +++
this_graph_has -- 81 81 -- 0.00008 0.00008 -- _onnx_check_model.py:388:this_graph_has (this_graph_has)
this_or_ancestor_graph_has -- 60 80 -- 0.00013 0.00021 -- _onnx_check_model.py:392:this_or_ancestor_graph_has (this_or_ancestor_graph_has)
this_graph_has -- 80 80 -- 0.00008 0.00008 -- _onnx_check_model.py:388:this_graph_has (this_graph_has) +++
this_or_ancestor_graph_has -- 20 20 -- 0.00002 0.00003 -- _onnx_check_model.py:392:this_or_ancestor_graph_has (this_or_ancestor_graph_has) +++
_enforce_has_field -- 46 46 -- 0.00007 0.00024 -- _onnx_check_model.py:405:_enforce_has_field (_enforce_has_field)
<built-in method builtins.hasattr> -- 46 46 -- 0.00018 0.00018 -- ~:0:<built-in method builtins.hasattr> (<built-in method builtins.hasattr>) +++
_enforce_non_empty_field -- 23 23 -- 0.00003 0.00009 -- _onnx_check_model.py:417:_enforce_non_empty_field (_enforce_non_empty_field)
<built-in method builtins.getattr> -- 23 23 -- 0.00006 0.00006 -- ~:0:<built-in method builtins.getattr> (<built-in method builtins.getattr>) +++
<lambda> -- 1 1 -- 0.00000 0.04924 -- plot_benchmark_onnx_serialize.py:150:<lambda> (<lambda>)
check_model -- 1 1 -- 0.00002 0.04923 -- _onnx_check_model.py:1266:check_model (check_model)
__init__ -- 1 1 -- 0.00001 0.00001 -- _onnx_check_model.py:312:__init__ (__init__) +++
_check_model -- 1 1 -- 0.00008 0.04920 -- _onnx_check_model.py:1223:_check_model (_check_model)
get_ir_version -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:326:get_ir_version (get_ir_version) +++
set_ir_version -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:330:set_ir_version (set_ir_version)
set_opset_imports -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:338:set_opset_imports (set_opset_imports) +++
__init__ -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:377:__init__ (__init__) +++
_check_graph -- 1 1 -- 0.00149 0.04907 -- _onnx_check_model.py:962:_check_graph (_check_graph)
get_ir_version -- 20 20 -- 0.00004 0.00004 -- _onnx_check_model.py:326:get_ir_version (get_ir_version) +++
__init__ -- 1 1 -- 0.00000 0.00001 -- _onnx_check_model.py:377:__init__ (__init__) +++
add -- 41 41 -- 0.00014 0.00018 -- _onnx_check_model.py:384:add (add)
<method 'add' of 'set' objects> -- 41 41 -- 0.00004 0.00004 -- ~:0:<method 'add' of 'set' objects> (<method 'add' of 'set' objects>) +++
this_graph_has -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:388:this_graph_has (this_graph_has) +++
this_or_ancestor_graph_has -- 60 60 -- 0.00011 0.00021 -- _onnx_check_model.py:392:this_or_ancestor_graph_has (this_or_ancestor_graph_has) +++
_enforce_has_field -- 20 20 -- 0.00004 0.00016 -- _onnx_check_model.py:405:_enforce_has_field (_enforce_has_field) +++
_enforce_non_empty_field -- 1 1 -- 0.00001 0.00001 -- _onnx_check_model.py:417:_enforce_non_empty_field (_enforce_non_empty_field) +++
_check_value_info -- 2 2 -- 0.00016 0.00049 -- _onnx_check_model.py:423:_check_value_info (_check_value_info)
is_main_graph -- 2 2 -- 0.00000 0.00000 -- _onnx_check_model.py:342:is_main_graph (is_main_graph)
_enforce_has_field -- 6 6 -- 0.00001 0.00003 -- _onnx_check_model.py:405:_enforce_has_field (_enforce_has_field) +++
_enforce_non_empty_field -- 2 2 -- 0.00000 0.00001 -- _onnx_check_model.py:417:_enforce_non_empty_field (_enforce_non_empty_field) +++
<method 'ByteSize' ...CMessage' objects> -- 12 12 -- 0.00003 0.00003 -- ~:0:<method 'ByteSize' of 'google.protobuf.pyext._message.CMessage' objects> (<method 'ByteSize' of 'google.protobuf.pyext._message.CMessage' objects>)
<method 'endswith' of 'str' objects> -- 138 138 -- 0.00006 0.00006 -- ~:0:<method 'endswith' of 'str' objects> (<method 'endswith' of 'str' objects>) +++
<built-in method builtins.dir> -- 2 2 -- 0.00014 0.00014 -- ~:0:<built-in method builtins.dir> (<built-in method builtins.dir>)
<built-in method builtins.getattr> -- 12 12 -- 0.00005 0.00005 -- ~:0:<built-in method builtins.getattr> (<built-in method builtins.getattr>) +++
_check_tensor -- 20 20 -- 0.01124 0.04066 -- _onnx_check_model.py:484:_check_tensor (_check_tensor)
_enforce_has_field -- 20 20 -- 0.00002 0.00005 -- _onnx_check_model.py:405:_enforce_has_field (_enforce_has_field) +++
_check_data_field -- 100 100 -- 0.00043 0.01959 -- _onnx_check_model.py:465:_check_data_field (_check_data_field)
<built-in method builtins.getattr> -- 120 120 -- 0.01901 0.01901 -- ~:0:<built-in method builtins.getattr> (<built-in method builtins.getattr>) +++
<built-in method builtins.len> -- 100 100 -- 0.00015 0.00015 -- ~:0:<built-in method builtins.len> (<built-in method builtins.len>) +++
<built-in method builtins.hasattr> -- 40 40 -- 0.00971 0.00971 -- ~:0:<built-in method builtins.hasattr> (<built-in method builtins.hasattr>) +++
<built-in method builtins.len> -- 20 20 -- 0.00008 0.00008 -- ~:0:<built-in method builtins.len> (<built-in method builtins.len>) +++
_check_node -- 20 20 -- 0.00061 0.00579 -- _onnx_check_model.py:911:_check_node (_check_node)
__getattr__ -- 20 20 -- 0.00013 0.00031 -- _onnx_check_model.py:68:__getattr__ (__getattr__) +++
verify -- 20 20 -- 0.00141 0.00415 -- _onnx_check_model.py:83:verify (verify)
__init__ -- 20 20 -- 0.00006 0.00006 -- _onnx_check_model.py:31:__init__ (__init__)
__getattr__ -- 140 140 -- 0.00086 0.00248 -- _onnx_check_model.py:68:__getattr__ (__getattr__) +++
num_inputs_allowed -- 20 20 -- 0.00001 0.00001 -- _onnx_check_model.py:73:num_inputs_allowed (num_inputs_allowed)
num_outputs_allowed -- 20 20 -- 0.00001 0.00001 -- _onnx_check_model.py:78:num_outputs_allowed (num_outputs_allowed)
<built-in method builtins.len> -- 200 200 -- 0.00017 0.00017 -- ~:0:<built-in method builtins.len> (<built-in method builtins.len>) +++
GetSchema -- 20 20 -- 0.00003 0.00055 -- _onnx_check_model.py:302:GetSchema (GetSchema)
get_schema -- 20 20 -- 0.00008 0.00052 -- _onnx_check_model.py:295:get_schema (get_schema)
__init__ -- 20 20 -- 0.00003 0.00003 -- _onnx_check_model.py:65:__init__ (__init__)
<built-in metho...fs.get_schema> -- 20 20 -- 0.00041 0.00041 -- ~:0:<built-in method onnx.onnx_cpp2py_export.defs.get_schema> (<built-in method onnx.onnx_cpp2py_export.defs.get_schema>)
get_opset_imports -- 20 20 -- 0.00001 0.00001 -- _onnx_check_model.py:334:get_opset_imports (get_opset_imports) +++
get_schema_registry -- 20 20 -- 0.00001 0.00001 -- _onnx_check_model.py:354:get_schema_registry (get_schema_registry)
_enforce_non_empty_field -- 20 20 -- 0.00002 0.00007 -- _onnx_check_model.py:417:_enforce_non_empty_field (_enforce_non_empty_field) +++
check_is_experimental_op -- 20 20 -- 0.00007 0.00007 -- _onnx_check_model.py:1296:check_is_experimental_op (check_is_experimental_op)
<method 'append' of 'list' objects> -- 20 20 -- 0.00001 0.00001 -- ~:0:<method 'append' of 'list' objects> (<method 'append' of 'list' objects>)
<method 'add' of 'set' objects> -- 20 20 -- 0.00002 0.00002 -- ~:0:<method 'add' of 'set' objects> (<method 'add' of 'set' objects>) +++
_check_model_local_functions -- 1 1 -- 0.00002 0.00004 -- _onnx_check_model.py:1122:_check_model_local_functions (_check_model_local_functions)
__init__ -- 1 1 -- 0.00001 0.00001 -- _onnx_check_model.py:312:__init__ (__init__) +++
get_opset_imports -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:334:get_opset_imports (get_opset_imports) +++
set_opset_imports -- 1 1 -- 0.00000 0.00000 -- _onnx_check_model.py:338:set_opset_imports (set_opset_imports) +++
<built-in method builtins.len> -- 321 321 -- 0.00041 0.00041 -- ~:0:<built-in method builtins.len> (<built-in method builtins.len>)
<method 'add' of 'set' objects> -- 61 61 -- 0.00006 0.00006 -- ~:0:<method 'add' of 'set' objects> (<method 'add' of 'set' objects>)
<built-in method builtins.hasattr> -- 246 246 -- 0.01083 0.01083 -- ~:0:<built-in method builtins.hasattr> (<built-in method builtins.hasattr>)
<method 'endswith' of 'str' objects> -- 298 298 -- 0.00026 0.00026 -- ~:0:<method 'endswith' of 'str' objects> (<method 'endswith' of 'str' objects>)
<built-in method builtins.getattr> -- 315 315 -- 0.01978 0.01978 -- ~:0:<built-in method builtins.getattr> (<built-in method builtins.getattr>)
Total running time of the script: ( 2 minutes 9.090 seconds)