[GSoC][TMVA][SOFIE] Serialisation of RModel #8666

sanjibansg · 2021-07-14T00:08:16Z

Description

This PR implements serialisation of RModel by adding a custom streamer in class RModel and modifying the definition of structure TMVA::Experimental::SOFIE::InitializedTensor.

Checklist:

tested changes locally

Tests

Tests for Serialisation of Custom Models

Example usage

Writing the RModel object

using namespace TMVA::Experimental;
TFile file("model.root","CREATE");
SOFIE::RModelParser_ONNX parser;
SOFIE::RModel model = parser.Parse("Linear_2.onnx");
model.Write("model");
file.Close();

Reading the RModel object

using namespace TMVA::Experimental;
TFile file("model.root","READ");
SOFIE::RModel *model;
file.GetObject("model",model);
file.Close();
model->Generate();
model->OutputGenerated("model.hxx");

phsft-bot · 2021-07-14T00:08:19Z

Can one of the admins verify this patch?

jalopezg-git · 2021-07-14T09:34:32Z

@phsft-bot build

phsft-bot · 2021-07-14T09:34:37Z

Starting build on ROOT-debian10-i386/cxx14, ROOT-performance-centos8-multicore/default, ROOT-ubuntu16/nortcxxmod, mac1014/python3, mac11.0/cxx17, windows10/cxx14
How to customize builds

phsft-bot · 2021-07-14T10:15:41Z

Build failed on ROOT-debian10-i386/cxx14.
Running on pcepsft10.dyndns.cern.ch:/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-07-14T09:35:30.879Z] stderr: error: could not read '.git/rebase-apply/head-name': No such file or directory

Failing tests:

projectroot.roottest.python.cpp.roottest_python_cpp_cpp

phsft-bot · 2021-07-14T13:35:05Z

Build failed on windows10/cxx14.
Running on null:C:\build\workspace\root-pullrequests-build
See console output.

bellenot · 2021-07-14T13:48:42Z

@sanjibansg please fork also roottest to prevent timeouts on the Windows nodes. Thanks

lmoneta · 2021-07-21T14:17:59Z

@sanjibansg : can you please rebase it to fix the conflict file , happening after merging your other PR on restructuring Sofie. Thank you

sanjibansg · 2021-07-21T15:09:16Z

@sanjibansg : can you please rebase it to fix the conflict file , happening after merging your other PR on restructuring Sofie. Thank you

@lmoneta Resolved the merge conflict.

lmoneta · 2021-08-04T15:11:57Z

@phsft-bot build just on ROOT-ubuntu16/nortcxxmod with flags -Dtmva-sofie=On

phsft-bot · 2021-08-04T15:12:05Z

Starting build on ROOT-ubuntu16/nortcxxmod with flags -Dtmva-sofie=On
How to customize builds

phsft-bot · 2021-08-04T15:13:36Z

Build failed on ROOT-ubuntu16/nortcxxmod.
Running on sft-ubuntu-1604-1.cern.ch:/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-08-04T15:13:35.602Z] CMake Error at /mnt/build/workspace/root-pullrequests-build/rootspi/jenkins/root-build.cmake:1045 (message):

lmoneta · 2021-08-05T09:01:05Z

@phsft-bot build just on ROOT-ubuntu2004/default with flags -Dtmva-sofie=On

phsft-bot · 2021-08-05T09:01:12Z

Starting build on ROOT-ubuntu2004/default with flags -Dtmva-sofie=On
How to customize builds

phsft-bot · 2021-08-05T11:58:04Z

Build failed on ROOT-ubuntu2004/default.
Running on root-ubuntu-2004-3.cern.ch:/home/sftnight/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-08-05T11:58:02.761Z] CMake Error at /home/sftnight/build/workspace/root-pullrequests-build/rootspi/jenkins/root-build.cmake:1045 (message):

lmoneta

Looks good, just a small comment on the names of member function and data members

tmva/sofie/inc/TMVA/SOFIE_common.hxx

tmva/sofie/test/CMakeLists.txt

lmoneta · 2021-08-06T09:08:01Z

@phsft-bot build just on ROOT-ubuntu18.04/default with flags -Dtmva-sofie=On

phsft-bot · 2021-08-06T09:08:10Z

Starting build on ROOT-ubuntu18.04/default with flags -Dtmva-sofie=On
How to customize builds

phsft-bot · 2021-08-06T09:10:29Z

Build failed on ROOT-ubuntu18.04/default.
Running on sft-ubuntu-1804-2.cern.ch:/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-08-06T09:10:24.228Z] CMake Error at /mnt/build/workspace/root-pullrequests-build/rootspi/jenkins/root-build.cmake:1045 (message):

lmoneta · 2021-08-10T08:01:02Z

@phsft-bot build just on ROOT-ubuntu2004/default with flags -Dtmva-sofie=On

phsft-bot · 2021-08-10T08:01:09Z

Starting build on ROOT-ubuntu2004/default with flags -Dtmva-sofie=On
How to customize builds

phsft-bot · 2021-08-10T08:07:41Z

Build failed on ROOT-ubuntu2004/default.
Running on root-ubuntu-2004-1.cern.ch:/home/sftnight/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-08-10T08:07:34.691Z] FAILED: tmva/sofie/test/CMakeFiles/emitFromONNX.dir///sofie_parsers/src/RModelParser_ONNX.cxx.o
[2021-08-10T08:07:35.415Z] /home/sftnight/build/workspace/root-pullrequests-build/root/tmva/sofie_parsers/src/RModelParser_ONNX.cxx:185:15: error: ‘class onnx::ModelProto’ has no member named ‘ParseFromIstream’; did you mean ‘ParseFromString’?
[2021-08-10T08:07:35.415Z] FAILED: tmva/sofie/test/CMakeFiles/emitFromROOT.dir///sofie_parsers/src/RModelParser_ONNX.cxx.o
[2021-08-10T08:07:36.011Z] /home/sftnight/build/workspace/root-pullrequests-build/root/tmva/sofie_parsers/src/RModelParser_ONNX.cxx:185:15: error: ‘class onnx::ModelProto’ has no member named ‘ParseFromIstream’; did you mean ‘ParseFromString’?

Warnings:

[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 32] from the object at ‘onnx::TensorProto_Segment_default_instance’ is out of the bounds of referenced subobject ‘onnx::TensorProto_Segment::begin’ with type ‘long int’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Tensor_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Tensor::shape’ with type ‘onnx::TensorShapeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Map_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Map::value_type’ with type ‘onnx::TypeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [49, 56] from the object at ‘onnx::SparseTensorProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::SparseTensorProto::values’ with type ‘onnx::TensorProto*’ at offset 40 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [73, 80] from the object at ‘onnx::TrainingInfoProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::TrainingInfoProto::initialization’ with type ‘onnx::GraphProto*’ at offset 64 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 32] from the object at ‘onnx::TensorProto_Segment_default_instance’ is out of the bounds of referenced subobject ‘onnx::TensorProto_Segment::begin’ with type ‘long int’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Tensor_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Tensor::shape’ with type ‘onnx::TensorShapeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.475Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Map_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Map::value_type’ with type ‘onnx::TypeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T08:07:40.476Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [49, 56] from the object at ‘onnx::SparseTensorProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::SparseTensorProto::values’ with type ‘onnx::TensorProto*’ at offset 40 [-Warray-bounds]
[2021-08-10T08:07:40.476Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [73, 80] from the object at ‘onnx::TrainingInfoProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::TrainingInfoProto::initialization’ with type ‘onnx::GraphProto*’ at offset 64 [-Warray-bounds]

And 1 more

lmoneta · 2021-08-10T09:50:53Z

@phsft-bot build just on ROOT-ubuntu18.04/default with flags -Dtmva-sofie=On

phsft-bot · 2021-08-10T09:50:59Z

Starting build on ROOT-ubuntu18.04/default with flags -Dtmva-sofie=On
How to customize builds

…dTensor

phsft-bot · 2021-08-10T10:26:22Z

Build failed on ROOT-ubuntu18.04/default.
Running on sft-ubuntu-1804-2.cern.ch:/build/workspace/root-pullrequests-build
See console output.

Errors:

[2021-08-10T10:26:16.753Z] FAILED: tmva/sofie_parsers/CMakeFiles/ROOTTMVASofieParser.dir/src/RModelParser_ONNX.cxx.o
[2021-08-10T10:26:17.011Z] /mnt/build/workspace/root-pullrequests-build/root/tmva/sofie_parsers/src/RModelParser_ONNX.cxx:185:15: error: ‘class onnx::ModelProto’ has no member named ‘ParseFromIstream’; did you mean ‘ParseFromString’?

Warnings:

[2021-08-10T10:26:14.987Z] Warning in <CheckModuleValid>: warning: Couldn't find in the following specified headers in the module ROOTTMVASofieParser:

lmoneta · 2021-08-10T10:54:08Z

@phsft-bot build just on ROOT-ubuntu18.04/default, ROOT-ubuntu2004/default with flags -Dtmva-sofie=On

phsft-bot · 2021-08-10T10:54:14Z

Starting build on ROOT-ubuntu18.04/default, ROOT-ubuntu2004/default with flags -Dtmva-sofie=On
How to customize builds

phsft-bot · 2021-08-10T11:44:58Z

Build failed on ROOT-ubuntu2004/default.
Running on root-ubuntu-2004-1.cern.ch:/home/sftnight/build/workspace/root-pullrequests-build
See console output.

Warnings:

[2021-08-10T11:25:00.049Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 32] from the object at ‘onnx::TensorProto_Segment_default_instance’ is out of the bounds of referenced subobject ‘onnx::TensorProto_Segment::begin’ with type ‘long int’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.049Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Tensor_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Tensor::shape’ with type ‘onnx::TensorShapeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.049Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Map_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Map::value_type’ with type ‘onnx::TypeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.049Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [49, 56] from the object at ‘onnx::SparseTensorProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::SparseTensorProto::values’ with type ‘onnx::TensorProto*’ at offset 40 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [73, 80] from the object at ‘onnx::TrainingInfoProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::TrainingInfoProto::initialization’ with type ‘onnx::GraphProto*’ at offset 64 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 32] from the object at ‘onnx::TensorProto_Segment_default_instance’ is out of the bounds of referenced subobject ‘onnx::TensorProto_Segment::begin’ with type ‘long int’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Tensor_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Tensor::shape’ with type ‘onnx::TensorShapeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [25, 28] from the object at ‘onnx::TypeProto_Map_default_instance’ is out of the bounds of referenced subobject ‘onnx::TypeProto_Map::value_type’ with type ‘onnx::TypeProto*’ at offset 16 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [49, 56] from the object at ‘onnx::SparseTensorProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::SparseTensorProto::values’ with type ‘onnx::TensorProto*’ at offset 40 [-Warray-bounds]
[2021-08-10T11:25:00.308Z] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:33: warning: ‘void* _builtin_memset(void*, int, long unsigned int)’ offset [73, 80] from the object at ‘onnx::TrainingInfoProto_default_instance’ is out of the bounds of referenced subobject ‘onnx::TrainingInfoProto::initialization’ with type ‘onnx::GraphProto*’ at offset 64 [-Warray-bounds]

phsft-bot · 2021-08-10T11:45:25Z

Build failed on ROOT-ubuntu18.04/default.
Running on sft-ubuntu-1804-2.cern.ch:/build/workspace/root-pullrequests-build
See console output.

Warnings:

[2021-08-10T11:16:04.803Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:1295:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:04.803Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:2422:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:04.803Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:3010:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:04.803Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:3757:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:4417:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:5190:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:5566:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:6099:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:6884:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]
[2021-08-10T11:16:05.060Z] /mnt/build/workspace/root-pullrequests-build/build/tmva/sofie_parsers/onnx_proto3.pb.cc:7483:10: warning: unused parameter ‘deterministic’ [-Wunused-parameter]

And 44 more

lmoneta

The Warnings are caused by using an old protobuf version in the build nodes. When using protobuf version 3.17 they should be fixed.
The PR can then be merged.
Thank you @sanjibansg for this contribution!

* Initial commit for serialisation of RModel * Modify: Casting of shared_ptr to persistent pointer and vice-versa * Add: Tests for serialisation of RModel * Resolve: Merge Conflict * Modify: Use CMAKE_BINARY_DIRECTORY/ginclude instead of /include * Modify: Names of Data members & member functions in struct InitializedTensor

sanjibansg marked this pull request as ready for review July 14, 2021 00:14

sanjibansg requested review from ashlaban, lmoneta, sitongan and stwunsch as code owners July 14, 2021 00:14

jalopezg-git assigned lmoneta and sitongan Jul 14, 2021

jalopezg-git added improvement in:TMVA labels Jul 14, 2021

This was referenced Aug 3, 2021

[GSoC][TMVA][ROOT Storage] PyKeras Parser TMVA #8430

Merged

[GSoC][TMVA][SOFIE] PyTorch Parser TMVA #8684

Merged

sanjibansg force-pushed the serialisation branch from ed2befe to be48426 Compare August 4, 2021 17:42

sanjibansg requested a review from bellenot as a code owner August 5, 2021 22:44

sanjibansg force-pushed the serialisation branch from ab0aa79 to fc35654 Compare August 6, 2021 08:43

lmoneta approved these changes Aug 6, 2021

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tmva/sofie/inc/TMVA/SOFIE_common.hxx Outdated Show resolved Hide resolved

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sanjibansg force-pushed the serialisation branch from 88678d7 to f88da31 Compare August 9, 2021 20:48

sanjibansg added 6 commits August 10, 2021 15:36

Initial commit for serialisation of RModel

2e7c5fc

Modify: Casting of shared_ptr to persistent pointer and vice-versa

99337aa

Add: Tests for serialisation of RModel

aada54a

Resolve: Merge Conflict

c4f8abc

Modify: Use CMAKE_BINARY_DIRECTORY/ginclude instead of /include

17e72a3

Modify: Names of Data members & member functions in struct Initialize…

f09983f

…dTensor

sanjibansg force-pushed the serialisation branch from f88da31 to f09983f Compare August 10, 2021 10:10

lmoneta approved these changes Aug 10, 2021

View reviewed changes

lmoneta merged commit 0bd9252 into root-project:master Aug 10, 2021

sanjibansg deleted the serialisation branch September 5, 2021 13:58

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[GSoC][TMVA][SOFIE] Serialisation of RModel #8666

[GSoC][TMVA][SOFIE] Serialisation of RModel #8666

sanjibansg commented Jul 14, 2021 •

edited

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[GSoC][TMVA][SOFIE] Serialisation of RModel #8666

[GSoC][TMVA][SOFIE] Serialisation of RModel #8666

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sanjibansg commented Jul 14, 2021 • edited

Description

Checklist:

Tests

Example usage

phsft-bot commented Jul 14, 2021

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Errors:

Failing tests:

phsft-bot commented Jul 14, 2021

bellenot commented Jul 14, 2021 • edited

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Errors:

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sanjibansg commented Jul 14, 2021 •

edited

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edited