onnxruntime build is not compatible with onnx build. Protobuf loaded twice. #7597

xkszltl · 2021-05-06T18:20:03Z

Describe the bug

Custom build of protobuf+onnx+ort shared libs doesn't work.
onnx-ml.proto is loaded twice.

# sudo docker run --rm -it <docker_image> bash -c 'ldconfig -p | grep onnx && python3 -c '"'"'print("-" * 30); import onnx; print("-" * 30); import onnxruntime'"'"
        libonnxruntime_providers_tensorrt.so (libc6,x86-64) => /usr/local/lib/libonnxruntime_providers_tensorrt.so
        libonnxruntime_providers_shared.so (libc6,x86-64) => /usr/local/lib/libonnxruntime_providers_shared.so
        libonnxruntime_providers_dnnl.so (libc6,x86-64) => /usr/local/lib/libonnxruntime_providers_dnnl.so
        libonnxruntime.so.1.7.2 (libc6,x86-64) => /usr/local/lib/libonnxruntime.so.1.7.2
        libonnxruntime.so (libc6,x86-64) => /usr/local/lib/libonnxruntime.so
        libonnxifi_dummy.so (libc6,x86-64) => /usr/local/lib/libonnxifi_dummy.so
        libonnxifi.so (libc6,x86-64) => /usr/local/lib/libonnxifi.so
        libonnx_proto.so (libc6,x86-64) => /usr/local/lib/libonnx_proto.so
        libonnx.so (libc6,x86-64) => /usr/local/lib/libonnx.so
        libnvonnxparser.so.7 (libc6,x86-64) => /usr/local/lib/libnvonnxparser.so.7
        libnvonnxparser.so.7 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libnvonnxparser.so.7
        libnvonnxparser.so (libc6,x86-64) => /usr/local/lib/libnvonnxparser.so
        libnvonnxparser.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libnvonnxparser.so
------------------------------
------------------------------
[libprotobuf ERROR ../src/google/protobuf/descriptor_database.cc:641] File already exists in database: onnx/onnx-ml.proto
[libprotobuf FATAL ../src/google/protobuf/descriptor.cc:1371] CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size): 
terminate called after throwing an instance of 'google::protobuf::FatalException'
  what():  CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size):

Here are ldd logs to show libs used by onnx/ort:

# sudo docker run --rm -it <docker_image> ldd /usr/local/lib/libonnx.so
        linux-vdso.so.1 (0x00007fff90dff000)
        libonnx_proto.so => /usr/local/lib/libonnx_proto.so (0x00007f2dc45dc000)
        libprotobuf.so.3.15.8.0 => /usr/local/lib/libprotobuf.so.3.15.8.0 (0x00007f2dc4112000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2dc3ef3000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f2dc3b6a000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2dc37cc000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2dc35b4000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2dc31c3000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2dc2fa6000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f2dc4cbd000)

# sudo docker run --rm -it <docker_image> ldd /usr/local/lib/libonnxruntime.so
        linux-vdso.so.1 (0x00007ffebefeb000)
        libcublas.so.11 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublas.so.11 (0x00007f6851c5e000)
        libcudnn.so.8 => /usr/lib/x86_64-linux-gnu/libcudnn.so.8 (0x00007f6851a35000)
        libnsync_cpp.so.1 => /usr/local/lib/libnsync_cpp.so.1 (0x00007f685182a000)
        libcudart.so.11.0 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so.11.0 (0x00007f68515a5000)
        libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f685121c000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6850e7e000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6850c66000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6850875000)
        libprotobuf.so.3.15.8.0 => /usr/local/lib/libprotobuf.so.3.15.8.0 (0x00007f68503ab000)
        libre2.so => /usr/local/lib/libre2.so (0x00007f685012e000)
        libcufft.so.10 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcufft.so.10 (0x00007f6841dca000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6841bc6000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f68419a7000)
        libpython3.6m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.6m.so.1.0 (0x00007f68412fc000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f6862b93000)
        libcublasLt.so.11 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublasLt.so.11 (0x00007f6833308000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6833100000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6832ee3000)
        libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f6832cb1000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f6832aae000)

We've had similar issue previously (#5035), not sure if it has the same root cause so I file a new issue for this.

Urgency

This is blocking the use of onnx and ort in the same process and would be a big concern in our product, where we usually want to:

Verify exported onnx model with ort.
Preprocess onnx proto before sending to ort.

System information

OS Platform and Distribution (e.g., Linux Ubuntu 16.04): Ubuntu 18.04
ONNX Runtime installed from (source or binary): source
ONNX Runtime version: 1.7.2
Python version: 3.6 (distro stock)
GCC/Compiler version (if compiling from source): gcc-8

The text was updated successfully, but these errors were encountered:

jywu-msft · 2021-05-09T18:26:20Z

@snnn any ideas?

snnn · 2021-05-10T16:28:45Z

Hi @xkszltl , could you please run ldd with "-v" like

# sudo docker run --rm -it <docker_image> ldd -v /usr/local/lib/libonnxruntime.so

and give us the output. So that we we could know who was consuming libprotobuf.so.3.15.8.0

xkszltl · 2021-05-10T16:54:11Z

Glad to.
Indentation removed to reduce log size:

linux-vdso.so.1 (0x00007ffe4dfff000)
libcublas.so.11 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublas.so.11 (0x00007f0396663000)
libcudnn.so.8 => /usr/lib/x86_64-linux-gnu/libcudnn.so.8 (0x00007f039643a000)
libnsync_cpp.so.1 => /usr/local/lib/libnsync_cpp.so.1 (0x00007f039622f000)
libcudart.so.11.0 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so.11.0 (0x00007f0395faa000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f0395c21000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f0395883000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f039566b000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f039527a000)
libprotobuf.so.3.15.8.0 => /usr/local/lib/libprotobuf.so.3.15.8.0 (0x00007f0394db0000)
libre2.so => /usr/local/lib/libre2.so (0x00007f0394b33000)
libcufft.so.10 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcufft.so.10 (0x00007f03867cf000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f03865cb000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f03863ac000)
libpython3.6m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.6m.so.1.0 (0x00007f0385d01000)
/lib64/ld-linux-x86-64.so.2 (0x00007f03a7598000)
libcublasLt.so.11 => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublasLt.so.11 (0x00007f0377d0d000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0377b05000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f03778e8000)
libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f03776b6000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f03774b3000)

Version information:
/usr/local/lib/libonnxruntime.so:
        libgcc_s.so.1 (GCC_3.3.1) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libpthread.so.0 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libcufft.so.10 (libcufft.so.10) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcufft.so.10
        libcudart.so.11.0 (libcudart.so.11.0) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so.11.0
        libcublas.so.11 (libcublas.so.11) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublas.so.11
        libm.so.6 (GLIBC_2.27) => /lib/x86_64-linux-gnu/libm.so.6
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        libcudnn.so.8 (libcudnn.so.8) => /usr/lib/x86_64-linux-gnu/libcudnn.so.8
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libstdc++.so.6 (GLIBCXX_3.4.14) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.8) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.17) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.18) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.19) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.5) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.7) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.15) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.20) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.21) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
/usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublas.so.11:
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
        librt.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/librt.so.1
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        libcublasLt.so.11 (libcublasLt.so.11) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublasLt.so.11
        libstdc++.so.6 (GLIBCXX_3.4.10) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
/usr/lib/x86_64-linux-gnu/libcudnn.so.8:
        librt.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/librt.so.1
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
/usr/local/lib/libnsync_cpp.so.1:
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.19) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
/usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so.11.0:
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        librt.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/librt.so.1
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/usr/lib/x86_64-linux-gnu/libstdc++.so.6:
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libgcc_s.so.1 (GCC_4.2.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        libgcc_s.so.1 (GCC_3.3) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.18) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.16) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.17) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libm.so.6:
        ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libgcc_s.so.1:
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libc.so.6:
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
/usr/local/lib/libprotobuf.so.3.15.8.0:
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libstdc++.so.6 (GLIBCXX_3.4.20) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.8) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.18) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.14) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.5) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.21) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
/usr/local/lib/libre2.so:
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libstdc++.so.6 (GLIBCXX_3.4.18) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.8) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.20) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.21) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
/usr/local/cuda-11.1/targets/x86_64-linux/lib/libcufft.so.10:
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
        librt.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/librt.so.1
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
/lib/x86_64-linux-gnu/libdl.so.2:
        ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
        libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libpthread.so.0:
        ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
        ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/usr/lib/x86_64-linux-gnu/libpython3.6m.so.1.0:
        libz.so.1 (ZLIB_1.2.0) => /lib/x86_64-linux-gnu/libz.so.1
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
        libutil.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libutil.so.1
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        libc.so.6 (GLIBC_2.15) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.10) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.7) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.6) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.25) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.17) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.9) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/usr/local/cuda-11.1/targets/x86_64-linux/lib/libcublasLt.so.11:
        libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
        ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
        librt.so.1 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/librt.so.1
        libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libstdc++.so.6 (GLIBCXX_3.4.10) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
        libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.3) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
/lib/x86_64-linux-gnu/librt.so.1:
        libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libpthread.so.0
        libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libz.so.1:
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libexpat.so.1:
        libc.so.6 (GLIBC_2.25) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.3.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libutil.so.1:
        libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6

snnn · 2021-05-10T19:00:23Z

So, in your custom build, both libonnx.so and libonnxruntime.so depend on libprotobuf.so, which is the full version protobuf.
I don't know who was using onnx.so, but the reason should be same:

#5035 (comment)

xkszltl · 2021-05-10T20:15:17Z

I don't know who was using onnx.so

Whatever uses onnx will use libonnx.so, e.g. the import onnx in python.

ytaous added the build build issues; typically submitted using template label May 7, 2021

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onnxruntime build is not compatible with onnx build. Protobuf loaded twice. #7597

onnxruntime build is not compatible with onnx build. Protobuf loaded twice. #7597

xkszltl commented May 6, 2021

jywu-msft commented May 9, 2021

snnn commented May 10, 2021

xkszltl commented May 10, 2021 •

edited

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snnn commented May 10, 2021

xkszltl commented May 10, 2021

onnxruntime build is not compatible with onnx build. Protobuf loaded twice. #7597

onnxruntime build is not compatible with onnx build. Protobuf loaded twice. #7597

Comments

xkszltl commented May 6, 2021

jywu-msft commented May 9, 2021

snnn commented May 10, 2021

xkszltl commented May 10, 2021 • edited Loading

snnn commented May 10, 2021

xkszltl commented May 10, 2021

xkszltl commented May 10, 2021 •

edited

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