Failed to compile cpp_wrappers

[zjjdes]

Hi there,

Firstly thanks for the excellent work. I'm having trouble compiling the grid_subsampling extention (compile_wrappers.sh). The error log is here:

running build_ext
building 'grid_subsampling' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: gcc -pthread -B /home/des/anaconda3/envs/D3Feat/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/cpp_wrappers
creating build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils
creating build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud
creating build/temp.linux-x86_64-3.6/grid_subsampling
compile options: '-I/home/des/anaconda3/envs/D3Feat/lib/python3.6/site-packages/numpy/core/include -I/home/des/anaconda3/envs/D3Feat/include/python3.6m -c'
extra options: '-std=c++11'
gcc: ../cpp_utils/cloud/cloud.cpp
gcc: grid_subsampling/grid_subsampling.cpp
gcc: wrapper.cpp
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /home/des/anaconda3/envs/D3Feat/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /home/des/anaconda3/envs/D3Feat/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/des/anaconda3/envs/D3Feat/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from wrapper.cpp:2:
/home/des/anaconda3/envs/D3Feat/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
grid_subsampling/grid_subsampling.cpp: In function ‘void grid_subsampling(std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, float, int)’:
grid_subsampling/grid_subsampling.cpp:99:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
99 | for (int i = 0; i < ldim; i++)
wrapper.cpp: In function ‘PyObject* grid_subsampling_compute(PyObject*, PyObject*, PyObject*)’:
wrapper.cpp:70:27: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
70 | static char kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
wrapper.cpp:70:37: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
70 | static char kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
wrapper.cpp:70:49: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
70 | static char kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
wrapper.cpp:70:60: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
70 | static char kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
wrapper.cpp:70:72: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
70 | static char kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
wrapper.cpp:70:82: warning: ISO C++ forbids converting a string constant to ‘char’ [-Wwrite-strings]
70 | static char *kwlist[] = {"points", "features", "classes", "sampleDl", "method", "verbose", NULL };
g++ -pthread -shared -B /home/des/anaconda3/envs/D3Feat/compiler_compat -L/home/des/anaconda3/envs/D3Feat/lib -Wl,-rpath=/home/des/anaconda3/envs/D3Feat/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o build/temp.linux-x86_64-3.6/grid_subsampling/grid_subsampling.o build/temp.linux-x86_64-3.6/wrapper.o -o /mnt/G/LiDAR datasets/d3feat/cpp_wrappers/cpp_subsampling/grid_subsampling.cpython-36m-x86_64-linux-gnu.so
/home/des/anaconda3/envs/D3Feat/compiler_compat/ld: build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: unable to initialize decompress status for section .debug_info
/home/des/anaconda3/envs/D3Feat/compiler_compat/ld: build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: unable to initialize decompress status for section .debug_info
/home/des/anaconda3/envs/D3Feat/compiler_compat/ld: build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: unable to initialize decompress status for section .debug_info
/home/des/anaconda3/envs/D3Feat/compiler_compat/ld: build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: Command "g++ -pthread -shared -B /home/des/anaconda3/envs/D3Feat/compiler_compat -L/home/des/anaconda3/envs/D3Feat/lib -Wl,-rpath=/home/des/anaconda3/envs/D3Feat/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o build/temp.linux-x86_64-3.6/grid_subsampling/grid_subsampling.o build/temp.linux-x86_64-3.6/wrapper.o -o /mnt/G/LiDAR datasets/d3feat/cpp_wrappers/cpp_subsampling/grid_subsampling.cpython-36m-x86_64-linux-gnu.so" failed with exit status 1

My environment:

• Anaconda on ArchLinux
• CUDA 9.0
• tensorflow=1.12.0
• cudatoolkit=9.0
• cudnn=7.6.0
• Default system GCC version: 10.2
• Default CUDA9.0 GCC version: 6.5

I suspected the version of GCC might be the cause, so I tried changing both the versions of GCC in the system and in CUDA to 5.5 but the problem persists.

Could you please advise how to solve this issue? Thanks.

[XuyangBai]

Hi @zjjdes Thanks for your interest. I haven't met such problems before. It seems like the object file is corrupted somehow. Could you first remove the *.o in cpp_wrappers and then rerun compile.sh?

[zjjdes]

@XuyangBai Thanks for your reply. I tried removing the build folder and compiling again, no luck. My guess is that the problem is in the following two lines:

build/temp.linux-x86_64-3.6/cpp_wrappers/cpp_utils/cloud/cloud.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status

So I think I still have issues with the GCC version. The original installation guide of KPConv suggests Ubuntu 16.04, which includes gcc 5.4 by default. I tried using gcc 5.5 but it did not work. Can I ask which version of gcc you used to successfully compile this?

[XuyangBai]

Hi @zjjdes I use gcc 6.5 with Ubuntu 18.04

[zjjdes]

@XuyangBai Thanks for your swift reply! I think I just found the solution here. I followed this guide and ran the script again, this time the aforementioned errors did not occur, and it generated grid_subsampling.cpython-36m-x86_64-linux-gnu.so in cpp_subsampling/grid_subsampling. Does this mean it has been successfully compiled? If so, please feel free to close the issue, and thanks again for your help.

[XuyangBai]

Hi @zjjdes yes, it should be successfully compiled now. You can try the training or evaluation code to verify.