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undefined reference error in compiling #458

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X-Bruce-Y opened this issue Apr 6, 2021 · 4 comments
Open

undefined reference error in compiling #458

X-Bruce-Y opened this issue Apr 6, 2021 · 4 comments
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@aguenette

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@X-Bruce-Y
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X-Bruce-Y commented Apr 6, 2021 •
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Dear developers,

I want to thank you for creating this comprehensive point cloud toolkit, and some of the filters are exactly what I need now. I'm literally new to C++ language and not very familiar with Linux, so it took me ~20 hrs to set up eigen, boost and libnabo and "successfully" make install libpointmatcher through trials and errors. However, when I try compiling examples/demo_cmake/convert.cpp, the following error messages were thrown:

/tmp/ccokO4LU.o: In function `main':
convert.cpp:(.text+0x163): undefined reference to `PointMatcher<float>::get()'
convert.cpp:(.text+0x202): undefined reference to `PointMatcherSupport::setLogger(std::shared_ptr<PointMatcherSupport::Logger>)'
convert.cpp:(.text+0x28d): undefined reference to `PointMatcher<float>::DataPoints::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
convert.cpp:(.text+0x360): undefined reference to `PointMatcher<float>::DataPointsFilters::DataPointsFilters(std::istream&)'
convert.cpp:(.text+0x379): undefined reference to `PointMatcher<float>::DataPointsFilters::apply(PointMatcher<float>::DataPoints&)'
convert.cpp:(.text+0x3fa): undefined reference to `PointMatcher<float>::DataPoints::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) const'
/tmp/ccokO4LU.o: In function `PointMatcherSupport::Registrar<PointMatcherSupport::Logger>::getDescriptor(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
convert.cpp:(.text._ZNK19PointMatcherSupport9RegistrarINS_6LoggerEE13getDescriptorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK19PointMatcherSupport9RegistrarINS_6LoggerEE13getDescriptorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x11c): undefined reference to `PointMatcherSupport::InvalidElement::InvalidElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status

Which I don't even know how to debug and almost destroyed my will to make use of libpointmatcher as I have spend too much time on merely setting it up. So I'm giving myself a last chance to open an issue here, hoping to get some guidance.

Related environment is:

boost 1.70.0 (non-conda)
eigen 3.3.9
libnabo 1.07
g++ 9.3.0 and gcc 9.3.0 (non-conda)
cmake 3.18.4 (conda)
make 3.82
system (on HPC cluster with slurm) 
    LSB Version:	:core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
    Distributor ID:	CentOS
    Description:	CentOS Linux release 7.6.1810 (Core) 
    Release:	7.6.1810
    Codename:	Core

I have put boost, eigen, libnabo and libpointmatcher into CPATH.

What I have tried:

  1. The head part of examples/demo_cmake/convert.cpp can be compiled successfully.

     #include "pointmatcher/PointMatcher.h"
 #include <cassert>
 #include <iostream>
 #include <fstream>
 
 using namespace std;
 using namespace PointMatcherSupport;
 
 typedef PointMatcher<float> PM;
 typedef PM::DataPoints DP;

while any more than that would cause error message.

  1. Compiling libnabo/examples/usage.cpp throws the following error:

     /tmp/cc1taue8.o: In function `main':
 usage.cpp:(.text+0x94): undefined reference to `Nabo::NearestNeighbourSearch<float, Eigen::Matrix<float, -1, -1, 0, -1, -1> >::createKDTreeLinearHeap(Eigen::Matrix<float, -1, -1, 0, -1, -1> const&, int, unsigned int, Nabo::Parameters const&)'
 collect2: error: ld returned 1 exit status

Compiling libnabo/examples/trivial.cpp throws the following error:

    /tmp/ccXKCvIU.o: In function `main':
    trivial.cpp:(.text+0x89): undefined reference to `Nabo::NearestNeighbourSearch<float, Eigen::Matrix<float, -1, -1, 0, -1, -1> >::createKDTreeLinearHeap(Eigen::Matrix<float, -1, -1, 0, -1, -1> const&, int, unsigned int, Nabo::Parameters const&)'
    trivial.cpp:(.text+0x10e): undefined reference to `Nabo::NearestNeighbourSearch<float, Eigen::Matrix<float, -1, -1, 0, -1, -1> >::knn(Eigen::Matrix<float, -1, 1, 0, -1, 1> const&, Eigen::Matrix<int, -1, 1, 0, -1, 1>&, Eigen::Matrix<float, -1, 1, 0, -1, 1>&, int, float, unsigned int, float) const'
    collect2: error: ld returned 1 exit status

Please allow me to put it here as that might be the cause of libpointmatcher failure and the repo of libnabo is short of maintenance.

  1. Changing boost 1.70.0 to 1.74.0 or 1.75.0 would cause some "undefined reference" error during making libpointmatcher, let alone to say using it.

Please forgive my possible informality in describing the situation. If any other information should be required, please just ask and I'll add it as long as I'm able to.

Bests.
@pomerlef
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pomerlef commented Apr 6, 2021

@aguenette could you have a look?

@aguenette aguenette self-assigned this Apr 6, 2021
@aguenette
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Hi @Seikegn! Can you add below's lines to the demo_cmake CMakeLists.txt file after the find_package(libpointmatcher REQUIRED) line and give me the output please?

message("libpointmatcher_INCLUDE_DIRS: ${libpointmatcher_INCLUDE_DIRS}\n")
message("libpointmatcher_LIBRARIES: ${libpointmatcher_LIBRARIES}\n")

@X-Bruce-Y
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Thanks a lot! @aguenette @pomerlef
@aguenette I assume you asked me to add the two lines and then run cmake .. Below is the direct output with cmake 3.18.4.

-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: //appsnew/usr/gcc/gcc-9.3.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /appsnew/usr/gcc/gcc-9.3.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning (dev) at /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/FindBoost.cmake:1922 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "thread" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/share/libpointmatcher/cmake/libpointmatcherConfig.cmake:10 (find_package)
  CMakeLists.txt:10 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/FindBoost.cmake:2053 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "thread" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/share/libpointmatcher/cmake/libpointmatcherConfig.cmake:10 (find_package)
  CMakeLists.txt:10 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/FindBoost.cmake:2108 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "thread" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/share/libpointmatcher/cmake/libpointmatcherConfig.cmake:10 (find_package)
  CMakeLists.txt:10 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/FindBoost.cmake:2346 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "thread" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/share/libpointmatcher/cmake/libpointmatcherConfig.cmake:10 (find_package)
  CMakeLists.txt:10 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

libpointmatcher_INCLUDE_DIRS: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/pointmatcher;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/PUBLIC;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/inclue

libpointmatcher_LIBRARIES: $<TARGET_FILE:pointmatcher>;libnabo::nabo;Threads::Threads;$<TARGET_FILE:yaml-cpp-pm>;/appsnew/usr/boost/boost_1_70_0/lib/libboost_thread.so;-lpthread;/appsnew/usr/boost/boost_1_70_0/lib/libboost_filesystem.so;/appsnew/usr/boost/boost_1_70_0/lib/libboost_system.so;/appsnew/usr/boost/boost_1_70_0/lib/libboost_program_options.so;/appsnew/usr/boost/boost_1_70_0/lib/libboost_date_time.so;/appsnew/usr/boost/boost_1_70_0/lib/libboost_chrono.so;/appsnew/usr/boost/boost_1_70_0/lib/libboost_atomic.so

-- Configuring done
-- Generating done
-- Build files have been written to: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake

And below is the CMakeOutput.log:

The system is: Linux - 3.10.0-957.el7.x86_64 - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: //appsnew/usr/gcc/gcc-9.3.0/bin/gcc 
Build flags: -march=nocona;-mtune=haswell;-ftree-vectorize;-fPIC;-fstack-protector-strong;-fno-plt;-O2;-ffunction-sections;-pipe;-isystem;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/include
Id flags:  

The output was:
0


Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/3.18.4/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /appsnew/usr/gcc/gcc-9.3.0/bin/g++ 
Build flags: -fvisibility-inlines-hidden;-std=c++17;-fmessage-length=0;-march=nocona;-mtune=haswell;-ftree-vectorize;-fPIC;-fstack-protector-strong;-fno-plt;-O2;-ffunction-sections;-pipe;-isystem;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/include
Id flags:  

The output was:
0


Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is GNU, found in "/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/3.18.4/CompilerIdCXX/a.out"

Detecting C compiler ABI info compiled with the following output:
Change Dir: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_5e924/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_5e924.dir/build.make CMakeFiles/cmTC_5e924.dir/build
gmake[1]: Entering directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o
//appsnew/usr/gcc/gcc-9.3.0/bin/gcc   -v -o CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o -c /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCCompilerABI.c
Using built-in specs.
COLLECT_GCC=//appsnew/usr/gcc/gcc-9.3.0/bin/gcc
Target: x86_64-pc-linux-gnu
Configured with: ../gcc-9.3.0/configure --prefix=/appsnew/usr/gcc/gcc-9.3.0 --disable-multilib
Thread model: posix
gcc version 9.3.0 (GCC) 
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
 /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/cc1 -quiet -v /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCCompilerABI.c -quiet -dumpbase CMakeCCompilerABI.c -mtune=generic -march=x86-64 -auxbase-strip CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o -version -o /tmp/cc9ZpB0h.s
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /appsnew/usr/boost/boost_1_70_0/include/
 /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9
 /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/
 /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/
 /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include
 /usr/local/include
 /appsnew/usr/gcc/gcc-9.3.0/include
 /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed
 /usr/include
End of search list.
GNU C17 (GCC) version 9.3.0 (x86_64-pc-linux-gnu)
    compiled by GNU C version 9.3.0, GMP version 6.1.0, MPFR version 3.1.4, MPC version 1.0.3, isl version isl-0.18-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: e923a81a69f5c7cc4d7c1200d362f05c
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
 as -v --64 -o CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o /tmp/cc9ZpB0h.s
GNU assembler version 2.27 (x86_64-redhat-linux) using BFD version version 2.27-34.base.el7
COMPILER_PATH=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/:/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/:/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/
LIBRARY_PATH=/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
Linking C executable cmTC_5e924
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//appsnew/usr/gcc/gcc-9.3.0/bin/gcc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -Wl,-rpath-link,/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -v -rdynamic CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o -o cmTC_5e924 
Using built-in specs.
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Thread model: posix
gcc version 9.3.0 (GCC) 
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LIBRARY_PATH=/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../:/lib/:/usr/lib/
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gmake[1]: Leaving directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp'



Parsed C implicit include dir info from above output: rv=done
  found start of include info
  found start of implicit include info
    add: [/appsnew/usr/boost/boost_1_70_0/include/]
    add: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9]
    add: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/]
    add: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
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    arg [/lib/../lib64/crt1.o] ==> ignore
    arg [/lib/../lib64/crti.o] ==> ignore
    arg [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtbegin.o] ==> ignore
    arg [-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib] ==> dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib]
    arg [-L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0] ==> dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0]
    arg [-L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64] ==> dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64]
    arg [-L/lib/../lib64] ==> dir [/lib/../lib64]
    arg [-L/usr/lib/../lib64] ==> dir [/usr/lib/../lib64]
    arg [-L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../..] ==> dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../..]
    arg [-O2] ==> ignore
    arg [--sort-common] ==> ignore
    arg [--as-needed] ==> ignore
    arg [-zrelro] ==> ignore
    arg [-znow] ==> ignore
    arg [--disable-new-dtags] ==> ignore
    arg [--gc-sections] ==> ignore
    arg [-rpath] ==> ignore
    arg [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib] ==> ignore
    arg [-rpath-link] ==> ignore
    arg [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib] ==> ignore
    arg [CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
    arg [-lstdc++] ==> lib [stdc++]
    arg [-lm] ==> lib [m]
    arg [-lgcc_s] ==> lib [gcc_s]
    arg [-lgcc] ==> lib [gcc]
    arg [-lc] ==> lib [c]
    arg [-lgcc_s] ==> lib [gcc_s]
    arg [-lgcc] ==> lib [gcc]
    arg [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtend.o] ==> ignore
    arg [/lib/../lib64/crtn.o] ==> ignore
  collapse library dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib]
  collapse library dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0]
  collapse library dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib64]
  collapse library dir [/lib/../lib64] ==> [/lib64]
  collapse library dir [/usr/lib/../lib64] ==> [/usr/lib64]
  collapse library dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../..] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib]
  implicit libs: [stdc++;m;gcc_s;gcc;c;gcc_s;gcc]
  implicit dirs: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib;/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0;/appsnew/usr/gcc/gcc-9.3.0/lib64;/lib64;/usr/lib64;/appsnew/usr/gcc/gcc-9.3.0/lib]
  implicit fwks: []

So sorry to distract you with a log this lengthy, but I'm not sure which part might be pertinent.

Please let me know if any other information should be needed.

@aguenette
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@aguenette I assume you asked me to add the two lines and then run cmake .. Below is the direct output with cmake 3.18.4.

Yes, that's what I meant, thanks for the feedback!

It looks like your libpointmatcher_INCLUDE_DIRS variable is different from what I get on Ubuntu:

libpointmatcher_INCLUDE_DIRS: /usr/local/include;/usr/include/eigen3

Yours is:

libpointmatcher_INCLUDE_DIRS: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/pointmatcher;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/PUBLIC;/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/inclue

For example, when I build libpointmatcher or libnabo on Ubuntu, there's no include directory in my build directory (plus there's a typo in your libnabo's one). So it might be that... or not.

Also, I thought that it could be your cmake 3.18.4 that you are using, you get policy errors that I don't get even if I use cmake 3.20.0. Maybe, you could try to install it from CentOS package manager instead of anaconda?

You also mentioned that you struggled installing the library and its dependencies, can you tell me what you had to do in order to build the library? Like, have you installed libnabo and libpointmatcher? Did you have to manually specified the path to both libraries? Have you change the `CMakeLists.txt. file in the demo project? That kind of stuff.

It also looks like you're doing an in-source build for demo project:

-- Build files have been written to: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake

I recommend you to create a build directory and do an out-of-source build like you did for libpointmatcher and libnabo. Doing so, you will be able to remove the directory and start with a new configuration if something goes wrong with the building process.

Finally, if you have installed libointmatcher and libnabo on your system, I suggest you to uninstall them and try to rebuild them with another version of cmake and maybe use cmake-gui to set some variable a little more easily and don't forget to remove the build directory and create a new one. I hope this will help you to successfully install and use libpointmatcher. If you have any questions about what I said, don't hesitate.

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