Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

undefined reference error in compiling #458

Open
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
Assignees

Comments

@X-Bruce-Y
Copy link

X-Bruce-Y commented Apr 6, 2021

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
Copy link
Collaborator

pomerlef commented Apr 6, 2021

@aguenette could you have a look?

@aguenette aguenette self-assigned this Apr 6, 2021
@aguenette
Copy link
Member

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
Copy link
Author

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
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
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
/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5e924.dir/link.txt --verbose=1
//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.
COLLECT_GCC=//appsnew/usr/gcc/gcc-9.3.0/bin/gcc
COLLECT_LTO_WRAPPER=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper
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) 
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='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_5e924' '-mtune=generic' '-march=x86-64'
 /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2 -plugin /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so -plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccLColzc.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTC_5e924 /lib/../lib64/crt1.o /lib/../lib64/crti.o /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtbegin.o -L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../.. -O2 --sort-common --as-needed -z relro -z now --disable-new-dtags --gc-sections -rpath /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -rpath-link /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtend.o /lib/../lib64/crtn.o
COLLECT_GCC_OPTIONS='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_5e924' '-mtune=generic' '-march=x86-64'
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]
    add: [/usr/local/include]
    add: [/appsnew/usr/gcc/gcc-9.3.0/include]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
    add: [/usr/include]
  end of search list found
  collapse include dir [/appsnew/usr/boost/boost_1_70_0/include/] ==> [/appsnew/usr/boost/boost_1_70_0/include]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
  collapse include dir [/usr/local/include] ==> [/usr/local/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/include] ==> [/appsnew/usr/gcc/gcc-9.3.0/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
  collapse include dir [/usr/include] ==> [/usr/include]
  implicit include dirs: [/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]


Parsed C implicit link information from above output:
  link line regex: [^( *|.*[/\])(ld|CMAKE_LINK_STARTFILE-NOTFOUND|([^/\]+-)?ld|collect2)[^/\]*( |$)]
  ignore line: [Change Dir: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp]
  ignore line: []
  ignore line: [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]
  ignore line: [gmake[1]: Entering directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp']
  ignore line: [Building C object CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o]
  ignore line: [//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]
  ignore line: [Using built-in specs.]
  ignore line: [COLLECT_GCC=//appsnew/usr/gcc/gcc-9.3.0/bin/gcc]
  ignore line: [Target: x86_64-pc-linux-gnu]
  ignore line: [Configured with: ../gcc-9.3.0/configure --prefix=/appsnew/usr/gcc/gcc-9.3.0 --disable-multilib]
  ignore line: [Thread model: posix]
  ignore line: [gcc version 9.3.0 (GCC) ]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64']
  ignore line: [ /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]
  ignore line: [GNU C17 (GCC) version 9.3.0 (x86_64-pc-linux-gnu)]
  ignore line: [	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]
  ignore line: []
  ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
  ignore line: [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"]
  ignore line: [#include "..." search starts here:]
  ignore line: [#include <...> search starts here:]
  ignore line: [ /appsnew/usr/boost/boost_1_70_0/include/]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
  ignore line: [ /usr/local/include]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/include]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
  ignore line: [ /usr/include]
  ignore line: [End of search list.]
  ignore line: [GNU C17 (GCC) version 9.3.0 (x86_64-pc-linux-gnu)]
  ignore line: [	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]
  ignore line: []
  ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
  ignore line: [Compiler executable checksum: e923a81a69f5c7cc4d7c1200d362f05c]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64']
  ignore line: [ as -v --64 -o CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o /tmp/cc9ZpB0h.s]
  ignore line: [GNU assembler version 2.27 (x86_64-redhat-linux) using BFD version version 2.27-34.base.el7]
  ignore line: [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/]
  ignore line: [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/]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64']
  ignore line: [Linking C executable cmTC_5e924]
  ignore line: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5e924.dir/link.txt --verbose=1]
  ignore line: [//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 ]
  ignore line: [Using built-in specs.]
  ignore line: [COLLECT_GCC=//appsnew/usr/gcc/gcc-9.3.0/bin/gcc]
  ignore line: [COLLECT_LTO_WRAPPER=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper]
  ignore line: [Target: x86_64-pc-linux-gnu]
  ignore line: [Configured with: ../gcc-9.3.0/configure --prefix=/appsnew/usr/gcc/gcc-9.3.0 --disable-multilib]
  ignore line: [Thread model: posix]
  ignore line: [gcc version 9.3.0 (GCC) ]
  ignore line: [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/]
  ignore line: [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/]
  ignore line: [COLLECT_GCC_OPTIONS='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_5e924' '-mtune=generic' '-march=x86-64']
  link line: [ /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2 -plugin /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so -plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccLColzc.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTC_5e924 /lib/../lib64/crt1.o /lib/../lib64/crti.o /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtbegin.o -L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../.. -O2 --sort-common --as-needed -z relro -z now --disable-new-dtags --gc-sections -rpath /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -rpath-link /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib CMakeFiles/cmTC_5e924.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtend.o /lib/../lib64/crtn.o]
    arg [/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2] ==> ignore
    arg [-plugin] ==> ignore
    arg [/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so] ==> ignore
    arg [-plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper] ==> ignore
    arg [-plugin-opt=-fresolution=/tmp/ccLColzc.res] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
    arg [-plugin-opt=-pass-through=-lc] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
    arg [--eh-frame-hdr] ==> ignore
    arg [-m] ==> ignore
    arg [elf_x86_64] ==> ignore
    arg [-export-dynamic] ==> ignore
    arg [-dynamic-linker] ==> ignore
    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
    arg [-o] ==> ignore
    arg [cmTC_5e924] ==> ignore
    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_5e924.dir/CMakeCCompilerABI.c.o] ==> ignore
    arg [-lgcc] ==> lib [gcc]
    arg [--as-needed] ==> ignore
    arg [-lgcc_s] ==> lib [gcc_s]
    arg [--no-as-needed] ==> ignore
    arg [-lc] ==> lib [c]
    arg [-lgcc] ==> lib [gcc]
    arg [--as-needed] ==> ignore
    arg [-lgcc_s] ==> lib [gcc_s]
    arg [--no-as-needed] ==> ignore
    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: [gcc;gcc_s;c;gcc;gcc_s]
  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: []


Detecting CXX 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_7293b/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_7293b.dir/build.make CMakeFiles/cmTC_7293b.dir/build
gmake[1]: Entering directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o
/appsnew/usr/gcc/gcc-9.3.0/bin/g++   -v -o CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -c /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCXXCompilerABI.cpp
Using built-in specs.
COLLECT_GCC=/appsnew/usr/gcc/gcc-9.3.0/bin/g++
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_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/cc1plus -quiet -v -D_GNU_SOURCE /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpbase CMakeCXXCompilerABI.cpp -mtune=generic -march=x86-64 -auxbase-strip CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -version -o /tmp/ccAKNxp4.s
GNU C++14 (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
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/c++/9.3.0
 /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/x86_64-pc-linux-gnu
 /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/backward
 /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 C++14 (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: e19d96d1233eb6e336d130138c38f7c2
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v --64 -o CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccAKNxp4.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_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
Linking CXX executable cmTC_7293b
/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7293b.dir/link.txt --verbose=1
/appsnew/usr/gcc/gcc-9.3.0/bin/g++ -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_7293b.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_7293b 
Using built-in specs.
COLLECT_GCC=/appsnew/usr/gcc/gcc-9.3.0/bin/g++
COLLECT_LTO_WRAPPER=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper
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) 
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='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_7293b' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2 -plugin /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so -plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/cc7HQqN9.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTC_7293b /lib/../lib64/crt1.o /lib/../lib64/crti.o /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtbegin.o -L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../.. -O2 --sort-common --as-needed -z relro -z now --disable-new-dtags --gc-sections -rpath /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -rpath-link /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtend.o /lib/../lib64/crtn.o
COLLECT_GCC_OPTIONS='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_7293b' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
gmake[1]: Leaving directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp'



Parsed CXX 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/c++/9.3.0]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/x86_64-pc-linux-gnu]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/backward]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
    add: [/usr/local/include]
    add: [/appsnew/usr/gcc/gcc-9.3.0/include]
    add: [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
    add: [/usr/include]
  end of search list found
  collapse include dir [/appsnew/usr/boost/boost_1_70_0/include/] ==> [/appsnew/usr/boost/boost_1_70_0/include]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include]
  collapse include dir [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/] ==> [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0] ==> [/appsnew/usr/gcc/gcc-9.3.0/include/c++/9.3.0]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/x86_64-pc-linux-gnu] ==> [/appsnew/usr/gcc/gcc-9.3.0/include/c++/9.3.0/x86_64-pc-linux-gnu]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/backward] ==> [/appsnew/usr/gcc/gcc-9.3.0/include/c++/9.3.0/backward]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
  collapse include dir [/usr/local/include] ==> [/usr/local/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/include] ==> [/appsnew/usr/gcc/gcc-9.3.0/include]
  collapse include dir [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed] ==> [/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
  collapse include dir [/usr/include] ==> [/usr/include]
  implicit include dirs: [/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/include/c++/9.3.0;/appsnew/usr/gcc/gcc-9.3.0/include/c++/9.3.0/x86_64-pc-linux-gnu;/appsnew/usr/gcc/gcc-9.3.0/include/c++/9.3.0/backward;/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]


Parsed CXX implicit link information from above output:
  link line regex: [^( *|.*[/\])(ld|CMAKE_LINK_STARTFILE-NOTFOUND|([^/\]+-)?ld|collect2)[^/\]*( |$)]
  ignore line: [Change Dir: /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp]
  ignore line: []
  ignore line: [Run Build Command(s):/usr/bin/gmake cmTC_7293b/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_7293b.dir/build.make CMakeFiles/cmTC_7293b.dir/build]
  ignore line: [gmake[1]: Entering directory `/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/examples/demo_cmake/CMakeFiles/CMakeTmp']
  ignore line: [Building CXX object CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o]
  ignore line: [/appsnew/usr/gcc/gcc-9.3.0/bin/g++   -v -o CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -c /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCXXCompilerABI.cpp]
  ignore line: [Using built-in specs.]
  ignore line: [COLLECT_GCC=/appsnew/usr/gcc/gcc-9.3.0/bin/g++]
  ignore line: [Target: x86_64-pc-linux-gnu]
  ignore line: [Configured with: ../gcc-9.3.0/configure --prefix=/appsnew/usr/gcc/gcc-9.3.0 --disable-multilib]
  ignore line: [Thread model: posix]
  ignore line: [gcc version 9.3.0 (GCC) ]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64']
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/cc1plus -quiet -v -D_GNU_SOURCE /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/share/cmake-3.18/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpbase CMakeCXXCompilerABI.cpp -mtune=generic -march=x86-64 -auxbase-strip CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -version -o /tmp/ccAKNxp4.s]
  ignore line: [GNU C++14 (GCC) version 9.3.0 (x86_64-pc-linux-gnu)]
  ignore line: [	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]
  ignore line: []
  ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
  ignore line: [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"]
  ignore line: [#include "..." search starts here:]
  ignore line: [#include <...> search starts here:]
  ignore line: [ /appsnew/usr/boost/boost_1_70_0/include/]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/eigen-3.3.9]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libnabo/built/include/]
  ignore line: [ /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/libpointmatcher/built/include/]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/x86_64-pc-linux-gnu]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../include/c++/9.3.0/backward]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include]
  ignore line: [ /usr/local/include]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/include]
  ignore line: [ /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/include-fixed]
  ignore line: [ /usr/include]
  ignore line: [End of search list.]
  ignore line: [GNU C++14 (GCC) version 9.3.0 (x86_64-pc-linux-gnu)]
  ignore line: [	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]
  ignore line: []
  ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
  ignore line: [Compiler executable checksum: e19d96d1233eb6e336d130138c38f7c2]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64']
  ignore line: [ as -v --64 -o CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccAKNxp4.s]
  ignore line: [GNU assembler version 2.27 (x86_64-redhat-linux) using BFD version version 2.27-34.base.el7]
  ignore line: [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/]
  ignore line: [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/]
  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64']
  ignore line: [Linking CXX executable cmTC_7293b]
  ignore line: [/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib/python3.7/site-packages/cmake/data/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7293b.dir/link.txt --verbose=1]
  ignore line: [/appsnew/usr/gcc/gcc-9.3.0/bin/g++ -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_7293b.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_7293b ]
  ignore line: [Using built-in specs.]
  ignore line: [COLLECT_GCC=/appsnew/usr/gcc/gcc-9.3.0/bin/g++]
  ignore line: [COLLECT_LTO_WRAPPER=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper]
  ignore line: [Target: x86_64-pc-linux-gnu]
  ignore line: [Configured with: ../gcc-9.3.0/configure --prefix=/appsnew/usr/gcc/gcc-9.3.0 --disable-multilib]
  ignore line: [Thread model: posix]
  ignore line: [gcc version 9.3.0 (GCC) ]
  ignore line: [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/]
  ignore line: [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/]
  ignore line: [COLLECT_GCC_OPTIONS='-L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib' '-v' '-rdynamic' '-o' 'cmTC_7293b' '-shared-libgcc' '-mtune=generic' '-march=x86-64']
  link line: [ /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2 -plugin /appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so -plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/cc7HQqN9.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTC_7293b /lib/../lib64/crt1.o /lib/../lib64/crti.o /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtbegin.o -L/lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../.. -O2 --sort-common --as-needed -z relro -z now --disable-new-dtags --gc-sections -rpath /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib -rpath-link /lustre2/jdhan_pkuhpc/yangxinyu/SoftRepo/Anaconda3/envs/PCT/lib CMakeFiles/cmTC_7293b.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /appsnew/usr/gcc/gcc-9.3.0/lib/gcc/x86_64-pc-linux-gnu/9.3.0/crtend.o /lib/../lib64/crtn.o]
    arg [/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/collect2] ==> ignore
    arg [-plugin] ==> ignore
    arg [/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/liblto_plugin.so] ==> ignore
    arg [-plugin-opt=/appsnew/usr/gcc/gcc-9.3.0/libexec/gcc/x86_64-pc-linux-gnu/9.3.0/lto-wrapper] ==> ignore
    arg [-plugin-opt=-fresolution=/tmp/cc7HQqN9.res] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
    arg [-plugin-opt=-pass-through=-lc] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
    arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
    arg [--eh-frame-hdr] ==> ignore
    arg [-m] ==> ignore
    arg [elf_x86_64] ==> ignore
    arg [-export-dynamic] ==> ignore
    arg [-dynamic-linker] ==> ignore
    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
    arg [-o] ==> ignore
    arg [cmTC_7293b] ==> ignore
    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
Copy link
Member

@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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants