CMakeError.log

Issue #10 new
Former user created an issue

Professor: Hello,

when i use [chaiqz@tns3 build]$ CC=gcc CXX=g++ Fortan=gfortran /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/bin/cmake -DENABLE_MOVIE=no -DSKYNET_MATRIX_SOLVER=pardiso -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

the output are: -- The CXX compiler identification is GNU 4.9.0 -- The C compiler identification is GNU 4.9.0 -- The Fortran compiler identification is GNU -- Check for working CXX compiler: /usr/local/bin/g++ -- Check for working CXX compiler: /usr/local/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/local/bin/gcc -- Check for working C compiler: /usr/local/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes -- Found HDF5: /home/chaiqz/local/hdf5-1.12.0-linux-centos7-x86_64-static/lib/libhdf5_cpp.a;/home/chaiqz/local/hdf5-1.12.0-linux-centos7-x86_64-static/lib/libhdf5.a;/home/chaiqz/local/hdf5-1.12.0-linux-centos7-x86_64-static/lib/libsz.a;/home/chaiqz/local/hdf5-1.12.0-linux-centos7-x86_64-static/lib/libz.a;/usr/lib64/libdl.so;/usr/lib64/libm.so
-- Found GSL: /home/chaiqz/lib/gsl/lib/libgsl.so;/home/chaiqz/lib/gsl/lib/libgslcblas.so
-- Boost version: 1.74.0 -- Found the following Boost libraries: -- system -- filesystem -- serialization -- Found SWIG: /home/chaiqz/lib/swig/bin/swig (found suitable version "3.0.0", minimum required is "3") -- Found PythonLibs: /usr/local/lib/libpython2.7.a (found suitable version "2.7.14", minimum required is "2.6") -- Found Pardiso : /home/chaiqz/lib/libpardiso600-GNU720-X86-64.so;/home/chaiqz/lib/libpardiso600-GNU720-X86-64.so -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- A library with BLAS API found. -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP Fortran flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
-- -- -- Configuration options: -- -- CMAKE_CXX_FLAGS: -Wall -Wextra -std=c++11 -g -fPIC -DSKYNET_USE_PARDISO -- CMAKE_CXX_LINK_FLAGS: -- CMAKE_CXX_FLAGS_DEBUG: -g -DDEBUG -- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG -- CMAKE_Fortran_FLAGS: -g -fPIC -- CMAKE_Fortran_LINK_FLAGS: -- CMAKE_Fortran_FLAGS_DEBUG: -g -- CMAKE_Fortran_FLAGS_RELEASE: -O3 -- -- -- Matrix solver: pardiso (sparse) -- SWIG: enabled -- making movies: disabled -- -- -- Configuring done -- Generating done -- Build files have been written to: /home/chaiqz/Skynet/build

i found the build/CMakeError.log is

Determining if the pthread_create exist failed with the following output: Change Dir: /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2471864884/fast" /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2471864884.dir/build.make CMakeFiles/cmTryCompileExec2471864884.dir/build gmake[1]: Entering directory /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp' /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/bin/cmake -E cmake_progress_report /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec2471864884.dir/CheckSymbolExists.c.o /usr/local/bin/gcc -o CMakeFiles/cmTryCompileExec2471864884.dir/CheckSymbolExists.c.o -c /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c Linking C executable cmTryCompileExec2471864884 /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2471864884.dir/link.txt --verbose=1 /usr/local/bin/gcc CMakeFiles/cmTryCompileExec2471864884.dir/CheckSymbolExists.c.o -o cmTryCompileExec2471864884 -rdynamic CMakeFiles/cmTryCompileExec2471864884.dir/CheckSymbolExists.c.o: In functionmain': CheckSymbolExists.c:(.text+0x16): undefined reference to pthread_create' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTryCompileExec2471864884] Error 1 gmake[1]: Leaving directory/home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp' gmake: *** [cmTryCompileExec2471864884/fast] Error 2

File /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c: / / #include <pthread.h>

int main(int argc, char* argv) { (void)argv; #ifndef pthread_create return ((int)(&pthread_create))[argc]; #else (void)argc; return 0; #endif }

Determining if the function pthread_create exists in the pthreads failed with the following output: Change Dir: /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTryCompileExec3554605195/fast" /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3554605195.dir/build.make CMakeFiles/cmTryCompileExec3554605195.dir/build gmake[1]: Entering directory /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp' /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/bin/cmake -E cmake_progress_report /home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec3554605195.dir/CheckFunctionExists.c.o /usr/local/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTryCompileExec3554605195.dir/CheckFunctionExists.c.o -c /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/share/cmake-3.1/Modules/CheckFunctionExists.c Linking C executable cmTryCompileExec3554605195 /home/chaiqz/local/cmake-3.1.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3554605195.dir/link.txt --verbose=1 /usr/local/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTryCompileExec3554605195.dir/CheckFunctionExists.c.o -o cmTryCompileExec3554605195 -rdynamic -lpthreads /usr/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status gmake[1]: *** [cmTryCompileExec3554605195] Error 1 gmake[1]: Leaving directory/home/chaiqz/Skynet/build/CMakeFiles/CMakeTmp' gmake: *** [cmTryCompileExec3554605195/fast] Error 2

Then "make -j install" as attachments,, could you help me? thank you very much.

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