Build error on Rhea

[keichi]

I'm getting link errors when trying to build ADIOS2 on Rhea.

Error message:

[ 63%] Linking C executable ../../../bin/hello_bpWriter_c
../../../lib/libadios2.so.2.2.0: undefined reference to `std::this_thread::__sleep_for(std::chrono::duration<long, std::ratio<1l, 1l> >, std::chrono::duration<long, std::ratio<1l, 1000000000l> >)@GLIBCXX_3.4.18'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__future_base::_Result_base::_Result_base()@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `typeinfo for std::__future_base::_State_base@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__detail::_Prime_rehash_policy::_M_need_rehash(unsigned long, unsigned long, unsigned long) const@GLIBCXX_3.4.18'
../../../lib/libadios2.so.2.2.0: undefined reference to `vtable for std::nested_exception@CXXABI_1.3.5'
../../../lib/libadios2.so.2.2.0: undefined reference to `vtable for std::__future_base::_State_base@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__future_base::_State_base::~_State_base()@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__detail::_Prime_rehash_policy::_M_next_bkt(unsigned long) const@GLIBCXX_3.4.18'
../../../lib/libadios2.so.2.2.0: undefined reference to `typeinfo for std::nested_exception@CXXABI_1.3.5'
../../../lib/libadios2.so.2.2.0: undefined reference to `typeinfo for std::__future_base::_Result_base@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__future_base::_Result_base::~_Result_base()@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::invalid_argument::~invalid_argument()@GLIBCXX_3.4.15'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::chrono::_V2::system_clock::now()@GLIBCXX_3.4.19'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__throw_future_error(int)@GLIBCXX_3.4.14'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::nested_exception::~nested_exception()@CXXABI_1.3.5'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::_Hash_bytes(void const*, unsigned long, unsigned long)@CXXABI_1.3.5'
../../../lib/libadios2.so.2.2.0: undefined reference to `std::__throw_bad_function_call()@GLIBCXX_3.4.14'
collect2: error: ld returned 1 exit status

CMake command:

CC=`which gcc` CXX=`which g++` cmake -DADIOS2_USE_Fortran=OFF -DCMAKE_INSTALL_PREFIX=/lustre/atlas/proj-shared/csc143/keichi/rhea ..

(CC and CXX are set because module load PE-gnu does not update these variables on Rhea)

CMake output:

ADIOS2 build configuration:
  ADIOS Version: 2.2.0
  C++ Compiler : GNU 4.8.2
    /ccs/compilers/gcc/rhel6-x86_64/4.8.2/bin/g++

  Installation prefix: /lustre/atlas/proj-shared/csc143/keichi/rhea
        bin: bin
        lib: lib
    include: include
      cmake: lib/cmake/adios2

  Features:
    Library Type: shared
    Build Type:   Release
    Testing: ON
    Build Options:
      BZip2    : ON
      ZFP      : OFF
      SZ       : OFF
      MPI      : ON
      DataMan  : ON
      SST      : ON
      ZeroMQ   : OFF
      HDF5     : OFF
      ADIOS1   : OFF
      Python   : OFF
      Fortran  : OFF
      SysVShMem: ON

Loaded modules:

  1) lustredu/1.4         4) bbcp/15.02.03.00.1   7) openmpi/1.8.4
  2) xalt/0.5.3           5) DefApps              8) PE-gnu/4.8.2-1.8.4
  3) hsi/5.0.2.p1         6) gcc/4.8.2            9) cmake/3.6.1

[williamfgc]

@keichi Looks like is linking against the wrong libstdc++ (or stdc++) for the adios2 dependency. Try using -DBUILD_SHARED_LIBS=OFF for static linking, which is the preferred method anyways.

[keichi]

@williamfgc Problem solved once I have added -DBUILD_SHARED_LIBS=OFF. Thanks!