Known Errors

Some known compilation errors

  1. NetCDF error example:

    /usr/bin/ld: /project_shared/Libraries/netcdf-3.6.3_pgi_fortran_17.4-0//lib/libnetcdf.a(attr.o): relocation R_X86_64_32S against '.data' can not be used when making a shared object; recompile with -fPIC
/project_shared/Libraries/netcdf-3.6.3_pgi_fortran_17.4-0//lib/libnetcdf.a: error adding symbols: Bad value

The NetCDF library is not compiled using shared library. You need to re-install NetCDF, compile it with -fPIC, and check if libnetcdf.so file is generated.

  1. Link library issue example:

    /usr/bin/ld: cannot find -lmpi_cxx

The mpi_cxx library is not available now in the current OpenMPI version. Use -lmpi instead in the build_rule.mk file. Also, the following command can be used to check which library mlicxx depends on:

mpicxx -showme:libs

  1. C++ library issue example:

    /usr/bin/ld: ESMCI_StringSubr.o: undefined reference to symbol '_ZNKSt5ctypeIcE13_M_widen_initEv@@GLIBCXX_3.4.11'

It seems that the location of library that ESMC_StringSubr.o depend on is not known to the system. Check the library by using:

strings /usr/lib64/libstdc++.so.6 | grep _ZNKSt5ctypeIcE13_M_widen_initEv_ZNKSt5ctypeIcE13_M_widen_initEv

And, add /usr/lib64/ to LD_LIBRARY_PATH variable in ~/.bashrc

To see what a Library is linked to:

[cpapadop@ring lib64]$ ldd libstdc++.so.6
linux-vdso.so.1 =>  (0x00007ffd7bdf8000)
libm.so.6 => /lib64/libm.so.6 (0x00007f569cdd9000)
libc.so.6 => /lib64/libc.so.6 (0x00007f569ca17000)
/lib64/ld-linux-x86-64.so.2 (0x00007f569d3f9000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f569c801000)

  1. NetCDF issue:

    ./esmf/lib/libO/Linux.pgi.64.openmpi.default/libesmf.so: undefined reference to 'netcdf_nf90_put_var_4d_eightbytereal\_'

The undefined reference issue is because the the library is not added when compiling the unit test programs. The solution is to add “-netcdff” to the end of the compling command.

  1. error: namespace “std” has no member “addressof”

This is a problem due to c++11 library.