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Tips in case of errors during compilation

23.1. Tips in case of errors during compilation#

  1. In case of strange errors during compilation (*e.g. “catastrophic error: could not find …”), try one of these solutions*

    • check your home space is not full ;-)

    • check your paths to compilers and libraries (especially Netcdf library)

    • check that you have the good permissions, and check that your executable files (configure, make…) do are executable

    • check that your shell scripts headers are correct or add them if necessary (e.g. for bash: #!/bin/bash)

    • try to exit/log out the machine, log in back, clean and restart compilation

  2. Errors and tips related to netcdf library

    • with netcdf 4.3.3.1: need to add the following compilation flag for all models: -mt_mpi

      The error associated to a missing -mt_mpi flag is of this type: “ /opt/intel//impi/4.1.1.036/intel64/lib/libmpi_mt.so.4: could not read symbols: Bad value “

    • with netcdf 4.1.3: do NOT add -mt_mpi flag

    • with netcdf4, need to place hdf5 library path in your environment:

    export LD_LIBRARY_PATH=YOUR_HDF5_DIR/lib:$LD_LIBRARY_PATH

    • with netcdf 4, if you use the library splitted in 2: C part and Fortran part, you need to place links to C library before links to Fortran library and need to put both path in this same order in your LD_LIBRARY_PATH

  3. In case of ‘segmentation fault’ error

    • try to allocate more memory with “unlimited -s unlimited”

    • try to launch the compilation as a job (batch) with more allocated memory

  4. relocation truncated to fit: R_X86_64_32S against symbol at compilation in sequential mode

    • add option mcmodel=large in compile options (FLAGS) in jobcomp

  5. m2c error at the beginning of the compilation

    • the path to OCEAN directory in the jobcomp file may be wrong