Intel compiler + MPI support, cleaned makefiles, template bash environment setup...

[brodeau]

Modifications / new stuff for this pull request

All Makefiles have been modified so they take the following variables from the user environment, they are not defined anymore in a hard-coded way as before...

List of environment variables that must be set for Makefiles to do their job:

• NEXTSIMDIR
• CXX
• CC
• FC
• CFLAGS, minimal, ex: "-O3 -fPIC"; many other flags remain in the Makefiles, but not these!
• CXXFLAGS, minimal, ex: "-O3 -pthread -fPIC -fopenmp"; many other flags remain in the Makefiles, but not these!
• MPI_DIR, ex: "/usr" for OpenMPI on Linux
• MPI_LIB_DIR, normally: =${MPI_DIR}/lib
• MPI_INC_DIR, normally: =${MPI_DIR}/include
• NETCDF_DIR
• NETCDF_CXX_DIR, normally: =${NETCDF_DIR}
• GMSH_DIR
• BOOST_DIR
• BOOST_INCDIR, normally: =${BOOST_DIR}/include/boost
• BOOST_LIBDIR, normally: =${BOOST_DIR}/lib

To make it easy

Added two template bash scripts to be sourced to set these variables according to your machine/architecture:

• env_compile_gnu_linux.bash for Gnu/GCC/OpenMPI on Linux
• env_compile_intel_linux.bash for Intel compilers and Intel MPI on Linux

So that prior to using the make command, in the terminal:
. ./env_compile_gnu_linux.bash

/laurent

[einola]

Minor changes to get Dockerfile working. Tested in docker too (one-winter run).