Many codes need headers (C/C++) or modules (Fortran) for procedure prototypes, etc. This is especially common if it is using an external library. As was true for libraries, there is a system default search path for these “include files.”

The compiler flag is -I/path/to/includes

The path to Fortran module files is also specified by the -I flag.

The lmod modules system we use is hierarchical. You must first load your choice of compiler. From there you can type

module avail

The modules at the top will be for libraries built with that compiler. You will generally need to provide paths for these libraries by -L and -I flags. You can find the paths with

printenv | grep ROOT 

Most recent modules have an environment variable NAME_ROOT, e.g.

HDF5_ROOT

Example

A number of scientific and engineering codes need the input/output libraries HDF5 or NetCDF. We will use NetCDF for this example.

module load gcc
module load netcdf

printenv | grep ROOT 

The following should be typed on a single line:

gfortran -o myexec -L${NETCDF_ROOT}/lib -I${NETCDF_ROOT}/include mycode.f90 -lnetcdff -lnetcdf 

Exercises

Exercise 1. Multiple files (no C example here)

Copy from /share/resources/tutorials/compilers your choice of files

• Copy main.cxx or main.f90
• Copy sub1.cxx or sub1.f90
• Copy sub2.cxx or sub2.f90
• C++ copy sub1.h and sub2.h as well

Use these three files to create an executable.

Exercise 2. External Libraries

• Load the netcdf module for your choice of compiler suite as indicated above.

• Copy simple_xy_wr.c or simple_xy_wr.cpp or simple_xy_wr.f90 (note the C++ suffix is cpp here).

• Compile and link the examples. You will need to add -I${NETCDF_ROOT}/include and -L${NETCDF_ROOT}/lib to your link command. For C use -lnetcdf for the library. For Fortran use -lnetcdff -lnetcdf in that order. For C++ use -lnetcdf_c++ -lnetcdf in that order.