An example to add an option to autoconf in EMAN

Purpose

    Add openMP support for EMAN autoconf system, so that
    a user can compile openMP program optionally.

Requirements:

    1. default setup is no openMP. use option '--enable-openmp'
       to enable it.
       
    2. openMP library and include directories can be specified with
       '--with-openmp-lib=DIR', and '--with-openmp-inc=DIR'.

    3. 'omp.h' will be searched to determine whether openMP
       is installed on your computer.

    4. '-lmp' is added to linker flags; '-mp' is added to compiler
       flags for SGI machines. 

    5. add openMP support to 'eman/src' binaries only
    

Implementation

    Two files need to be edited.
        1) EMAN/src/eman/configure.in;
	2) EMAN/src/eman/src/Makefile.am

    
    1. add the following to configure.in:
    
       AC_ARG_ENABLE(openmp,	     [  --enable-openmp		enable OpenMP support [default=no]])
       AC_ARG_WITH(openmp-includes, [  --with-openmp-inc=DIR   OpenMP include files are in DIR])
       AC_ARG_WITH(openmp-libraries,[  --with-openmp-lib=DIR   OpenMP library files are in DIR])
		 	
       if test "$enable_openmp" = "yes"; then
	   search_headerdir "OpenMP" "omp.h" 0 $with_openmp_inc
	   
	   if test ! "X$found_incdir" = "X"; then
	       OPENMP_CXXFLAGS="-DOPENMP -I${found_incdir}"
	       if test ! $with_openmp_lib = "X"; then
	 	   openmp_libdir="-L$with_openmp_lib"
	       fi
	       OPENMP_LIB="$openmp_libdir -lmp"
	   else
	       AC_MSG_RESULT([WARNING: OpenMP support disabled])
	   fi        
       fi   

       # for SGI machine only
       if test ! "$OPENMP_CXXFLAGS" = "X"; then
	    OPENMP_CXXFLAGS="-mp ${OPENMP_CXXFLAGS}"
       fi
	 	

       AC_SUBST(OPENMP_CXXFLAGS)
       AC_SUBST(OPENMP_LIB)

	
    2. add the following to src/Makefile.am

       1) add '$(OPENMP_LIB)' to 'LDADD' macro
       2) add '$(OPENMP_CXXFLAGS)' to 'AM_CXXFLAGS' macro