This can be done in combination with conditional compilation and using the "D" option on the command line. Here is some example code:
program test_Dopt
character (len=1) :: pathsep
pathsep = "?"
#ifdef WOS
pathsep = ""
#endif
#ifdef UOS
pathsep = "/"
#endif
write (*, '( "pathsep is >", A1, "<")' ) pathsep
end program test_Dopt
Name the program with filetype F90 to cause gfortran to run the preprocessor or use -cpp on the compile line. Then pass options to the prepreprocessor by including them after D on the compile line, e.g., gfortran -DWOS. (This is more general then gfortran -- most Fortran compilers will process C-style pre-processor directives.) Then you can identify the OS outside of Fortran and pass the information to the Fortran program.
You can compile your code via using the filetype F90 or -cpp.
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