A sample SConstruct script for compiling your code(s) with NetCDF4 library.

SConstruct

# -*- coding: utf-8 -*-
#
# SConstruct for compiling Fortran90 code(s)
#
# coded by Takashi Unuma, Kyoto Univ.
# last modified: 2014/08/17
#

# load python modules
import os
import os.path
import sys

# check environmental value
FORTRAN  = os.environ.get('FC')

# check compiler
if FORTRAN == "":
    print u"Please set FORTRAN value as an environmental value"
    print u" ex 1) $ export FC=gfortran"
    print u" ex 2) $ export FC=ifort"
    print u" ex 3) $ export FC=pgfortran"
    print u" ex 4) $ export FC=f95"
    print u" ex 5) $ export FC=g95"
    sys.exit()

# define fortran flags
if FORTRAN == "gfortran":
    FFLAG   = ['-frecord-marker=4','-ffree-form','-fno-range-check','-O3','-ftree-vectorize','-funroll-loops','-fopenmp']
    DFLAG   = ['-frecord-marker=4','-ffree-form','-fno-range-check','-O','-fopenmp','-fbounds-check','-Wall','-Wuninitialized','-ffpe-trap=invalid,zero,overflow']

elif FORTRAN == "ifort":
    FFLAG   = ['-FR','-i-dynamic','-O3','-xHost','-fno-alias','-unroll0','-ipo','-openmp']
    DFLAG   = ['-FR','-i-dynamic','-O0','-openmp','-warn all','-check all','-gen_interfaces','-fpe0','-ftrapuv']

elif FORTRAN == "pgfortran":
    FFLAG   = ['-m64','-Mfree','-Kieee','-O3','-fast','-Ktrap=none','-mp','-Minfo']
    DFLAG   = ['-m64','-Mfree','-Kieee','-O0','-mp','-Minfo','-Ktrap=fp','-Minform=inform','-Mbounds','-Mlre=noassoc']

elif FORTRAN == "f95":
    FFLAG   = ['-ffree-form','-fno-range-check','-O3','-ftree-vectorize','-funroll-loops','-fopenmp']
    DFLAG   = ['-ffree-form','-fno-range-check','-O0','-fopenmp','-Wall','-Wuninitialized','-ffpe-trap=invalid,zero,overflow']

elif FORTRAN == "g95":
    FFLAG   = ['-ffree-form','-O3'] # not supported OpenMP directive
    DFLAG   = ['-ffree-form','-O0','-fbounds-check','-Wall','-Wuninitialized','-ftrace=full','-pedantic','-std=f95']

else:
    print FORTRAN + u"is not supported on this SConstruct (for now)"
    sys.exit()

# debug
#  This debug section will be enabled with the scons option of "debug=0". 
if ARGUMENTS.get('debug', 0):
    FFLAGS  = DFLAG
else:
    FFLAGS  = FFLAG

# define library path
#  These variables will use the system environmental setting. 
NETCDF = os.environ.get('NETCDF')
HDF = os.environ.get('HDF')
ZLIB = os.environ.get('ZLIB')

# check library path
if NETCDF == "":
    print u"Please set NETCDF value as an environmental value"
    sys.exit()
if HDF == "":
    print u"Please set HDF value as an environmental value"
    sys.exit()
if ZLIB == "":
    print u"Please set ZLIB value as an environmental value"
    sys.exit()

# define path to includes and libs
INCFLAG = [NETCDF + '/include', HDF5 + '/include', ZLIB + '/include']
LIBFLAG = [NETCDF + '/lib', HDF5 + '/lib', ZLIB + '/lib']

# define the required library
REQLIB = ['netcdf', 'netcdff', 'hdf5_hl', 'hdf5', 'z', 'm']

# set common env.
env = Environment(ENV=os.environ,F90=FORTRAN,LINK=FORTRAN,LINKFLAGS=FFLAGS,F90FLAGS=FFLAGS,F90PATH=INCFLAG)

# build your code(s)
env.Program('hoge.f90', LIBS=REQLIB, LIBPATH=LIBFLAG)