new package: wrf (#18398)

* wrf: new package

* wrf: fix install dir

* wrf: ndown location

* Add more compiler and nesting options to wrf package

* Fix configure that didn't find pgf90, use tempfile and compile in parallel

* WRF v4.2 with parallel I/O support through pnetcdf

Signed-off-by: michael laufer <michael.laufer@toganetworks.com>

* extend Package, compiler wrapper now used, small fixes

Signed-off-by: michael laufer <michael.laufer@toganetworks.com>

* Update var/spack/repos/builtin/packages/wrf/package.py

fixed typo

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Levi Baber <baberlevi@gmail.com>
Co-authored-by: eXact lab <info@exact-lab.it>
Co-authored-by: michael laufer <michael.laufer@toganetworks.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

16 files changed, 677 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/wrf/package.py b/var/spack/repos/builtin/packages/wrf/package.py
new file mode 100644
index 0000000000..c9d11a8ee0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/package.py
@@ -0,0 +1,150 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import glob
+import tempfile
+
+
+class Wrf(Package):
+    """The Weather Research and Forecasting (WRF) Model
+    is a next-generation mesoscale numerical weather prediction system designed
+    for both atmospheric research and operational forecasting applications.
+    """
+
+    homepage = "https://www.mmm.ucar.edu/weather-research-and-forecasting-model"
+    url      = "https://github.com/wrf-model/WRF/archive/v4.2.tar.gz"
+
+    version('4.2', sha256='c39a1464fd5c439134bbd39be632f7ce1afd9a82ad726737e37228c6a3d74706')
+    version('4.0', sha256='a5b072492746f96a926badda7e6b44cb0af26695afdd6c029a94de5e1e5eec73')
+
+    variant('build_type', default='dmpar',
+            values=('serial', 'smpar', 'dmpar', 'dmsm'))
+
+    variant('nesting', default='basic',
+            values=('basic', 'preset', 'vortex'))
+
+    variant('compile_type', default='em_real',
+            values=('em_real', 'em_quarter_ss', 'em_b_wave', 'em_les',
+                    'em_heldsuarez', 'em_tropical_cyclone', 'em_hill2d_x',
+                    'em_squall2d_x', 'em_squall2d_y', 'em_grav2d_x',
+                    'em_seabreeze2d_x', 'em_scm_xy'))
+
+    variant('pnetcdf', default=True,
+            description='Parallel IO support through Pnetcdf libray')
+
+    # These patches deal with netcdf & netcdf-fortran being two diff things
+    # Patches are based on:
+    # https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/w/WRF/WRF-3.5_netCDF-Fortran_separate_path.patch
+    patch('patches/4.0/arch.Config.pl.patch', when='@4.0')
+    patch('patches/4.0/arch.configure.defaults.patch', when='@4.0')
+    patch('patches/4.0/arch.conf_tokens.patch', when='@4.0')
+    patch('patches/4.0/arch.postamble.patch', when='@4.0')
+    patch('patches/4.0/configure.patch', when='@4.0')
+    patch('patches/4.0/external.io_netcdf.makefile.patch', when='@4.0')
+    patch('patches/4.0/Makefile.patch', when='@4.0')
+
+    patch('patches/4.2/arch.Config.pl.patch', when='@4.2')
+    patch('patches/4.2/arch.configure.defaults.patch', when='@4.2')
+    patch('patches/4.2/arch.conf_tokens.patch', when='@4.2')
+    patch('patches/4.2/arch.postamble.patch', when='@4.2')
+    patch('patches/4.2/configure.patch', when='@4.2')
+    patch('patches/4.2/external.io_netcdf.makefile.patch', when='@4.2')
+    patch('patches/4.2/var.gen_be.Makefile.patch', when='@4.2')
+    patch('patches/4.2/Makefile.patch', when='@4.2')
+
+    depends_on('mpi')
+    # According to:
+    # http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_v4/v4.0/users_guide_chap2.html#_Required_Compilers_and_1
+    # Section: "Required/Optional Libraries to Download"
+    depends_on('parallel-netcdf', when='+pnetcdf')
+    depends_on('netcdf-c+parallel-netcdf')
+    depends_on('netcdf-fortran')
+    depends_on('jasper')
+    depends_on('libpng')
+    depends_on('zlib')
+    depends_on('perl')
+    # not sure if +fortran is required, but seems like a good idea
+    depends_on('hdf5+fortran+hl+mpi')
+    # build script use csh
+    depends_on('tcsh', type=('build'))
+    # time is not installed on all systems b/c bash provides it
+    # this fixes that for csh install scripts
+    depends_on('time', type=('build'))
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('m4', type='build')
+    depends_on('libtool', type='build')
+    phases = ['configure', 'build', 'install']
+
+    def setup_build_environment(self, spack_env):
+        spack_env.set('NETCDF', self.spec['netcdf-c'].prefix)
+        if '+pnetcdf' in self.spec:
+            spack_env.set('PNETCDF', self.spec['parallel-netcdf'].prefix)
+        # This gets used via the applied patch files
+        spack_env.set('NETCDFF', self.spec['netcdf-fortran'].prefix)
+        spack_env.set('PHDF5', self.spec['hdf5'].prefix)
+        spack_env.set('JASPERINC', self.spec['jasper'].prefix.include)
+        spack_env.set('JASPERLIB', self.spec['jasper'].prefix.lib)
+
+        if self.spec.satisfies('%gcc@10:'):
+            args = '-w -O2 -fallow-argument-mismatch -fallow-invalid-boz'
+            spack_env.set('FCFLAGS', args)
+            spack_env.set('FFLAGS', args)
+
+    def patch(self):
+        # Let's not assume csh is intalled in bin
+        files = glob.glob('*.csh')
+
+        filter_file('^#!/bin/csh -f', '#!/usr/bin/env csh', *files)
+        filter_file('^#!/bin/csh', '#!/usr/bin/env csh', *files)
+
+    def configure(self, spec, prefix):
+        build_opts = {"gcc":   {"serial": '32',
+                                "smpar":  '33',
+                                "dmpar":  '34',
+                                "dmsm":   '35'},
+                      "intel": {"serial": '13',
+                                "smpar":  '14',
+                                "dmpar":  '15',
+                                "dmsm":   '16'},
+                      "pgi":   {"serial": '52',
+                                "smpar":  '53',
+                                "dmpar":  '54',
+                                "dmsm":   '55'},
+                      }
+
+        nesting_opts = {"basic":  "1",
+                        "preset": "2",
+                        "vortex": "3"}
+
+        try:
+            compiler_opts = build_opts[self.spec.compiler.name]
+        except KeyError:
+            raise InstallError("Compiler not recognized nor supported.")
+
+        # Spack already makes sure that the variant value is part of the set.
+        build_type = compiler_opts[spec.variants['build_type'].value]
+
+        nesting_value = nesting_opts[spec.variants['nesting'].value]
+
+        with tempfile.TemporaryFile(mode='w') as fp:
+            fp.write(build_type + '\n' + nesting_value + '\n')
+            fp.seek(0)
+            Executable('./configure')(input=fp)
+
+    def build(self, spec, prefix):
+        csh = which('csh')
+        # num of compile jobs capped at 20 in wrf
+        csh('./compile', '-j', str(min(int(make_jobs), 20)),
+            spec.variants['compile_type'].value)
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('./main/wrf.exe', prefix.bin)
+        install('./main/ndown.exe', prefix.bin)
+        install('./main/real.exe', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/Makefile.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/Makefile.patch
new file mode 100644
index 0000000000..5fb99e78ae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/Makefile.patch
@@ -0,0 +1,21 @@
+--- a/Makefile	2018-06-08 19:39:31.000000000 -0500
++++ b/Makefile	2018-11-02 13:33:12.273662388 -0500
+@@ -906,14 +906,14 @@
+ 	@ echo '--------------------------------------'
+ 	( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \
+           cd ../external/io_netcdf ; \
+-          $(MAKE) NETCDFPATH="$(NETCDFPATH)" \
+-               FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
++          $(MAKE) NETCDFPATH="$(NETCDFPATH)" FNETCDFFPATH="$(NETCDFFPATH)" \
++               C="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
+                CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \
+                LIB_LOCAL="$(LIB_LOCAL)" \
+                ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR" diffwrf; \
+           cd ../io_netcdf ; \
+-          $(MAKE) NETCDFPATH="$(NETCDFPATH)" \
+-               FC="$(SFC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
++          $(MAKE) NETCDFPATH="$(NETCDFPATH)" FNETCDFFPATH="$(NETCDFFPATH)" \
++               C="$(SFC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
+                CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \
+ 	       LIB_LOCAL="$(LIB_LOCAL)" \
+                ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR"; \
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.Config.pl.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.Config.pl.patch
new file mode 100644
index 0000000000..b9269ab5e2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.Config.pl.patch
@@ -0,0 +1,37 @@
+--- a/arch/Config.pl	2018-06-08 19:39:31.000000000 -0500
++++ b/arch/Config.pl	2018-11-02 13:33:12.165660199 -0500
+@@ -8,6 +8,7 @@
+ select((select(STDOUT), $|=1)[0]);
+ $sw_perl_path = perl ;
+ $sw_netcdf_path = "" ;
++$sw_netcdff_path = "" ;
+ $sw_pnetcdf_path = "" ;
+ $sw_hdf5_path=""; 
+ $sw_phdf5_path=""; 
+@@ -63,6 +64,10 @@
+   {
+     $sw_netcdf_path = substr( $ARGV[0], 8 ) ;
+   }
++  if (substr( $ARGV[0], 1, 8) eq "netcdff=" )
++  {
++    $sw_netcdff_path = substr( $ARGV[0], 9) ;
++  }
+   if ( substr( $ARGV[0], 1, 13 ) eq "dep_lib_path=" )
+   {
+     $sw_dep_lib_path = substr( $ARGV[0], 14 ) ;
+@@ -117,6 +122,7 @@
+   if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" )
+   {
+     $sw_usenetcdff = substr( $ARGV[0], 12 ) ;
++    $sw_usenetcdff =~ s/!/ /g ;
+   }
+   if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" )
+   {
+@@ -439,6 +445,7 @@
+   {
+     $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ;
+     $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ;
++    $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ;
+     $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ;
+     $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ;
+     $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ;
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.conf_tokens.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.conf_tokens.patch
new file mode 100644
index 0000000000..1be2361c53
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.conf_tokens.patch
@@ -0,0 +1,16 @@
+--- a/arch/conf_tokens	2018-06-08 19:39:31.000000000 -0500
++++ b/arch/conf_tokens	2018-11-02 13:33:12.347663887 -0500
+@@ -5,6 +5,7 @@
+        CONFIGURE_DMPARALLEL
+ CONFIGURE_RWORDSIZE
+ CONFIGURE_NETCDF_FLAG
++CONFIGURE_NETCDFF_FLAG
+ CONFIGURE_GRIB2_FLAG
+ CONFIGURE_NETCDF_LIB_PATH
+ CONFIGURE_GRIB2_LIB
+@@ -13,4 +14,5 @@
+ CONFIGURE_WRFIO_NF 
+ CONFIGURE_WRFIO_GRIB2 
+ CONFIGURE_NETCDF_PATH
++CONFIGURE_NETCDFF_PATH
+ CONFIGURE_GRIB2_INC
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.configure.defaults.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.configure.defaults.patch
new file mode 100644
index 0000000000..7de1273d18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.configure.defaults.patch
@@ -0,0 +1,10 @@
+--- a/arch/configure.defaults	2018-11-11 10:02:30.575095478 -0600
++++ b/arch/configure.defaults	2018-11-02 13:33:12.352663988 -0500
+@@ -1598,6 +1598,7 @@
+ 
+ LIB_EXTERNAL    = \
+                      ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \
++                     CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib
+                      ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a
+ ESMF_IO_LIB     =    ../external/esmf_time_f90/libesmf_time.a
+ LIB_BUNDLED     = \
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.postamble.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.postamble.patch
new file mode 100644
index 0000000000..59677edd9b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/arch.postamble.patch
@@ -0,0 +1,27 @@
+--- a/arch/postamble	2018-06-08 19:39:31.000000000 -0500
++++ b/arch/postamble	2018-11-02 13:33:12.162660138 -0500
+@@ -48,6 +48,7 @@
+                       -I$(WRF_SRC_ROOT_DIR)/wrftladj \
+                       -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \
+                       -I$(NETCDFPATH)/include \
++                      -I$(NETCDFFPATH)/include \
+                       CONFIGURE_RTTOV_INC
+ REGISTRY        =    Registry
+ CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE
+@@ -70,6 +71,7 @@
+ ENVCOMPDEFS     =    CONFIGURE_COMPILEFLAGS
+ CPPFLAGS        =    $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE
+ NETCDFPATH      =    CONFIGURE_NETCDF_PATH
++NETCDFFPATH     =    CONFIGURE_NETCDFF_PATH
+ HDF5PATH        =    CONFIGURE_HDF5_PATH
+ WRFPLUSPATH     =    CONFIGURE_WRFPLUS_PATH
+ RTTOVPATH       =    CONFIGURE_RTTOV_PATH
+@@ -101,7 +103,7 @@
+ 
+ wrfio_nf : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \
+-          make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
++          make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
+           CC="$(SCC)" CFLAGS="$(CFLAGS)" \
+           FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/configure.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/configure.patch
new file mode 100644
index 0000000000..4a56e867b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/configure.patch
@@ -0,0 +1,44 @@
+--- a/configure	2018-06-08 19:39:31.000000000 -0500
++++ b/configure	2018-11-02 13:33:12.344663826 -0500
+@@ -190,6 +190,13 @@
+   else
+     USENETCDF=" "
+   fi
++  # for netCDF 4.2 and greater, the Fortran library is a separate install
++  if [ -z "$NETCDFF" ]; then
++    NETCDFF="$NETCDF"
++  fi
++  if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then
++    USENETCDFF="-L$NETCDFF/lib!-lnetcdff" # ! will be replaced with space
++  fi
+   export USENETCDF=$USENETCDF
+   export USENETCDFF=$USENETCDFF
+ else
+@@ -549,7 +556,7 @@
+    srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"`
+    if [ -n "$srch" ] ; then
+      $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \
+-          -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
++          -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
+           -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \
+           -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \
+           -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH"
+@@ -629,14 +636,14 @@
+ echo "If you wish to change the default options, edit the file:"
+ echo "     arch/configure.defaults"
+ 
+-if test -n "$NETCDF" ; then
+-  if [ ! -f $NETCDF/include/netcdf.inc ] ; then
++if test -n "$NETCDFF" ; then
++  if [ ! -f $NETCDFF/include/netcdf.inc ] ; then
+     echo
+-    echo "Error : Not found $NETCDF/include/netcdf.inc"
++    echo "Error : Not found $NETCDFF/include/netcdf.inc"
+     echo "        Please check this installation of NetCDF and re-run this configure script"
+     exit -1
+   fi
+-  grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null
++  grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null
+   configure_aaaa=$? ; export configure_aaaa
+   if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then
+     echo "NetCDF users note:"
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.0/external.io_netcdf.makefile.patch b/var/spack/repos/builtin/packages/wrf/patches/4.0/external.io_netcdf.makefile.patch
new file mode 100644
index 0000000000..5572f63860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.0/external.io_netcdf.makefile.patch
@@ -0,0 +1,42 @@
+--- a/external/io_netcdf/makefile	2018-06-08 19:39:31.000000000 -0500
++++ b/external/io_netcdf/makefile	2018-11-02 13:33:12.280662529 -0500
+@@ -3,9 +3,9 @@
+ OBJSL   = wrf_io.o field_routines.o module_wrfsi_static.o
+ OBJS    = $(OBJSL)
+ CODE    = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code 
+-FFLAGS  =  $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share
+-LIBS    = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf
+-LIBFFS  = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
++FFLAGS  =  $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share
++LIBS    = $(LIB_LOCAL) -L$(NETCDFFPATH)/lib -lnetcdf
++LIBFFS  = $(LIB_LOCAL) -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
+ CPP1    = $(CPP) -P $(TRADFLAG)
+ M4      = m4 -Uinclude -Uindex -Ulen
+ AR      = ar
+@@ -24,7 +24,7 @@
+ 			$(RANLIB) $@
+ 
+ wrf_io.o:               wrf_io.F90 $(CODE)
+-			grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\
++			grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\
+                         a=$$? ; export a ; \
+ 			if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \
+                           $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \
+@@ -43,14 +43,14 @@
+ 	x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \
+ 	if [ $$x = "gfortran" ] ; then \
+            echo removing external declaration of iargc for gfortran ; \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
+         else \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
+         fi
+ 	$(FC) -c $(FFLAGS) diffwrf.f
+ 	@if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \
+ 	  echo "diffwrf io_netcdf is being built now. " ; \
+-          if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \
++          if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\
+           else \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/Makefile.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/Makefile.patch
new file mode 100644
index 0000000000..fe01efb756
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/Makefile.patch
@@ -0,0 +1,20 @@
+diff --git a/Makefile b/Makefile
+index 9b6600a..8805cd1 100644
+--- a/Makefile
++++ b/Makefile
+@@ -976,13 +976,13 @@ framework :
+ 	@ echo '--------------------------------------'
+ 	( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \
+           cd ../external/io_netcdf ; \
+-          $(MAKE) NETCDFPATH="$(NETCDFPATH)" \
++          $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \
+                FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
+                CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \
+                LIB_LOCAL="$(LIB_LOCAL)" \
+                ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR" diffwrf; \
+           cd ../io_netcdf ; \
+-          $(MAKE) NETCDFPATH="$(NETCDFPATH)" \
++          $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \
+                FC="$(SFC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
+                CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \
+ 	       LIB_LOCAL="$(LIB_LOCAL)" \
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.Config.pl.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.Config.pl.patch
new file mode 100644
index 0000000000..ca3840ac55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.Config.pl.patch
@@ -0,0 +1,62 @@
+diff --git a/arch/Config.pl b/arch/Config.pl
+index b6f45db..75fad32 100644
+--- a/arch/Config.pl
++++ b/arch/Config.pl
+@@ -8,6 +8,7 @@
+ select((select(STDOUT), $|=1)[0]);
+ $sw_perl_path = perl ;
+ $sw_netcdf_path = "" ;
++$sw_netcdff_path = "" ;
+ $sw_pnetcdf_path = "" ;
+ $sw_hdf5_path=""; 
+ $sw_phdf5_path=""; 
+@@ -63,6 +64,10 @@ while ( substr( $ARGV[0], 0, 1 ) eq "-" )
+   {
+     $sw_netcdf_path = substr( $ARGV[0], 8 ) ;
+   }
++  if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" )
++  {
++    $sw_netcdff_path = substr( $ARGV[0], 9 ) ;
++  }
+   if ( substr( $ARGV[0], 1, 13 ) eq "dep_lib_path=" )
+   {
+     $sw_dep_lib_path = substr( $ARGV[0], 14 ) ;
+@@ -117,6 +122,7 @@ while ( substr( $ARGV[0], 0, 1 ) eq "-" )
+   if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" )
+   {
+     $sw_usenetcdff = substr( $ARGV[0], 12 ) ;
++    $sw_usenetcdff =~ s/!/ /g ;
+   }
+   if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" )
+   {
+@@ -443,6 +449,7 @@ while ( <CONFIGURE_DEFAULTS> )
+   {
+     $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ;
+     $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ;
++    $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ;
+     $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ;
+     $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ;
+     $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ;
+@@ -484,17 +491,19 @@ while ( <CONFIGURE_DEFAULTS> )
+     if ( $sw_netcdf_path ) 
+       { $_ =~ s/CONFIGURE_WRFIO_NF/wrfio_nf/g ;
+ 	$_ =~ s:CONFIGURE_NETCDF_FLAG:-DNETCDF: ;
++	$_ =~ s:CONFIGURE_NETCDFF_FLAG:-DNETCDFF: ;
+         if ( $ENV{NETCDF_LDFLAGS} ) {
+-          $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a $ENV{NETCDF_LDFLAGS} : ;
++          $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a $ENV{NETCDF_LDFLAGS} $ENV{NETCDFF_LDFLAGS}: ;
+         } elsif ( $sw_os eq "Interix" ) {
+-	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
++	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         } else {
+-	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
++	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         }
+ 	 }
+     else                   
+       { $_ =~ s/CONFIGURE_WRFIO_NF//g ;
+ 	$_ =~ s:CONFIGURE_NETCDF_FLAG::g ;
++	$_ =~ s:CONFIGURE_NETCDFF_FLAG::g ;
+ 	$_ =~ s:CONFIGURE_NETCDF_LIB_PATH::g ;
+ 	 }
+ 
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.conf_tokens.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.conf_tokens.patch
new file mode 100644
index 0000000000..49de156934
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.conf_tokens.patch
@@ -0,0 +1,18 @@
+diff --git a/arch/conf_tokens b/arch/conf_tokens
+index 2695b30..7b1f7df 100644
+--- a/arch/conf_tokens
++++ b/arch/conf_tokens
+@@ -5,6 +5,7 @@
+        CONFIGURE_DMPARALLEL
+ CONFIGURE_RWORDSIZE
+ CONFIGURE_NETCDF_FLAG
++CONFIGURE_NETCDFF_FLAG
+ CONFIGURE_GRIB2_FLAG
+ CONFIGURE_NETCDF_LIB_PATH
+ CONFIGURE_GRIB2_LIB
+@@ -13,4 +14,5 @@ CONFIGURE_COMPILEFLAGS
+ CONFIGURE_WRFIO_NF 
+ CONFIGURE_WRFIO_GRIB2 
+ CONFIGURE_NETCDF_PATH
++CONFIGURE_NETCDFF_PATH
+ CONFIGURE_GRIB2_INC
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.configure.defaults.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.configure.defaults.patch
new file mode 100644
index 0000000000..58e6ffccf4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.configure.defaults.patch
@@ -0,0 +1,68 @@
+diff --git a/arch/configure.defaults b/arch/configure.defaults
+index 9098375..7767a81 100644
+--- a/arch/configure.defaults
++++ b/arch/configure.defaults
+@@ -74,7 +74,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =
+ TRADFLAG        =      CONFIGURE_TRADFLAG
+@@ -786,7 +786,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =     
+ TRADFLAG        =      CONFIGURE_TRADFLAG
+@@ -1007,7 +1007,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =
+ TRADFLAG        =      CONFIGURE_TRADFLAG
+@@ -1050,7 +1050,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =
+ TRADFLAG        =      CONFIGURE_TRADFLAG
+@@ -1598,7 +1598,8 @@ CC_TOOLS        =       $(SCC)
+ 
+ LIB_EXTERNAL    = \
+                      ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \
+-                     ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a
++                     ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a \
++                     CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib
+ ESMF_IO_LIB     =    ../external/esmf_time_f90/libesmf_time.a
+ LIB_BUNDLED     = \
+                      ../external/fftpack/fftpack5/libfftpack.a \
+@@ -1773,7 +1774,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =
+ TRADFLAG        =      CONFIGURE_TRADFLAG
+@@ -1947,7 +1948,7 @@ FORMAT_FIXED    =       -ffixed-form
+ FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+ FCSUFFIX        =       
+ BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+-FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO)
++FCBASEOPTS_NO_G =       -w $(FORMAT_FREE) $(BYTESWAPIO) $(FFLAGS)
+ FCBASEOPTS      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+ MODULE_SRCH_FLAG =     
+ TRADFLAG        =      -traditional
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.postamble.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.postamble.patch
new file mode 100644
index 0000000000..9d163c8785
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/arch.postamble.patch
@@ -0,0 +1,36 @@
+diff --git a/arch/postamble b/arch/postamble
+index c855259..93e4ae3 100644
+--- a/arch/postamble
++++ b/arch/postamble
+@@ -53,6 +53,7 @@ INCLUDE_MODULES =    $(MODULE_SRCH_FLAG) \
+                       -I$(WRF_SRC_ROOT_DIR)/wrftladj \
+                       -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \
+                       -I$(NETCDFPATH)/include \
++                      -I$(NETCDFFPATH)/include \
+                       CONFIGURE_RTTOV_INC
+ REGISTRY        =    Registry
+ CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE
+@@ -62,6 +63,7 @@ LDFLAGS         =    $(OMP) $(FCFLAGS) $(LDFLAGS_LOCAL) CONFIGURE_LDFLAGS
+ ENVCOMPDEFS     =    CONFIGURE_COMPILEFLAGS
+ CPPFLAGS        =    $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE
+ NETCDFPATH      =    CONFIGURE_NETCDF_PATH
++NETCDFFPATH     =    CONFIGURE_NETCDFF_PATH
+ HDF5PATH        =    CONFIGURE_HDF5_PATH
+ WRFPLUSPATH     =    CONFIGURE_WRFPLUS_PATH
+ RTTOVPATH       =    CONFIGURE_RTTOV_PATH
+@@ -93,13 +95,13 @@ module_dm_rsllite :
+ 
+ wrfio_nf : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \
+-          make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
++          make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
+           CC="$(SCC)" CFLAGS="$(CFLAGS)" \
+           FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
+ wrfio_pnf : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \
+-          make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
++          make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
+           FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
+ wrfio_grib_share :
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/configure.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/configure.patch
new file mode 100644
index 0000000000..26bdcd9714
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/configure.patch
@@ -0,0 +1,43 @@
+diff --git a/configure b/configure
+index c4fc28b..16a9ef5 100755
+--- a/configure
++++ b/configure
+@@ -179,8 +179,9 @@ USENETCDFF=""
+ USENETCDF=""
+ if [ -n "$NETCDF" ] ; then
+   echo "Will use NETCDF in dir: $NETCDF"
++  echo "Will use NETCDFF in dir: $NETCDFF"
+ # Oh UNIDATA, why make it so hard ...
+-  if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then
++  if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib/libnetcdff.dll.a" ] ; then
+     USENETCDFF="-lnetcdff"
+   else
+     USENETCDFF=" "
+@@ -552,7 +553,7 @@ if test -n "$PERL" ; then
+    srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"`
+    if [ -n "$srch" ] ; then
+      $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \
+-          -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
++          -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
+           -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \
+           -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \
+           -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH"
+@@ -634,14 +635,14 @@ echo "If you wish to change settings, please edit that file."
+ echo "If you wish to change the default options, edit the file:"
+ echo "     arch/configure.defaults"
+ 
+-if test -n "$NETCDF" ; then
+-  if [ ! -f $NETCDF/include/netcdf.inc ] ; then
++if test -n "$NETCDFF" ; then
++  if [ ! -f $NETCDFF/include/netcdf.inc ] ; then
+     echo
+-    echo "Error : Not found $NETCDF/include/netcdf.inc"
++    echo "Error : Not found $NETCDFF/include/netcdf.inc"
+     echo "        Please check this installation of NetCDF and re-run this configure script"
+     exit -1
+   fi
+-  grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null
++  grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null
+   configure_aaaa=$? ; export configure_aaaa
+   if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then
+     echo "NetCDF users note:"
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/external.io_netcdf.makefile.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/external.io_netcdf.makefile.patch
new file mode 100644
index 0000000000..00a6d3595c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/external.io_netcdf.makefile.patch
@@ -0,0 +1,43 @@
+diff --git a/external/io_netcdf/makefile b/external/io_netcdf/makefile
+index fa638d4..9778990 100644
+--- a/external/io_netcdf/makefile
++++ b/external/io_netcdf/makefile
+@@ -3,9 +3,9 @@
+ OBJSL   = wrf_io.o field_routines.o module_wrfsi_static.o
+ OBJS    = $(OBJSL)
+ CODE    = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code 
+-FFLAGS  =  $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share
++FFLAGS  =  $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share
+ LIBS    = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf
+-LIBFFS  = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
++LIBFFS  = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
+ CPP1    = $(CPP) -P $(TRADFLAG)
+ M4      = m4 -Uinclude -Uindex -Ulen
+ AR      = ar
+@@ -24,7 +24,7 @@ libwrfio_nf.a:         $(OBJS) $(CODE)
+ 			$(RANLIB) $@
+ 
+ wrf_io.o:               wrf_io.F90 $(CODE)
+-			grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\
++			grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\
+                         a=$$? ; export a ; \
+ 			if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \
+                           $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \
+@@ -43,14 +43,14 @@ diffwrf:                diffwrf.F90
+ 	x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \
+ 	if [ $$x = "gfortran" ] ; then \
+            echo removing external declaration of iargc for gfortran ; \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
+         else \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
+         fi
+ 	$(FC) -c $(FFLAGS) diffwrf.f
+ 	@if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \
+ 	  echo "diffwrf io_netcdf is being built now. " ; \
+-          if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \
++          if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib/libnetcdff.dll.a \) ] ; then \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\
+           else \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\
diff --git a/var/spack/repos/builtin/packages/wrf/patches/4.2/var.gen_be.Makefile.patch b/var/spack/repos/builtin/packages/wrf/patches/4.2/var.gen_be.Makefile.patch
new file mode 100644
index 0000000000..b9f65526f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wrf/patches/4.2/var.gen_be.Makefile.patch
@@ -0,0 +1,40 @@
+diff --git a/var/gen_be/Makefile b/var/gen_be/Makefile
+index 208c34d..20ae8d7 100644
+--- a/var/gen_be/Makefile
++++ b/var/gen_be/Makefile
+@@ -14,7 +14,7 @@ gen_be : 	gen_be_ensrf.exe	\
+ 		gen_be_ep1.exe	\
+ 		gen_be_ep2.exe	\
+ 		gen_be_vertloc.exe	\
+-		gen_be_addmean.exe	
++		gen_be_addmean.exe	\
+ 		gen_be_stage1.exe	\
+ 		gen_be_stage1_1dvar.exe	\
+ 		gen_be_stage2.exe	\
+@@ -70,7 +70,7 @@ gen_be_vertloc.exe     : gen_be_vertloc.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+         $(SFC) -o gen_be_vertloc.exe $(LDFLAGS) $(GEN_BE_OBJS)  gen_be_vertloc.o $(GEN_BE_LIB)
+ 
+ gen_be_addmean.exe : gen_be_addmean.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+-	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFPATH)/include gen_be_addmean.f90 > gen_be_addmean.f
++	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFFPATH)/include gen_be_addmean.f90 > gen_be_addmean.f
+ 	$(SFC) -c $(FCFLAGS) -I../da $(MODULE_DIRS) $(WRFVAR_INC) $(PROMOTION) gen_be_addmean.f
+ 	$(SFC) -o gen_be_addmean.exe $(LDFLAGS) $(GEN_BE_OBJS) gen_be_addmean.o $(GEN_BE_LIB)
+ 
+@@ -140,7 +140,7 @@ gen_be_diags_read.exe : gen_be_diags_read.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+ 	$(SFC) -o gen_be_diags_read.exe $(LDFLAGS) $(GEN_BE_OBJS) gen_be_diags_read.o $(GEN_BE_LIB)
+ 
+ gen_be_etkf.exe : gen_be_etkf.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+-	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFPATH)/include gen_be_etkf.f90 > gen_be_etkf.f
++	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFFPATH)/include gen_be_etkf.f90 > gen_be_etkf.f
+ 	$(SFC) -c $(FCFLAGS) -I../da $(MODULE_DIRS) $(WRFVAR_INC) $(PROMOTION) gen_be_etkf.f
+ 	$(SFC) -o gen_be_etkf.exe $(LDFLAGS) $(GEN_BE_OBJS) gen_be_etkf.o $(GEN_BE_LIB)
+ 
+@@ -150,7 +150,7 @@ gen_be_ensrf.exe : gen_be_ensrf.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+ 	$(SFC) -o gen_be_ensrf.exe $(LDFLAGS) $(GEN_BE_OBJS) gen_be_ensrf.o $(GEN_BE_LIB)
+ 
+ gen_be_ensmean.exe : gen_be_ensmean.f90 $(GEN_BE_OBJS) $(GEN_BE_LIBS)
+-	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFPATH)/include gen_be_ensmean.f90 > gen_be_ensmean.f
++	$(CPP) $(CPPFLAGS) -I$(WRF_SRC_ROOT_DIR)/inc -I$(NETCDFFPATH)/include gen_be_ensmean.f90 > gen_be_ensmean.f
+ 	$(SFC) -c $(FCFLAGS) -I../da $(MODULE_DIRS) $(WRFVAR_INC) $(PROMOTION) gen_be_ensmean.f
+ 	$(SFC) -o gen_be_ensmean.exe $(LDFLAGS) $(GEN_BE_OBJS) gen_be_ensmean.o $(GEN_BE_LIB)
+