Careful cygwin support

README

@@ -40,6 +40,7 @@ doc/README.irr_diag
 doc/README.rsl_output
 doc/README.windturbine
 doc/README_test_cases
+doc/README.cygwin.md
 
 - Beginning with version 4.0, for more information on the releases, visit 
   the WRF GitHub Release Page:

arch/Config.pl

@@ -42,7 +42,7 @@
 $sw_usenetcdf = "" ;    
 $sw_time = "" ;          # name of a timer to time fortran compiles, e.g. timex or time
 $sw_ifort_r8 = 0 ;
-$sw_hdf5 = "-lhdf5 -lhdf5_hl";
+$sw_hdf5 = "-lhdf5_hl -lhdf5";
 $sw_zlib = "-lz";
 $sw_dep_lib_path = "";
 $sw_gpfs_path = "";
@@ -604,8 +604,7 @@
                  $_ .= " \$\(NETCDF4_IO_OPTS\)\n" ; 
                }
              if (/^LIB.*=/) 
-               { $_  =~ s/\r|\n//g ;
-                 $_ .=" \$\(NETCDF4_DEP_LIB\)\n" ;
+               { $_  =~ s/(\\?)[\r\n]/ \$\(NETCDF4_DEP_LIB\)\1\n/g ;
                }
            }
        }
@@ -756,6 +755,9 @@
 # apply substitutions to the preamble...
 while ( <ARCH_PREAMBLE> )
   {
+    if ( $sw_os ne "CYGWIN_NT" ) {
+      $_ =~ s/#NOWIN// ;
+    }
   # ESMF substitutions in preamble
   if ( $sw_esmflib_path && $sw_esmfinc_path )
     {
@@ -797,6 +799,76 @@
 
   $_ =~ s/CONFIGURE_DEP_LIB_PATH/$sw_dep_lib_path/g ;
 
+    $_ =~ s/CONFIGURE_COMMS_LIB/$sw_comms_lib/g ;
+    if ( $sw_os ne "CYGWIN_NT" ) {
+      $_ =~ s/#NOWIN// ;
+    }
+    if ( $sw_netcdf_path )
+      { $_ =~ s/CONFIGURE_WRFIO_NF/wrfio_nf/g ;
+	$_ =~ s:CONFIGURE_NETCDF_FLAG:-DNETCDF: ;
+        if ( $ENV{NETCDF_LDFLAGS} ) {
+          $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a $ENV{NETCDF_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 : ;
+        } 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 : ;
+        }
+	 }
+    else
+      { $_ =~ s/CONFIGURE_WRFIO_NF//g ;
+	$_ =~ s:CONFIGURE_NETCDF_FLAG::g ;
+	$_ =~ s:CONFIGURE_NETCDF_LIB_PATH::g ;
+	 }
+
+    if ( $sw_pnetcdf_path )
+      { $_ =~ s/CONFIGURE_WRFIO_PNF/wrfio_pnf/g ;
+	$_ =~ s:CONFIGURE_PNETCDF_FLAG:-DPNETCDF: ;
+        if ( $sw_os eq "Interix" ) {
+	  $_ =~ s:CONFIGURE_PNETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_pnetcdf/libwrfio_pnf.a -L$sw_pnetcdf_path/lib -lpnetcdf: ;
+        } else {
+	  $_ =~ s:CONFIGURE_PNETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_pnetcdf -lwrfio_pnf -L$sw_pnetcdf_path/lib -lpnetcdf: ;
+        }
+	 }
+    else
+      { $_ =~ s/CONFIGURE_WRFIO_PNF//g ;
+	$_ =~ s:CONFIGURE_PNETCDF_FLAG::g ;
+	$_ =~ s:CONFIGURE_PNETCDF_LIB_PATH::g ;
+	 }
+
+    if ( $sw_hdf5_path )
+      { $_ =~ s:CONFIGURE_HDF5_LIB_PATH:-L$sw_hdf5_path/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lm -lz: ;
+        $_ =~ s:CONFIGURE_HDF5_FLAG:-DHDF5: ;
+         }
+    else
+      { $_ =~ s:CONFIGURE_HDF5_LIB_PATH::g ;
+        $_ =~ s:CONFIGURE_HDF5_FLAG::g ;
+         }
+
+    if ( $sw_phdf5_path )
+
+      { $_ =~ s/CONFIGURE_WRFIO_PHDF5/wrfio_phdf5/g ;
+	$_ =~ s:CONFIGURE_PHDF5_FLAG:-DPHDF5: ;
+	$_ =~ s:CONFIGURE_PHDF5_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_phdf5 -lwrfio_phdf5 -L$sw_phdf5_path/lib -lhdf5_fortran -lhdf5 -lm -lz -L$sw_phdf5_path/lib -lsz: ;
+	 }
+    else
+      { $_ =~ s/CONFIGURE_WRFIO_PHDF5//g ;
+	$_ =~ s:CONFIGURE_PHDF5_FLAG::g ;
+	$_ =~ s:CONFIGURE_PHDF5_LIB_PATH::g ;
+	 }
+
+    if ( $sw_jasperlib_path && $sw_jasperinc_path )
+      { $_ =~ s/CONFIGURE_WRFIO_GRIB2/wrfio_grib2/g ;
+        $_ =~ s:CONFIGURE_GRIB2_FLAG:-DGRIB2:g ;
+        $_ =~ s:CONFIGURE_GRIB2_INC:-I$sw_jasperinc_path:g ;
+        $_ =~ s:CONFIGURE_GRIB2_LIB:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_grib2 -lio_grib2 -L$sw_jasperlib_path -ljasper:g ;
+      }
+    else
+      { $_ =~ s/CONFIGURE_WRFIO_GRIB2//g ;
+        $_ =~ s:CONFIGURE_GRIB2_FLAG::g ;
+        $_ =~ s:CONFIGURE_GRIB2_INC::g ;
+        $_ =~ s:CONFIGURE_GRIB2_LIB::g ;
+      }
+
   if ( $sw_gpfs_path ne "" )
     { if (/^GPFS.*=/)
         { $_  =~ s/\r|\n//g;

arch/configure.defaults

@@ -1556,7 +1556,7 @@ CC_TOOLS        =      $(SCC)
 ###########################################################
 #ARCH    CYGWIN_NT i686, PGI compiler on Windows # serial smpar dmpar dm+sm
 #
-DESCRIPTION     =       PGI ($SFC/$SCC): Windows
+DESCRIPTION     =       PGI ($SFC/$SCC): Windows POSIX native
 DMPARALLEL      =       # 1
 OMPCPP          =       # -D_OPENMP
 OMP             =       # -mp -Minfo=mp
@@ -1916,6 +1916,64 @@ RANLIB          =      ranlib
 RLFLAGS		=	
 CC_TOOLS        =      $(SCC) 
 
+###########################################################
+#ARCH    CYGWIN_NT i686 x86_64 Cygwin, gfortran compiler with gcc  #serial smpar dmpar dm+sm
+#
+DESCRIPTION     =       GNU ($SFC/$SCC)
+DMPARALLEL      =       # 1
+OMPCPP          =       # -D_OPENMP
+OMP             =       # -fopenmp
+OMPCC           =       # -fopenmp
+SFC             =       gfortran
+SCC             =       gcc
+CCOMP           =       gcc
+DM_FC           =       mpif90
+DM_CC           =       mpicc
+FC              =       CONFIGURE_FC
+CC              =       CONFIGURE_CC
+LD              =       $(FC)
+RWORDSIZE       =       CONFIGURE_RWORDSIZE
+PROMOTION       =       #-fdefault-real-8
+ARCH_LOCAL      =       -DNONSTANDARD_SYSTEM_SUBR  -DWRF_USE_CLM
+CFLAGS_LOCAL    =       -w -O3 -c
+LDFLAGS_LOCAL   =       
+CPLUSPLUSLIB    =       
+ESMF_LDFLAG     =       $(CPLUSPLUSLIB)
+FCOPTIM         =       -O2 -ftree-vectorize -funroll-loops
+FCREDUCEDOPT	=       $(FCOPTIM)
+FCNOOPT		=       -O0
+FCDEBUG         =       # -g $(FCNOOPT) # -ggdb -fbacktrace
+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      =       $(FCBASEOPTS_NO_G) $(FCDEBUG)
+MODULE_SRCH_FLAG =     
+TRADFLAG        =      -traditional
+CPP             =      /lib/cpp -P
+AR              =      ar
+ARFLAGS         =      ru
+M4              =      m4 -G
+RANLIB          =      ranlib
+RLFLAGS		=	
+CC_TOOLS        =      $(SCC)
+
+LIB_EXTERNAL    = \
+                     $(WRF_SRC_ROOT_DIR)/external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.dll.a \
+		     -L CONFIGURE_NETCDF_PATH -lnetcdff -lnetcdf -lnetcdf -ltirpc -lhdf5_hl -lhdf5 -lm -lz \
+		     CONFIGURE_GRIB2_LIB
+ESMF_IO_LIB     =    $(WRF_SRC_ROOT_DIR)/external/esmf_time_f90/libesmf_time.a
+LIB_BUNDLED     = \
+                     $(WRF_SRC_ROOT_DIR)/external/fftpack/fftpack5/libfftpack.a \
+                     $(WRF_SRC_ROOT_DIR)/external/io_grib1/libio_grib1.a \
+                     $(WRF_SRC_ROOT_DIR)/external/io_grib_share/libio_grib_share.a \
+                     $(WRF_SRC_ROOT_DIR)/external/io_int/libwrfio_int.a \
+                     $(ESMF_IO_LIB) \
+                     CONFIGURE_COMMS_LIB \
+                     $(WRF_SRC_ROOT_DIR)/frame/module_internal_header_util.o \
+                     $(WRF_SRC_ROOT_DIR)/frame/pack_utils.o
+
 #insert new stanza here
 
 ###########################################################

arch/postamble

@@ -55,19 +55,6 @@ INCLUDE_MODULES =    $(MODULE_SRCH_FLAG) \
 REGISTRY        =    Registry
 CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE
 
-#NOWIN LIB_BUNDLED     = \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/fftpack/fftpack5/libfftpack.a \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_grib1/libio_grib1.a \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_grib_share/libio_grib_share.a \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_int/libwrfio_int.a \
-#NOWIN                      $(ESMF_IO_LIB) \
-#NOWIN                      CONFIGURE_COMMS_LIB \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/frame/module_internal_header_util.o \
-#NOWIN                      $(WRF_SRC_ROOT_DIR)/frame/pack_utils.o 
-
-#NOWIN LIB_EXTERNAL    = \
-#NOWIN                      CONFIGURE_NETCDF_LIB_PATH CONFIGURE_PNETCDF_LIB_PATH CONFIGURE_GRIB2_LIB CONFIGURE_ATMOCN_LIB CONFIGURE_HDF5_LIB_PATH
-
 LIB             =    $(LIB_BUNDLED) $(LIB_EXTERNAL) $(LIB_LOCAL) $(LIB_WRF_HYDRO)
 LDFLAGS         =    $(OMP) $(FCFLAGS) $(LDFLAGS_LOCAL) CONFIGURE_LDFLAGS
 ENVCOMPDEFS     =    CONFIGURE_COMPILEFLAGS

arch/preamble

@@ -105,6 +105,19 @@ NETCDF4_DEP_LIB = $(DEP_LIB_PATH) $(HDF5) $(ZLIB) $(GPFS) $(CURL)
 
 LIBWRFLIB = libwrflib.a
 
+#NOWIN LIB_BUNDLED     = \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/fftpack/fftpack5/libfftpack.a \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_grib1/libio_grib1.a \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_grib_share/libio_grib_share.a \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/external/io_int/libwrfio_int.a \
+#NOWIN                      $(ESMF_IO_LIB) \
+#NOWIN                      CONFIGURE_COMMS_LIB \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/frame/module_internal_header_util.o \
+#NOWIN                      $(WRF_SRC_ROOT_DIR)/frame/pack_utils.o
+
+#NOWIN LIB_EXTERNAL    = \
+#NOWIN                      CONFIGURE_NETCDF_LIB_PATH CONFIGURE_PNETCDF_LIB_PATH CONFIGURE_GRIB2_LIB CONFIGURE_ATMOCN_LIB CONFIGURE_HDF5_LIB_PATH
+
 
 #### Architecture specific settings ####
 

configure

@@ -180,12 +180,12 @@ USENETCDF=""
 if [ -n "$NETCDF" ] ; then
   echo "Will use NETCDF in dir: $NETCDF"
 # Oh UNIDATA, why make it so hard ...
-  if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then
+  if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then
     USENETCDFF="-lnetcdff"
   else
     USENETCDFF=" "
   fi
-  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then
+  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then
     USENETCDF="-lnetcdf"
   else
     USENETCDF=" "
@@ -204,7 +204,7 @@ fi
 
 # If the user asked for classic netcdf, acquiesce to the request.
 
-if [ "`uname`" = "Linux" ] ; then
+if [ "`uname`" = "Linux" -o "`uname -o`" = "Cygwin" ] ; then
   ans="`whereis nf-config`"
 elif [ "`uname`" = "Darwin" ] ; then
   ans="`which nf-config`"

doc/README.cygwin.md

@@ -0,0 +1,79 @@
+# Installing WRF on Cygwin
+
+1. Download https://cygwin.com/setup-x86_64.exe
+2. (Optional) Download https://cygwin.com/setup-x86_64.exe.sig and verify the signature
+3. Run `setup-x86_64.exe`
+	- Select `Install from Internet`
+	- Pick an installation root (installing directly into `C:\` is not
+	  recommended)
+	- Pick a directory for a download cache
+		- If installing Cygwin on multiple computers, these files can
+          be re-used, skipping the download step on those computers
+	- `Direct Connection` is nice if it works, but `System Proxy Settings`
+	  may fill in useful data from your OS.
+	- Select a mirror near you
+    - Change package view to `Full`
+    - Select for install at least:
+		- gcc-core (OpenMP for smpar)
+		- gcc-fortran
+		- libnetcdf-fortran-devel
+		- openmpi (MPI for dmpar)
+		- libopenmpi-devel (MPI for dmpar)
+		- libjasper-devel (GRIB)
+		- perl
+		- tcsh
+	- Select install
+	- Accept the packages pulled in as dependencies
+	- Wait for download, install, and postinstall steps.  This will
+      take about an hour the first time through
+	- Decide whether you want shortcuts from the Desktop or Start Menu
+4. Open mintty
+   - If you didn't install shortcuts, you can run the `Cygwin.bat`
+     file in the root of the Cygwin install tree
+5. Follow usual instructions for installing WRF
+   - Download and unpack source
+   - `./clean -a`
+   - Export variables so WRF can find everything:
+	 - `export NETCDF=/usr/ NETCDF4=1 HDF5=/usr`
+	 - (Optional) `export JASPER=/usr JASPERLIB=/usr/lib JASPERINC=/usr/include`
+	 - (Optional) `export WRFIO_NCD_NO_LARGE_FILE_SUPPORT=0 NETCDF_classic=0`
+   - `./configure`, follow directions
+   - `./compile`, follow directions
+   - ...
+
+
+If the compiler reports problems due to `mpi.mod` or `netcdf.mod`
+being compiled with a different version of gfortran, subscribe to the
+[cygwin mailing list](https://cygwin.com/lists.html) and send a
+message there to remind the maintainer that `openmpi` or
+`netcdf-fortran` was built with an old version of `gfortran` and to
+ask them nicely to update it.
+
+If the (volunteer) maintainer does not have time, or you want to build
+this yourself, re-run `setup-x86_64.exe` and check the `Source?` box
+next to `openmpi` or `libnetcdf-fortran-devel`, install `cygport` and
+finish the install.  Unpack the archives in `/usr/src` (`tar xaf ...`
+should do the trick), and `cd` into the new directory.  There will be
+a `.cygport` file with the build script.  Edit this to add a `.1`
+after the current release field.  Save this file, then run
+`cygport ${package}.cygport download prep compile test install package`
+If there are errors, try to fix them, then re-run
+`cygport ${package}.cygport compile test install package`
+Once it compiles, you can follow the directions in
+https://cygwin.com/package-server.html#overlay
+to set up a local package server and install from that, or you can run
+```bash
+cd /
+for name in /usr/src/${package}-${version}*/${package}-${version}*/dist/**.tar.xz;
+do
+    tar xaf ${name}
+done
+```
+then re-run setup to make sure everything still works.
+The first method plays much nicer with other tools.
+
+If you feel nice, you can tell the maintainer whether the package
+compiled, whether the tests passed and what you needed to do to make
+it do that.  The contents of
+`/usr/src/${package}-${version}*/${package}-${version}*/patch` might
+help with that.

external/io_netcdf/makefile

@@ -50,7 +50,7 @@ diffwrf:                diffwrf.F90
 	$(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 [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; 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) ;\

tools/Makefile

@@ -12,6 +12,7 @@ OBJ = registry.o my_strtok.o reg_parse.o data.o type.o misc.o \
 
 registry : $(OBJ) standard.exe
 	$(CC_TOOLS) -o registry $(DEBUG) $(LDFLAGS) $(OBJ)
+	if [ -x /usr/bin/peflags.exe ] ; then /usr/bin/peflags.exe --stack-reserve=33554432 registry; fi
 
 standard.exe : standard.o
 	$(CC_TOOLS) -o standard.exe $(DEBUG) $(LDFLAGS) standard.o