Building NetCDF, HDF4 and HDF5 on Windows

There are binaries available, and they're probably fine, but the headers are not, because HDF4 / HDF5 install different headers depending on which compiler they were built with (which in itself is a bug). Luckily, building them from source is fairly easy.

First, get the latest source (currently 4.0.1) from http://www.unidata.ucar.edu/software/netcdf/ and extract it in a convenient place, then configure, build and install:

$ LDFLAGS=-L/c/met.no/lib CPPFLAGS=-I/c/met.no/include ./configure --prefix=/c/met.no --disable-f90 --disable-examples
$ make all install

Note the --enable-shared part; you can leave out --disable-f90 and --disable-examples if you want, but keep --enable-shared.

First, get the latest source (currently 4.2r4) from http://www.hdfgroup.org/release4/obtain.html and extract it in a convenient place.

HDF4's autoconf infrastructure is a weird mix of too-old and too-new. Open configure.ac, look for “Libtool initialization” (around line 660) and replace the following two lines

LT_INIT(dlopen)
LT_OUTPUT

with these:

AC_LIBTOOL_DLOPEN
AM_PROG_LIBTOOL

Next, there is a spot in configure.ac that checks which OS you're running on and bails if it doesn't recognize it… which is stupid, because it controls code that is only used *only* if you want to use HDF4's own version of NetCDF, which we don't. We can work around this by changing cygwin to mingw32 on line 695. It's wrong, but it doesn't matter, because the result is never used (see below).

Finally, in mfhdf/libsrc/Makefile.am, there is a missing INCLUDES line. We need to add the following line inside the if HDF_BUILD_XDR block:

INCLUDES += -I$(top_srcdir)/mfhdf/xdr

Then regenerate everything:

$ aclocal
$ libtoolize --copy --force
$ autoheader
$ automake --add-missing --copy --foreign
$ autoconf

XXX automake warns about F77LINK, check if that requires fixing. harmless since we don't build the Fortran interface

Finally, configure, build and install:

$ LDFLAGS=-L/c/met.no/lib CPPFLAGS="-I/c/met.no/include -DNO_SYS_XDR_INC" ./configure --prefix=/c/met.no --disable-fortran --disable-netcdf
$ make all install

The -DNO_SYS_XDR_INC part fixes more xdr-related breakage.

You must specify --disable-netcdf, otherwise HDF4 will clobber NetCDF's header files!

XXX I'm worried that the xdr stuff may cause more trouble down the line

First, get the latest source (currently 1.8.3) from http://www.hdfgroup.org/HDF5/release/obtain5.html and extract it in a convenient place.

In HDF5 1.8.3, there are several issues we need to address before we can build the library.

note: the first two issues have been reported to the HDF Group and will be fixed in the next release.

The first is a bug in perform/sio_engine.c: on line 376, replace mkdir with HDmkdir.

The second is that the test scripts use Winsock (ws2_32.lib), but don't link against it. This can be fixed by running the following commands before configure:

$ echo 'libh5test_la_LIBADD=-lws2_32' >>test/Makefile.am

The third is that several HDF5 libraries have a dependency on libhdf5, but libtool isn't told about this. This can be fixed in the same manner as the ws2_32 issue:

$ echo 'libhdf5_cpp_la_LIBADD=$(LIBHDF5)' >>c++/src/Makefile.am
$ echo 'libhdf5_hl_la_LIBADD=$(LIBHDF5)' >>hl/src/Makefile.am
$ echo 'libhdf5_hl_cpp_la_LIBADD=$(LIBH5_HL)' >>hl/c++/src/Makefile.am

Finally, HDF5's configure.in uses the LT_INIT macro, which only works with very recent versions of automake. Edit configure.in and replace these two lines:

LT_PREREQ([2.2])
LT_INIT([dlopen])

with this:

AC_LIBTOOL_DLOPEN
AM_PROG_LIBTOOL

XXX alternative: use more recent autotools versions, but this has repercussions for all other components

Now we need to regenerate everything:

$ aclocal
$ libtoolize --copy --force
$ autoheader
$ automake --add-missing --copy --foreign
$ autoconf

The fourth and final issue is that C++ support is not enabled by default. To enable it, add –enable-cxx to the configure command line.

Finally:

$ LDFLAGS=-L/c/met.no/lib CPPFLAGS=-I/c/met.no/include ./configure --prefix=/c/met.no --enable-cxx
$ make all install

TODO fix large file support!