hdf5.h: No such file or directory (Ubuntu 15.04)

[sid-kap]

When I try to build bindings-hdf5, I get the following error:

bindings-hdf5-0.1.1: build
Preprocessing library bindings-hdf5-0.1.1...
Types.hsc:1:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
compiling .stack-work/dist/x86_64-linux/Cabal-1.22.5.0/build/Bindings/HDF5/Types_hsc_make.c failed (exit code 1)
command was: /usr/bin/gcc -c .stack-work/dist/x86_64-linux/Cabal-1.22.5.0/build/Bindings/HDF5/Types_hsc_make.c -o .stack-work/dist/x86_64-linux/Cabal-1.22.5.0/build/Bindings/HDF5/Types_hsc_make.o -fno-stack-protector -D__GLASGOW_HASKELL__=710 -Dlinux_BUILD_OS=1 -Dx86_64_BUILD_ARCH=1 -Dlinux_HOST_OS=1 -Dx86_64_HOST_ARCH=1 -I.stack-work/dist/x86_64-linux/Cabal-1.22.5.0/build/autogen -include .stack-work/dist/x86_64-linux/Cabal-1.22.5.0/build/autogen/cabal_macros.h -I/home/sidharth/.stack/snapshots/x86_64-linux/lts-4.1/7.10.3/lib/x86_64-linux-ghc-7.10.3/bindings-DSL-1.0.23-Es09zjDpTFQCqScuh7qYEQ/include -I/home/sidharth/.stack/programs/x86_64-linux/ghc-7.10.3/lib/ghc-7.10.3/base_HQfYBxpPvuw8OunzQu6JGM/include -I/home/sidharth/.stack/programs/x86_64-linux/ghc-7.10.3/lib/ghc-7.10.3/integ_2aU3IZNMF9a7mQ0OzsZ0dS/include -I/home/sidharth/.stack/programs/x86_64-linux/ghc-7.10.3/lib/ghc-7.10.3/include -I/home/sidharth/.stack/programs/x86_64-linux/ghc-7.10.3/lib/ghc-7.10.3/include/

--  While building package bindings-hdf5-0.1.1 using:
      /home/sidharth/clones/bindings-dsl/bindings-hdf5/.stack-work/dist/x86_64-linux/Cabal-1.22.5.0/setup/setup --builddir=.stack-work/dist/x86_64-linux/Cabal-1.22.5.0 build lib:bindings-hdf5 --ghc-options " -ddump-hi -ddump-to-file"
    Process exited with code: ExitFailure 1

I'm using Ubuntu 15.04.
I believe this issue may be related to the following issues: NVIDIA/DIGITS#156, BVLC/caffe#2690, https://groups.google.com/forum/#!topic/caffe-users/cdyqjNpoFRY.
(Apparently, the location of hdf5.h changed in the newest Ubuntu HDF5 packages, which is why the build script can't find the header file.)
It seems like we might need to update bindings-hdf5/configure to look in the right directory for hdf5.h, but I'm not sure exactly how to do this.

Does anyone here know how we can fix this?

[sid-kap]

I fixed it by adding the following to bindings-hdf5.cabal, under library:

  include-dirs: /usr/include/hdf5/serial
  extra-lib-dirs: /usr/lib/x86_64-linux-gnu/hdf5/serial

Should we add this to the repo? That would be useful so that other people using Ubuntu 15.04 can run stack install bindings-hdf5 globally and it would just work, rather than having to manually clone the repo, update the cabal file, and build manually.

[jwiegley]

The cabal file is really not the place for such system-specific settings. They should become arguments to the stack install command.

[RyanGlScott]

FWIW, I can reproduce the error.

I wonder if it would be a better idea to use pkgconfig-depends: hdf5 instead of a configure script?

[sid-kap]

Out of curiosity, what usually happens in this situation? In my /usr/include directory on my Ubuntu 15.04 machine, I can see many libraries that keep their header files in a directory under /usr/include: X11, boost, cairo, curl, gsl, gtk-3.0, etc. Do people usually have to specify the directory when including these libraries (i.e. #include <cairo/cairo.h>)?

[RyanGlScott]

Er, disregard my advice: it appears that hdf5 does not ship with a .pc file. That is an Ubuntu-ism. (source: https://github.com/mokus0/bindings-hdf5#installation)

[sid-kap]

@RyanGlScott I'm not sure how pkg-config works, but on my (Ubuntu 15.04) machine, pkg-config --libs hdf5 yields

-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 

and pkg-config --cflags hdf5 yields

-I/usr/include/hdf5/serial

which looks to me like the desired output.