Error installing abinit with hdf5 enabled

[Fabricio Cannini]

Hello there.

While trying to install abinit as described above, the error below happens:

$ spack install abinit +hdf5
==> libsigsegv is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/libsigsegv-2.11-nwbx3xloeloijlyclcpkhaffbhcv4ac2
==> m4 is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/m4-1.4.18-l5ndpki5yduibmsz7dywpopnlx2s7sxr
==> libtool is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/libtool-2.4.6-z7osdpc5jrpjdoyrr5gkmo345sknbijn
==> pkgconf is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/pkgconf-1.4.0-5ix6hdueykp6keate4matz6bgf6oda6k
==> util-macros is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/util-macros-1.19.1-ttsbvbkpzqvo7mondef6nb6lu7dxxp72
==> libpciaccess is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/libpciaccess-0.13.5-f5k35g4jnofnql3akgfs5iuhijsfbjsq
==> xz is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/xz-5.2.3-f6q324m73chcvvq2mdv33txshpir7uck
==> zlib is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/zlib-1.2.11-zknfwanbwk6tnyaplsykwghx7cvnz4cr
==> libxml2 is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/libxml2-2.9.4-etonamb2xg6nhsgxakkkh7bdett64lmw
==> ncurses is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/ncurses-6.0-5utro5xxtp2ijwnx6fiwze4qksfdi7vg
==> readline is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/readline-7.0-hlk3dniagkghsp5kmrfxloql4hht36jt
==> gdbm is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gdbm-1.14.1-codgpslsr5agetrxl3se5mq6dxi3n7yw
==> perl is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/perl-5.24.1-ahzi5hrefrxdwcpdx7d5rrv5yquckr2b
==> autoconf is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/autoconf-2.69-sbkwtazgf7h523d4ogwsrtuz3qwb56tl
==> automake is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/automake-1.15.1-mttg4bsxkpj6iftodzhzlojez5j3kop7
==> numactl is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/numactl-2.0.11-52qome7tntxkrxudhotcwroubbw23vvo
==> hwloc is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/hwloc-1.11.9-7xxgxbg65an7zmrztfcuu3hs73puj6v3
==> openmpi is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/openmpi-3.0.0-7pxjmspapnh6zg5m2phr6zm4fnxd5ixh
==> fftw is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/fftw-3.3.7-db4x27omzkjdoffw52mss4kyjez2xajd

==> Installing hdf5
==> Using cached archive: /opt/spack/var/spack/cache/hdf5/hdf5-1.10.1.tar.gz
==> Staging archive: /opt/spack/var/spack/stage/hdf5-1.10.1-5avdytbtj5hzzl5paccvcff7vwudspxm/hdf5-1.10.1.tar.gz
==> Created stage in /opt/spack/var/spack/stage/hdf5-1.10.1-5avdytbtj5hzzl5paccvcff7vwudspxm
==> No patches needed for hdf5
==> Building hdf5 [AutotoolsPackage]
==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'
==> Executing phase: 'install'
==> Successfully installed hdf5
  Fetch: 0.03s.  Build: 2m 30.05s.  Total: 2m 30.09s.
[+] /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/hdf5-1.10.1-5avdytbtj5hzzl5paccvcff7vwudspxm
==> libxc is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/libxc-2.2.2-6dlnp6ddthqsa3wmjz3ydriutd4ggvqp

==> Installing netcdf
==> Using cached archive: /opt/spack/var/spack/cache/netcdf/netcdf-4.4.1.1.tar.gz
==> Staging archive: /opt/spack/var/spack/stage/netcdf-4.4.1.1-iu2ocujd2xqapss7zaq4w4jhiqk47lyg/netcdf-4.4.1.1.tar.gz
==> Created stage in /opt/spack/var/spack/stage/netcdf-4.4.1.1-iu2ocujd2xqapss7zaq4w4jhiqk47lyg
==> Ran patch() for netcdf
==> Building netcdf [AutotoolsPackage]
==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'
==> Executing phase: 'install'
==> Successfully installed netcdf
  Fetch: 0.01s.  Build: 46.42s.  Total: 46.43s.
[+] /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/netcdf-4.4.1.1-iu2ocujd2xqapss7zaq4w4jhiqk47lyg

==> Installing netcdf-fortran
==> Using cached archive: /opt/spack/var/spack/cache/netcdf-fortran/netcdf-fortran-4.4.4.tar.gz
==> Staging archive: /opt/spack/var/spack/stage/netcdf-fortran-4.4.4-4wuiozygj7prfmh734zx52affutetwdx/netcdf-fortran-4.4.4.tar.gz
==> Created stage in /opt/spack/var/spack/stage/netcdf-fortran-4.4.4-4wuiozygj7prfmh734zx52affutetwdx
==> No patches needed for netcdf-fortran
==> Building netcdf-fortran [AutotoolsPackage]
==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'
==> Executing phase: 'install'
==> Successfully installed netcdf-fortran
  Fetch: 0.00s.  Build: 1m 22.11s.  Total: 1m 22.12s.
[+] /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/netcdf-fortran-4.4.4-4wuiozygj7prfmh734zx52affutetwdx
==> openblas is already installed in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/openblas-0.2.20-tq4e7crjp5kedl55ubqkq5mf77kbdwbp

==> Installing abinit
==> Fetching https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz
######################################################################## 100,0%
==> Staging archive: /opt/spack/var/spack/stage/abinit-8.6.3-tboqvkkotgm4povtnxbp2ljdkicql7pe/abinit-8.6.3.tar.gz
==> Created stage in /opt/spack/var/spack/stage/abinit-8.6.3-tboqvkkotgm4povtnxbp2ljdkicql7pe
==> No patches needed for abinit
==> Building abinit [AutotoolsPackage]
==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Error: RuntimeError: Unable to locate netcdf-fortran headers in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/netcdf-fortran-4.4.4-4wuiozygj7prfmh734zx52affutetwdx/include
RuntimeError: RuntimeError: Unable to locate netcdf-fortran headers in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/netcdf-fortran-4.4.4-4wuiozygj7prfmh734zx52affutetwdx/include

/opt/spack/var/spack/repos/builtin/packages/abinit/package.py:165, in configure_args:
     55                hdf5 = spec['hdf5:hl']
     56                netcdff = spec['netcdf-fortran:shared'] 
     57                options.extend([
  >> 58                    '--with-netcdf-incs={0'.format(netcdff.headers.cpp_flags),}
     59                    '--with-netcdf-libs={0}'.format(
     60                        netcdff.libs.ld_flags + ' ' + hdf5.libs.ld_flags
     61                    ),

But the following './configure' incantation works just fine:

./configure --enable-mpi --with-mpi-prefix=$(spack location -i openmpi) --with-trio-flavor=netcdf --with-netcdf-incs="-I$(spack location -i netcdf-fortran)/include" --with-netcdf-libs="-L$(spack location -i netcdf-fortran)/lib -lnetcdff"

 
Any help to the cause of the error is appreciated.
TIA