Bug 440682 – =sci-libs/hdf5-1.8.9-r2 please stabilize

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Sean Santos 2012-11-01 02:45:02 UTC]

hdf5 seems to require quad precision to compile, which was only added to gfortran via libquadmath in 4.6 (at least for common architectures; I wouldn't know if there was some machine that had quad support earlier). For me, emerging hdf5 (the first and only stable version right now) stopped on a line with "KIND=16", with gfortran noting that the kind was unsupported.

Hopefully gcc 4.6 is stabilized soon. Even so, I think that the dependency should be added.

[Comment 1 François Bissey 2012-11-01 02:56:23 UTC]

which versions of hdf5? I compile hdf-1.8.9 with gcc-4.3 on SLES11 box at work so I am bit surprised by this claim.
Can you attach a build log of a failed install with gcc<4.6?

[Comment 2 Sean Santos 2012-11-01 03:24:53 UTC]

This is sci-libs/hdf5-1.8.8-r1. To be clear, compiling with the fortran USE flag is the problem, because this is an issue specific to gfortran. I would not be surprised if everything else works fine with gcc-4.3.

Here's the error message:

mpif90 -O2 -pipe -march=native   -I../../src -I../../fortran/src -O2 -pipe -march=native -c -o H5fortran_detect.o  H5fortran_detect.f90
H5fortran_detect.f90:175.16:

   REAL(KIND= 16) :: a
                1
Error: Kind 16 not supported for type REAL at (1)
H5fortran_detect.f90:178.21:

    a_size = SIZEOF(a)
                     1
Error: Symbol 'a' at (1) has no IMPLICIT type
make[2]: *** [H5fortran_detect.o] Error 1

There are a prodigous number of warnings, so the log is too large to attach, but I think this is the only relevant part as I can reproduce the error in a short program:

  program test
    integer, parameter :: qk = 16
    real(qk) :: a = 1._qk
    write(*,*) a
  end program test

With gfortran 4.5.4 this yields:

test.F90:5.9:

  real(qk) :: a = 1._qk
         1
Error: Kind 16 not supported for type REAL at (1)

[Comment 3 Kacper Kowalik (Xarthisius) (RETIRED) 2012-11-01 08:45:10 UTC]

It's a dupe of bug 419895. Please use hdf5-1.8.9. I'll reuse this bug for stabilization.

[Comment 4 Kacper Kowalik (Xarthisius) (RETIRED) 2012-11-01 08:50:54 UTC]

Couple of bug fixes, notably the one described originally in this report. Arches please do your magic!

[Comment 5 Anthony Basile 2012-11-01 16:59:40 UTC]

stable on ppc ppc64

[Comment 6 Agostino Sarubbo 2012-11-04 14:09:20 UTC]

amd64 stable

[Comment 7 Agostino Sarubbo 2012-11-21 11:26:21 UTC]

x86 stable

[Comment 8 Kacper Kowalik (Xarthisius) (RETIRED) 2012-12-04 07:01:42 UTC]

@alpha, @ia64, @sparc
Guys you may consider skipping this version and go ahead straight to 1.8.10. I'll request stablereq for it later this week.

[Comment 9 Agostino Sarubbo 2012-12-18 16:47:37 UTC]

(In reply to comment #8)
> @alpha, @ia64, @sparc
> Guys you may consider skipping this version and go ahead straight to 1.8.10.
> I'll request stablereq for it later this week.

Don't forget to file the stablereq for the new autoconf before asking 1.8.10 stable

[Comment 10 Agostino Sarubbo 2012-12-30 14:29:48 UTC]

sparc stable

[Comment 11 Agostino Sarubbo 2012-12-30 15:07:09 UTC]

alpha stable. Last arch, closing