H5dread_f symbol missing in hdf5 (fortran) libraries

Question

I am facing an issue while compiling WRF-DA code (code is here)

The compilation line which fails -

ftn -c -ip -O3  -w -ftz -fno-alias -align all -FR -convert big_endian   -r8        -real-size `expr 8 \* 8` -i4 -I../external/crtm_2.2.3/libsrc   -I/opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/include   -L/opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/lib/  -lhdf5hl_fortran -lhdf5_fortran -lhdf5  da_radiance.f 

  da_radiance.f(5884): error #6285: There is no matching specific subroutine for this generic subroutine call.   [H5DREAD_F]
      call H5Dread_f(dhnd1, &
-----------^

I tried searching relevant symbol in library, and as expected the symbol was not present (h5dread_f_c is present instead).

nm /opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/lib/libhdf5*|grep -i h5dread_f
nm: /opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/lib/libhdf5.settings: File format not recognized
nm: /opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/lib/libhdf5_cpp_intel_160.la: File format not recognized
                 U h5dread_f_c
                 U h5dread_f_c
0000000000001290 T h5dread_f_c
0000000000035320 T h5dread_f_c
                 U h5dread_f_c
                 U h5dread_f_c
0000000000001290 T h5dread_f_c
0000000000035320 T h5dread_f_c
                 U h5dread_f_c
                 U h5dread_f_c
0000000000001290 T h5dread_f_c
0000000000035320 T h5dread_f_c
0000000000035320 T h5dread_f_c
0000000000035320 T h5dread_f_c

I tried compiling hdf5-1.10.2. With a quick peek at the code, I saw that the function seems to have been declared (& commented) in fortran/src/H5Dff.F90 as -

!  M. Scot Breitenfeld
!  September 17, 2011
!
! Fortran2003 Interface:
!!  SUBROUTINE h5dread_f(dset_id, mem_type_id, buf, hdferr, &
!!                       mem_space_id, file_space_id, xfer_prp)
!!    INTEGER(HID_T), INTENT(IN)              :: dset_id
!!    INTEGER(HID_T), INTENT(IN)              :: mem_type_id
!!    TYPE(C_PTR)   , INTENT(INOUT)           :: buf
!!    INTEGER       , INTENT(OUT)             :: hdferr
!!    INTEGER(HID_T), INTENT(IN)   , OPTIONAL :: mem_space_id
!!    INTEGER(HID_T), INTENT(IN)   , OPTIONAL :: file_space_id
!!    INTEGER(HID_T), INTENT(IN)   , OPTIONAL :: xfer_prp
!*****
  SUBROUTINE h5dread_ptr(dset_id, mem_type_id, buf, hdferr, &
       mem_space_id, file_space_id, xfer_prp)

has this function been phased out in latest versions of HDF5? If yes then please share an appropriate (older) version of library (& relevant compilation flags) for the HDF5 in which i can find this symbol.

Please let me know if i can provide any further information.

score 1 · Answer 1 · answered May 12 '18 at 02:39

h5dread_f is an interface, which maps to one of the following

INTERFACE h5dread_f
   MODULE PROCEDURE h5dread_reference_obj
   MODULE PROCEDURE h5dread_reference_dsetreg
   MODULE PROCEDURE h5dread_char_scalar
   MODULE PROCEDURE h5dread_ptr
END INTERFACE

It seems that there are invalid types being passed into the function.

(thanks to Dave Allured from HDF5 group)

H5dread_f symbol missing in hdf5 (fortran) libraries

1 Answers1