parallel processing - HDF5 Real attribute writing in Fortran -


i trying write attribute in hdf file, code manages write proper value attribute if of type integer, not reals. code

! number of processes assumed 4  ! program dataset_by_chunk    use hdf5 ! module contains necessary modules  !     use mpi   implicit none   include 'mpif.h'   character(len=7), parameter :: filename = "test.h5"  ! file name  character(len=9), parameter :: dsetname = "data_test" ! dataset name   integer(hsize_t), dimension(1) :: data_dims   integer(hid_t) :: file_id       ! file identifier   integer(hid_t) :: dset_id       ! dataset identifier   integer(hid_t) :: filespace     ! dataspace identifier in file   integer(hid_t) :: memspace      ! dataspace identifier in memory  integer(hid_t) :: plist_id      ! property list identifier  integer(hid_t) :: attr_id       ! attribute identifier  integer(hid_t) :: aspace_id     ! attribute dataspace identifier  integer(hid_t) :: atype_id      ! attribute dataspace identifier   integer(hsize_t), dimension(2) :: dimsf = (/4,8/) ! dataset dimensions  ! in file.  !     integer, dimension(7) :: dimsfi = (/4,8,0,0,0,0,0/)   integer(hsize_t), dimension (2) :: dimsfi = (/4,8/)   integer(hsize_t), dimension(2) :: chunk_dims = (/2,4/) ! chunks dimensions   integer(hsize_t),  dimension(2) :: count    integer(hssize_t), dimension(2) :: offset   integer(hsize_t),  dimension(2) :: stride  integer(hsize_t),  dimension(2) :: block     integer(hsize_t), dimension(1) :: adims ! attribute dimension  integer          :: arank = 1     ! attribure rank  integer(size_t)  :: attrlen     ! length of attribute string   character(len=80) ::  attr_data  ! attribute data    integer, allocatable :: data (:,:)  ! data write  integer :: rank = 2 ! dataset rank   real re   integer :: error, error_n  ! error flags  !  ! mpi definitions , calls.  !  integer :: mpierror       ! mpi error flag  integer :: comm, info  integer :: mpi_size, mpi_rank   comm = mpi_comm_world  info = mpi_info_null   call mpi_init(mpierror)  call mpi_comm_size(comm, mpi_size, mpierror)  call mpi_comm_rank(comm, mpi_rank, mpierror)   ! quit if mpi_size not 4   if (mpi_size .ne. 4)     write(*,*) 'this example set use 4 processes'     write(*,*) 'quitting....'     goto 100  endif   attr_data = "dataset character attribute"  !  ! initialize hdf5 library , fortran interfaces.  !  call h5open_f(error)    !   ! setup file access property list parallel i/o access.  !  call h5pcreate_f(h5p_file_access_f, plist_id, error)  call h5pset_fapl_mpio_f(plist_id, comm, info, error)   !  ! create file collectively.  !   call h5fcreate_f(trim(filename), h5f_acc_trunc_f, file_id, error, access_prp = plist_id)  call h5pclose_f(plist_id, error)  !  ! create attribute  !  re = 20.0  !  ! create scalar data space attribute.  !  call h5screate_f(h5s_scalar_f,aspace_id,error)  adims=80  !     -----------------------------  !     reynolds number  call h5acreate_f(file_id,'re',h5t_native_double,aspace_id, &       attr_id, error)  call h5awrite_f(attr_id,h5t_native_double,re,adims,error)  call h5aclose_f(attr_id, error)   !  ! terminate access data space.  !  call h5sclose_f(aspace_id, error)   !  ! create data space  dataset.   !  call h5screate_simple_f(rank, dimsf, filespace, error)  call h5screate_simple_f(rank, chunk_dims, memspace, error)  !  ! create chunked dataset.  !  call h5pcreate_f(h5p_dataset_create_f, plist_id, error)  call h5pset_chunk_f(plist_id, rank, chunk_dims, error)  call h5dcreate_f(file_id, dsetname, h5t_native_integer, filespace, &                   dset_id, error, plist_id)  call h5sclose_f(filespace, error)  !  ! each process defines dataset in memory , writes hyperslab  ! in file.   !  stride(1) = 1   stride(2) = 1   count(1) =  1   count(2) =  1   block(1) = chunk_dims(1)  block(2) = chunk_dims(2)  if (mpi_rank .eq. 0)      offset(1) = 0      offset(2) = 0  endif  if (mpi_rank .eq. 1)      offset(1) = chunk_dims(1)       offset(2) = 0   endif  if (mpi_rank .eq. 2)      offset(1) = 0       offset(2) = chunk_dims(2)   endif  if (mpi_rank .eq. 3)      offset(1) = chunk_dims(1)       offset(2) = chunk_dims(2)   endif  !   ! select hyperslab in file.  !  call h5dget_space_f(dset_id, filespace, error)  call h5sselect_hyperslab_f (filespace, h5s_select_set_f, offset, count, error, &                              stride, block)  !   ! initialize data buffer trivial data.  !  allocate (data(chunk_dims(1),chunk_dims(2)))  data = mpi_rank + 1  !  ! create property list collective dataset write  !  call h5pcreate_f(h5p_dataset_xfer_f, plist_id, error)   call h5pset_dxpl_mpio_f(plist_id, h5fd_mpio_collective_f, error)   !  ! write dataset collectively.   !  call h5dwrite_f(dset_id, h5t_native_integer, data, dimsfi, error, &                  file_space_id = filespace, mem_space_id = memspace, xfer_prp = plist_id)  !  ! write dataset independently.   !  !    call h5dwrite_f(dset_id, h5t_native_integer, data, dimsfi,error, &  !                     file_space_id = filespace, mem_space_id = memspace)  !  ! deallocate data buffer.  !  deallocate(data)   !  ! close dataspaces.  !  call h5sclose_f(filespace, error)  call h5sclose_f(memspace, error)  !  ! close dataset.  !  call h5dclose_f(dset_id, error)  !  ! close property list.  !  call h5pclose_f(plist_id, error)  !  ! close file.  !  call h5fclose_f(file_id, error)   !  ! close fortran interfaces , hdf5 library.  !  call h5close_f(error)   100  continue  call mpi_finalize(mpierror)   end program dataset_by_chunk

the program runs satisfactorily, when checking in matlab h5disp, that:
attributes: 're': 0.000000

any suggestions how fix great! lot

a minimal, complete, , verifiable example (mcve) both (to spot mistake) , figure out doing.

so in saying that, here's one. please note there no error checking, bad, bad, bad.

program fa      use hdf5      implicit none      character(len=8), parameter :: filename = "test.h5"      integer(hid_t) :: file_id     integer(hid_t) :: attr_id     integer(hid_t) :: aspace_id     integer(size_t), dimension(1) :: adims = (/0/)      integer     :: ierr     real        :: re      re = 20.0      call h5open_f(ierr)     call h5fcreate_f(trim(filename), h5f_acc_trunc_f, file_id, ierr)     call h5screate_f(h5s_scalar_f, aspace_id, ierr)     call h5acreate_f(file_id, 'reynolds number', h5t_native_real, &                      aspace_id, attr_id, ierr)     call h5awrite_f(attr_id, h5t_native_real, re, adims, ierr)     call h5aclose_f(attr_id, ierr)     call h5sclose_f(aspace_id, ierr)     call h5fclose_f(file_id, ierr)     call h5close_f(ierr)  end program fa

if compile, run dump file:

$ h5fc -o fa fa.f90 $ ./fa $ h5dump test.h5 hdf5 "test.h5" { group "/" {     attribute "reynolds number" {       datatype  h5t_ieee_f32le       dataspace  scalar       data {       (0): 20       }     } } }

now question have ask code why adims set 80?

i highly suggest 3 things

  1. a mcve.
  2. error checking.

in regards using mpi should serial version (within reason) working parallelize it. yes, know might near impossible, if go route make life easier (at least begin with).


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