HDF5 Real attribute writing in Fortran - parallel-processing

Question

I am trying to write an attribute in my HDF file, my code manages to write the proper value for the attribute if it is of type integer, but not for reals. This is the code
! Number of processes is assumed to be 4
! PROGRAM DATASET_BY_CHUNK
USE HDF5 ! This module contains all 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 the 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 the attribute string
CHARACTER(LEN=80) :: attr_data ! Attribute data
INTEGER, ALLOCATABLE :: data (:,:) ! Data to write
INTEGER :: rank = 2 ! Dataset rank
real re
INTEGER :: error, error_n ! Error flags
!
! MPI definitions and 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 is not 4
if (mpi_size .NE. 4) then
write(*,*) 'This example is set up to use only 4 processes'
write(*,*) 'Quitting....'
goto 100
endif
attr_data = "Dataset character attribute"
!
! Initialize HDF5 library and Fortran interfaces.
!
CALL h5open_f(error)
!
! Setup file access property list with 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 the 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 some attribute
!
re = 20.0
!
! Create scalar data space for the 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 to the data space.
!
CALL h5sclose_f(aspace_id, error)
!
! Create the data space for the 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 and writes it to the hyperslab
! in the 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) then
offset(1) = 0
offset(2) = 0
endif
if (mpi_rank .EQ. 1) then
offset(1) = chunk_dims(1)
offset(2) = 0
endif
if (mpi_rank .EQ. 2) then
offset(1) = 0
offset(2) = chunk_dims(2)
endif
if (mpi_rank .EQ. 3) then
offset(1) = chunk_dims(1)
offset(2) = chunk_dims(2)
endif
!
! Select hyperslab in the 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 with trivial data.
!
ALLOCATE (data(chunk_dims(1),chunk_dims(2)))
data = mpi_rank + 1
!
! Create property list for 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 the 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 the 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 the dataset.
!
CALL h5dclose_f(dset_id, error)
!
! Close the property list.
!
CALL h5pclose_f(plist_id, error)
!
! Close the file.
!
CALL h5fclose_f(file_id, error)
!
! Close FORTRAN interfaces and HDF5 library.
!
CALL h5close_f(error)
100 continue
CALL MPI_FINALIZE(mpierror)
END PROGRAM DATASET_BY_CHUNK
The program runs satisfactorily, but when checking in Matlab with h5disp, I get that:
Attributes:
'Re': 0.000000
Any suggestions about how to fix it would be great! Thanks a lot

Answer 1

A Minimal, Complete, and Verifiable example (MCVE) would help both yourself (to spot your mistake) and us to figure out what you are really doing.
So in saying that, here's one. Please note there is no error checking, this is 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 you compile, run then dump the 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 the question I have to ask about your code is why is adims set to 80?
I would highly suggest three things
A MCVE.
Error checking.
In regards to using MPI you should always get a serial version (within reason) working then parallelize it. Yes, I know this might near be impossible, but if you do go this route it will make your life easier (at least to begin with).