Hyperslab to write columns one at a time in Fortran 90

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1

I have a Fortran 90 program that creates a large column of integers at the end of each loop. I would like to write this column into an HDF5 file with each new integer column being written as a new column in the HDF5 file. That is, at the end of the first loop, write column 1, then at the end of the second loop, write column 2, etc, until a 2D array with as many columns as there were loops is created.

Each of these integer columns will always be the same length and I know how many columns will be needed in the end. To do this, I create a dataspace large enough to hold the final 2D array. Then I select a hyperslab beginning with offset (0,0), then (0,1) for the next loop, (0,2) for the loop after that, etc., each time writing the data that my program creates.

This isn't quite working, however. Currently, with the offset (0,0) everything works. However, if I try to write to a hyperslab in any other column, I get nonsense values in my output .h5 file.

Am I implementing the hyperslab code correctly?

Here is a MWE which creates a dataspace of (20,10) and writes a column of twenty '5's into the first column of the .h5 file. If voffset is changed from (/0,0/) to (/0,1/), the '5's are not written and instead random numbers will appear in the second column of the .h5 file:

program hdf5_test
use hdf5
implicit none

! HDF5 file and path names
character(len=10), parameter :: outfilename = "OutData.h5" ! Output file name
character(len=8), parameter :: dsetvbinnedname = "velocity"

! Declare HDF5 IDs
integer(HID_T) :: outfile_id ! File identifier
integer(HID_T) :: dsetv_id
integer(HID_T) :: dataspacev_id

! Dataset dimensions in the file
integer(HSIZE_T), dimension(2) :: binned_vdims = (/20,1/) ! Chunk dimensions
integer(HSIZE_T), dimension(2) :: export_binned_vdims = (/20,10/) ! File dimensions

! Data buffers
integer, dimension(20) :: binned_vdata ! Chunk dimension

! Chunk parameters
integer(HSIZE_T), dimension(2) :: voffset, vchunkcount

integer :: rank = 2
integer :: error ! HDF5 error flag

! Initialize FORTRAN interface
call h5open_f(error)

! Create a new file using the default properties.
call h5fcreate_f(outfilename, H5F_ACC_TRUNC_F, outfile_id, error)

! Create the data space for the binned dataset.
call h5screate_simple_f(rank, export_binned_vdims, dataspacev_id, error)

! Create the chunked dataset.
call h5dcreate_f(outfile_id, dsetvbinnedname, H5T_NATIVE_INTEGER, dataspacev_id, dsetv_id, error)

! Select hyperslab
voffset = (/0,0/)
vchunkcount = (/20,1/)

call h5sselect_hyperslab_f(dataspacev_id, H5S_SELECT_SET_F, voffset, vchunkcount, error)

binned_vdata = 5 ! Write a column of '5's

! Write the data to the dataset.
call h5dwrite_f(dsetv_id, H5T_NATIVE_INTEGER, binned_vdata, export_binned_vdims, error, file_space_id=dataspacev_id)

! Close dataspace, dataset, and file
call h5dclose_f(dsetv_id, error)
call h5sclose_f(dataspacev_id, error)
call h5fclose_f(outfile_id, error)

call h5close_f(error)

end program hdf5_test

2

Hello Forrest,

I changed your program to write by columns to the dataset. (I added a memory space to the write call and a loop)
Is this more or less what you wanted to do? See the attached code.

-Barbara
help@hdfgroup.org

gasdia.f90 (2.02 KB)

ยทยทยท

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Gasdia, Forrest W
Sent: Friday, November 29, 2013 11:14 PM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Hyperslab to write columns one at a time in Fortran 90

I have a Fortran 90 program that creates a large column of integers at the end of each loop. I would like to write this column into an HDF5 file with each new integer column being written as a new column in the HDF5 file. That is, at the end of the first loop, write column 1, then at the end of the second loop, write column 2, etc, until a 2D array with as many columns as there were loops is created.

Each of these integer columns will always be the same length and I know how many columns will be needed in the end. To do this, I create a dataspace large enough to hold the final 2D array. Then I select a hyperslab beginning with offset (0,0), then (0,1) for the next loop, (0,2) for the loop after that, etc., each time writing the data that my program creates.

This isn't quite working, however. Currently, with the offset (0,0) everything works. However, if I try to write to a hyperslab in any other column, I get nonsense values in my output .h5 file.

Am I implementing the hyperslab code correctly?

Here is a MWE which creates a dataspace of (20,10) and writes a column of twenty '5's into the first column of the .h5 file. If voffset is changed from (/0,0/) to (/0,1/), the '5's are not written and instead random numbers will appear in the second column of the .h5 file:

program hdf5_test
use hdf5
implicit none

! HDF5 file and path names
character(len=10), parameter :: outfilename = "OutData.h5" ! Output file name
character(len=8), parameter :: dsetvbinnedname = "velocity"

! Declare HDF5 IDs
integer(HID_T) :: outfile_id ! File identifier
integer(HID_T) :: dsetv_id
integer(HID_T) :: dataspacev_id

! Dataset dimensions in the file
integer(HSIZE_T), dimension(2) :: binned_vdims = (/20,1/) ! Chunk dimensions
integer(HSIZE_T), dimension(2) :: export_binned_vdims = (/20,10/) ! File dimensions

! Data buffers
integer, dimension(20) :: binned_vdata ! Chunk dimension

! Chunk parameters
integer(HSIZE_T), dimension(2) :: voffset, vchunkcount

integer :: rank = 2
integer :: error ! HDF5 error flag

! Initialize FORTRAN interface
call h5open_f(error)

! Create a new file using the default properties.
call h5fcreate_f(outfilename, H5F_ACC_TRUNC_F, outfile_id, error)

! Create the data space for the binned dataset.
call h5screate_simple_f(rank, export_binned_vdims, dataspacev_id, error)

! Create the chunked dataset.
call h5dcreate_f(outfile_id, dsetvbinnedname, H5T_NATIVE_INTEGER, dataspacev_id, dsetv_id, error)

! Select hyperslab
voffset = (/0,0/)
vchunkcount = (/20,1/)

call h5sselect_hyperslab_f(dataspacev_id, H5S_SELECT_SET_F, voffset, vchunkcount, error)

binned_vdata = 5 ! Write a column of '5's

! Write the data to the dataset.
call h5dwrite_f(dsetv_id, H5T_NATIVE_INTEGER, binned_vdata, export_binned_vdims, error, file_space_id=dataspacev_id)

! Close dataspace, dataset, and file
call h5dclose_f(dsetv_id, error)
call h5sclose_f(dataspacev_id, error)
call h5fclose_f(outfile_id, error)

call h5close_f(error)

end program hdf5_test

3

Hi Barabara,

Thanks! That's exactly what I was looking for. I had attempted to use a memory space earlier, but your solution works and requires fewer lines of code.

Forrest