I've got a problem with excessive memory leakage using HDF5 in a Fortran
program. Here's a simple example of adding a large fixed size matrix to
a H5 file. It Iterates through a loop where the dataspace is enlarged,
another matrix is added to the file and the dataspace is closed.
Shouldn't it free all the memory at the end of each loop and return to a
certain base memory footprint? Instead it continues to grow throughout
the process.
Jack Berkery
GE Energy Applications
Schenectady, NY
!
************************************************************************
******
! *
! * Project: memtest.f90
! * Subject: Test appending a matrix to H5 file.
! *
!
************************************************************************
******
program main
use HDF5
implicit none
integer :: i, j, h5err
integer :: nrows = 1000
integer :: ncols = 500
real, dimension(500,1000) :: matrix
integer(HID_T) :: file ! File id
integer(HID_T) :: hdata ! Group id for storing hourly data
integer(HID_T) :: dset ! Dataset id
integer(HID_T) :: dspc ! Dataspace id
integer(HID_T) :: dprp ! Dataproperties id
integer(HID_T) :: dtyp ! Datatype id
integer(HID_T) :: mset ! Memory Dataset id
integer(HID_T) :: mspc ! Memory Dataspace id
! Variables for fetching dimension sizes from dataspaces within the
file.
integer(HSIZE_T) :: dimd(2), maxdim(2)
! Initialize FORTRAN interface.
call H5open_f ( h5err )
! Create a new file using default properties.
call H5Fcreate_f ( "test03.h5", H5F_ACC_TRUNC_F, file, h5err )
! Hourly data - Stores info about the settings at a given year.
call H5Gcreate_f ( file, "HData", hdata, h5err )
! Create dataspace to store expandable matrix of values
call H5Screate_simple_f ( 2, (/0, nrows/), dspc, h5err,
(/H5S_UNLIMITED_F, nrows/) )
! Define the datatype for this set
call H5Tcopy_f ( H5T_NATIVE_REAL, dtyp, h5err )
! Create property objects
call H5Pcreate_f ( H5P_DATASET_CREATE_F, dprp, h5err )
! Set properties - chunked (one at a time)
call H5Pset_chunk_f ( dprp, 2, (/1, nrows/), h5err )
! Set properties - using compression level 7 [0-9] (9 most
compression)
call H5Pset_deflate_f ( dprp, 7, h5err )
! Create the dataset with modified properties.
call H5Dcreate_f ( hdata, "vals", dtyp, dspc, dset, h5err, dprp )
! Create memory dataspaces to enable chunked write
call H5Screate_simple_f ( 2, (/ncols, nrows/), mspc, h5err )
! Fill in data variables
do i = 1, ncols
do j = 1, nrows
matrix (i,j) = 100.0 * real(i) + real(j)
end do
end do
! Write dataspace in a loop
! New data has to be appended to the dataset already in the file.
do i = 1, 30
print *, "Loop", i
! Get a new pointer to a copy of the dataspace for this set
call H5Dget_space_f ( dset, dspc, h5err )
! Figure out how big is the dataset in the file.
call H5Sget_simple_extent_dims_f ( dspc, dimd, maxdim, h5err )
! Extend size of the dataset in the file
call H5Dextend_f ( dset, dimd+(/ncols,0/), h5err )
! Close the dataspace now that it has been extended
call H5Sclose_f ( dspc, h5err )
! Fetch the dataspace of the extended dataset
call H5Dget_space_f ( dset, dspc, h5err )
! Select the appropriate slab in the extended dataset
call H5Sselect_hyperslab_f ( dspc, H5S_SELECT_SET_F, &
(/dimd(1),0/), (/1,1/), h5err, (/1,1/), shape(matrix) )
! Write the data from memory to the selected slab
call H5Dwrite_f ( dset, H5T_NATIVE_REAL, matrix, shape(matrix),
h5err, &
mspc, dspc, H5P_DEFAULT_F )
! Close the extended dataspace to free memory
call H5Sclose_f ( dspc, h5err )
call sleep (3) ! for a better view of process explorer
graph
end do
! Cleanup, end access and release resources
call sleep (5) ! for a better view of process
explorer graph
call H5Dclose_f ( dset, h5err ) ! dataset
!call H5Sclose_f ( dspc, h5err ) ! dataspace (released inside loop)
call H5Pclose_f ( dprp, h5err ) ! properties
call H5Tclose_f ( dtyp, h5err ) ! data types
call H5Fclose_f ( file, h5err ) ! file id
call H5close_f ( h5err ) ! fortran interface
call sleep (5)
end program main
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