223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

always chunk data 

for small datasets:
- only one chunk
- no compression
This commit is contained in:
Martin Diehl 2021-08-14 15:07:01 +02:00
parent 1d402a3d0c
commit 595cc4e59e
2 changed files with 42 additions and 30 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
python/damask/_result.py
View File

@ -1355,15 +1355,17 @@ class Result:
dataset[...] = result['data']
dataset.attrs['overwritten'] = True
else:
shape = result['data'].shape
if result['data'].size >= chunk_size*2:
shape = result['data'].shape
chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
dataset = f[group].create_dataset(result['label'],data=result['data'],
maxshape=shape, chunks=chunks,
compression='gzip', compression_opts=6,
shuffle=True,fletcher32=True)
compression = ('gzip',6)
else:
dataset = f[group].create_dataset(result['label'],data=result['data'])
chunks = shape
compression = (None,None)
dataset = f[group].create_dataset(result['label'],data=result['data'],
maxshape=shape, chunks=chunks,
compression=compression[0], compression_opts=compression[1],
shuffle=True,fletcher32=True)
now = datetime.datetime.now().astimezone()
dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \

58
src/HDF5_utilities.f90
View File

@ -77,10 +77,12 @@ module HDF5_utilities
end interface HDF5_addAttribute
#ifdef PETSC
logical, parameter, private :: parallel_default = .true.
logical, parameter :: parallel_default = .true.
#else
logical, parameter, private :: parallel_default = .false.
logical, parameter :: parallel_default = .false.
#endif
logical :: compression_possible
public :: &
HDF5_utilities_init, &
HDF5_read, &
@ -103,26 +105,33 @@ contains
!--------------------------------------------------------------------------------------------------
subroutine HDF5_utilities_init
integer :: hdferr
integer :: hdferr, HDF5_major, HDF5_minor, HDF5_release, deflate_info
integer(SIZE_T) :: typeSize
print'(/,a)', ' <<<+- HDF5_Utilities init -+>>>'
!--------------------------------------------------------------------------------------------------
!initialize HDF5 library and check if integer and float type size match
call h5open_f(hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (hdferr < 0) error stop 'HDF5 error'
if (int(bit_size(0),SIZE_T)/=typeSize*8) &
error stop 'Default integer size does not match H5T_NATIVE_INTEGER'
call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (hdferr < 0) error stop 'HDF5 error'
if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) &
error stop 'pReal does not match H5T_NATIVE_DOUBLE'
call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call H5Zget_filter_info_f(H5Z_FILTER_DEFLATE_F,deflate_info,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
compression_possible = (HDF5_major == 1 .and. HDF5_minor >= 12) .and. & ! https://forum.hdfgroup.org/t/6186
ior(H5Z_FILTER_ENCODE_ENABLED_F,deflate_info) > 0
end subroutine HDF5_utilities_init
@ -1907,11 +1916,12 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
totalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id
integer, dimension(worldsize) :: writeSize !< contribution of all processes
integer, dimension(worldsize) :: writeSize !< contribution of all processes
integer(HID_T) :: dcpl
integer :: ierr, hdferr, HDF5_major, HDF5_minor, HDF5_release
integer :: ierr, hdferr
integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective when writing in parallel)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
@ -1938,23 +1948,23 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)]
!--------------------------------------------------------------------------------------------------
! compress (and chunk) larger datasets
! chunk dataset, enable compression for larger datasets
call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if(product(totalShape) >= chunkSize*2_HSIZE_T) then
call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_shuffle_f(dcpl, hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_Fletcher32_f(dcpl,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
if (product(totalShape) >= chunkSize*2_HSIZE_T) then
call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
if (hdferr < 0) error stop 'HDF5 error'
if (HDF5_major == 1 .and. HDF5_minor >= 12) then ! https://forum.hdfgroup.org/t/6186
call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_shuffle_f(dcpl, hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_deflate_f(dcpl, 6, hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_Fletcher32_f(dcpl,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
endif
if (compression_possible) call h5pset_deflate_f(dcpl, 6, hdferr)
else
call h5pset_chunk_f(dcpl, size(totalShape), totalShape, hdferr)
endif
if (hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) and in file (global shape)