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DAMASK_EICMD
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workaround for HDF5: https://forum.hdfgroup.org/t/6186 

writing chunked/compressed data can cause problems with MPI. Even though not 100%
clear from the reference, it seems that the issue only appears for HDF5
< 1.12.
Of special importance for Ubuntu since the Debian package is still at 1.10.6
This commit is contained in:
Martin Diehl 2021-05-03 15:20:59 +02:00
parent 45ace810d1
commit b353f8ed92
1 changed files with 13 additions and 9 deletions
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22
src/HDF5_utilities.f90
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@ -1775,7 +1775,7 @@ subroutine initialize_write(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(HID_T) :: dcpl
integer :: ierr, hdferr integer :: ierr, hdferr, HDF5_major, HDF5_minor, HDF5_release
integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
@ -1808,14 +1808,18 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr) call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
if(hdferr < 0) error stop 'HDF5 error' if(hdferr < 0) error stop 'HDF5 error'
if(product(totalShape) >= chunkSize*2_HSIZE_T) then if(product(totalShape) >= chunkSize*2_HSIZE_T) then
call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr) call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
if(hdferr < 0) error stop 'HDF5 error' if (hdferr < 0) error stop 'HDF5 error'
call h5pset_shuffle_f(dcpl, hdferr) if (HDF5_major == 1 .and. HDF5_minor >= 12) then ! https://forum.hdfgroup.org/t/6186
if(hdferr < 0) error stop 'HDF5 error' call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
call h5pset_deflate_f(dcpl, 6, hdferr) if (hdferr < 0) error stop 'HDF5 error'
if(hdferr < 0) error stop 'HDF5 error' call h5pset_shuffle_f(dcpl, hdferr)
call h5pset_Fletcher32_f(dcpl,hdferr) if (hdferr < 0) error stop 'HDF5 error'
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
endif endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------