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avoid HDF5 error in case of empty dataset

This commit is contained in:
Martin Diehl 2022-10-19 20:46:17 +02:00
parent 51f0ac5d01
commit bf0113a737
2 changed files with 40 additions and 70 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit 583beecdcf806c5249574fd599f0b763f3461c3b
Subproject commit 36c2fe3cde7fc1397ddd0fef71b2f4b40b72bba8

108
src/HDF5_utilities.f90
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@ -673,13 +673,9 @@ subroutine HDF5_read_real1(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -687,6 +683,7 @@ subroutine HDF5_read_real1(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -713,13 +710,9 @@ subroutine HDF5_read_real2(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -727,6 +720,7 @@ subroutine HDF5_read_real2(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -753,13 +747,9 @@ subroutine HDF5_read_real3(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -767,6 +757,7 @@ subroutine HDF5_read_real3(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -793,13 +784,10 @@ subroutine HDF5_read_real4(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -807,6 +795,7 @@ subroutine HDF5_read_real4(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -833,13 +822,10 @@ subroutine HDF5_read_real5(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -847,6 +833,7 @@ subroutine HDF5_read_real5(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -873,13 +860,10 @@ subroutine HDF5_read_real6(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -887,6 +871,7 @@ subroutine HDF5_read_real6(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -913,13 +898,10 @@ subroutine HDF5_read_real7(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -927,6 +909,7 @@ subroutine HDF5_read_real7(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -955,13 +938,8 @@ subroutine HDF5_read_int1(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -969,6 +947,7 @@ subroutine HDF5_read_int1(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -995,13 +974,10 @@ subroutine HDF5_read_int2(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1009,6 +985,7 @@ subroutine HDF5_read_int2(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -1035,13 +1012,9 @@ subroutine HDF5_read_int3(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1049,6 +1022,7 @@ subroutine HDF5_read_int3(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -1075,13 +1049,9 @@ subroutine HDF5_read_int4(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1089,6 +1059,7 @@ subroutine HDF5_read_int4(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -1115,13 +1086,9 @@ subroutine HDF5_read_int5(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
myShape = int(shape(dataset),HSIZE_T)
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1129,6 +1096,7 @@ subroutine HDF5_read_int5(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -1155,13 +1123,10 @@ subroutine HDF5_read_int6(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1169,6 +1134,7 @@ subroutine HDF5_read_int6(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -1195,13 +1161,10 @@ subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
@ -1209,6 +1172,7 @@ subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
end if
if (any(totalShape == 0)) return
call H5Dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
@ -2031,6 +1995,12 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
if (any(globalShape == 0)) then
call H5Pclose_f(plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
return
end if
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call H5Screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)