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keep order of objects in groups
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@MarDiehl
MarDiehl committed Dec 18, 2024
1 parent a14503c commit f1603fe
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Showing 2 changed files with 52 additions and 26 deletions.
51 changes: 31 additions & 20 deletions src/HDF5_utilities.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -190,49 +190,49 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
logical, intent(in), optional :: parallel

character :: m
integer(HID_T) :: p_access,p_create
integer(HID_T) :: plist_access_id,plist_create_id
integer :: hdferr
logical :: exist


m = misc_optional(mode,'r')

call H5Pcreate_f(H5P_FILE_CREATE_F, p_create, hdferr)
call H5Pcreate_f(H5P_FILE_CREATE_F,plist_create_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
call H5Pset_link_creation_order_f(p_create, ior(H5P_CRT_ORDER_INDEXED_F,H5P_CRT_ORDER_TRACKED_F), hdferr)
call H5Pset_link_creation_order_f(plist_create_id,ior(H5P_CRT_ORDER_INDEXED_F,H5P_CRT_ORDER_TRACKED_F),hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

call H5Pcreate_f(H5P_FILE_ACCESS_F, p_access, hdferr)
call H5Pcreate_f(H5P_FILE_ACCESS_F, plist_access_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
#ifdef PETSC
if (misc_optional(parallel,.true.)) &
#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
call H5Pset_fapl_mpio_f(p_access, PETSC_COMM_WORLD, MPI_INFO_NULL_F90, hdferr)
call H5Pset_fapl_mpio_f(plist_access_id, PETSC_COMM_WORLD, MPI_INFO_NULL_F90, hdferr)
#else
call H5Pset_fapl_mpio_f(p_access, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
call H5Pset_fapl_mpio_f(plist_access_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
#endif
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
#endif

if (m == 'w') then
call H5Fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,&
access_prp=p_access,creation_prp=p_create)
access_prp=plist_access_id,creation_prp=plist_create_id)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
elseif (m == 'a') then
call H5Fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp=p_access)
call H5Fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp=plist_access_id)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
elseif (m == 'r') then
inquire(file=fileName,exist=exist)
if (.not. exist) call IO_error(100,trim(fileName))
call H5Fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp=p_access)
call H5Fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp=plist_access_id)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
else
error stop 'unknown access mode'
end if

call H5Pclose_f(p_access, hdferr)
call H5Pclose_f(plist_access_id, hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
call H5Pclose_f(p_create, hdferr)
call H5Pclose_f(plist_create_id, hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

end function HDF5_openFile
Expand All @@ -247,6 +247,7 @@ subroutine HDF5_closeFile(fileHandle)

integer :: hdferr


call H5Fclose_f(fileHandle,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

Expand All @@ -262,26 +263,35 @@ integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
character(len=*), intent(in) :: groupName

integer :: hdferr
integer(HID_T) :: aplist_id
integer(HID_T) :: gapl_id, gcpl_id

!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call H5Pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

!-------------------------------------------------------------------------------------------------
! setting I/O mode to collective
! set I/O mode to collective (for MPI parallel simulations)
call H5Pcreate_f(H5P_GROUP_ACCESS_F,gapl_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
#ifdef PETSC
call H5Pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
call H5Pset_all_coll_metadata_ops_f(gapl_id,.true.,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
#endif

!-------------------------------------------------------------------------------------------------
! keep creation order in group
call H5Pcreate_f(H5P_GROUP_CREATE_F,gcpl_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
call H5Pset_link_creation_order_f(gcpl_id,ior(H5P_CRT_ORDER_INDEXED_F,H5P_CRT_ORDER_TRACKED_F),hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

!-------------------------------------------------------------------------------------------------
! Create group
call H5Gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id)
call H5Gcreate_f(fileHandle,trim(groupName),HDF5_addGroup,hdferr, &
OBJECT_NAMELEN_DEFAULT_F,gcpl_id=gcpl_id,gapl_id=gapl_id)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

call H5Pclose_f(aplist_id,hdferr)
call H5Pclose_f(gcpl_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))
call H5Pclose_f(gapl_id,hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

end function HDF5_addGroup

Expand Down Expand Up @@ -331,6 +341,7 @@ subroutine HDF5_closeGroup(group_id)

integer :: hdferr


call H5Gclose_f(group_id, hdferr)
call HDF5_chkerr(hdferr,__FILE__//':'//IO_intAsStr(__LINE__))

Expand Down
27 changes: 21 additions & 6 deletions src/test/test_HDF5_utilities.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ end subroutine test_HDF5_utilities_run

subroutine read_write()

integer(HID_T) :: f, create_list
integer(HID_T) :: f,g, plist_create_id
integer :: hdferr, order

real(pREAL), dimension(3) :: real_d1_in,real_d1_out
Expand Down Expand Up @@ -89,20 +89,35 @@ subroutine read_write()
if (any(int_d4_in /= int_d4_out)) error stop 'test_read_write(w)/int_d4'
if (any(int_d5_in /= int_d5_out)) error stop 'test_read_write(w)/int_d5'

call HDF5_closeGroup(HDF5_addGroup(f,'grp'))

call HDF5_closeFile(f)


f = HDF5_openFile('test.hdf5','r')
call H5Fget_create_plist_f(f,create_list,hdferr)

call H5Fget_create_plist_f(f,plist_create_id,hdferr)
call HDF5_chkerr(hdferr)
call H5Pget_link_creation_order_f(create_list,order,hdferr)
call H5Pget_link_creation_order_f(plist_create_id,order,hdferr)
call HDF5_chkerr(hdferr)
! https://github.com/HDFGroup/hdf5/issues/5183
!if (iand(order,H5P_CRT_ORDER_INDEXED_F) /= H5P_CRT_ORDER_INDEXED_F) error stop 'CRT_ORDER_INDEXED'
!if (iand(order,H5P_CRT_ORDER_TRACKED_F) /= H5P_CRT_ORDER_TRACKED_F) error stop 'CRT_ORDER_TRACKED'
call H5Pclose_f(create_list,hdferr)
!if (iand(order,H5P_CRT_ORDER_INDEXED_F) /= H5P_CRT_ORDER_INDEXED_F) error stop 'CRT_ORDER_INDEXED/file'
!if (iand(order,H5P_CRT_ORDER_TRACKED_F) /= H5P_CRT_ORDER_TRACKED_F) error stop 'CRT_ORDER_TRACKED/file'
call H5Pclose_f(plist_create_id,hdferr)
call HDF5_chkerr(hdferr)

g = HDF5_openGroup(f,'grp')
call H5Gget_create_plist_f(g,plist_create_id,hdferr)
call HDF5_chkerr(hdferr,'H5Gget_create_plist_f')
call H5Pget_link_creation_order_f(plist_create_id,order,hdferr)
call HDF5_chkerr(hdferr,'H5Pget_link_creation_order_f')
if (iand(order,H5P_CRT_ORDER_INDEXED_F) /= H5P_CRT_ORDER_INDEXED_F) error stop 'CRT_ORDER_INDEXED/group'
if (iand(order,H5P_CRT_ORDER_TRACKED_F) /= H5P_CRT_ORDER_TRACKED_F) error stop 'CRT_ORDER_TRACKED/group'
call H5Pclose_f(plist_create_id,hdferr)
call HDF5_chkerr(hdferr,'H5Pclose_f')
call HDF5_closeGroup(g)


call HDF5_read(real_d1_out,f,'real_d1')
call HDF5_read(real_d2_out,f,'real_d2')
call HDF5_read(real_d3_out,f,'real_d3')
Expand Down

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