unify:read/write: stride optional arg

Author: scivision

src/interface.f90

@@ -104,15 +104,15 @@ module h5mpi
 interface !< write.f90
 module subroutine hdf_create(self, dname, dtype, mem_dims, dset_dims, &
   filespace_id, memspace, dset_id, dtype_id, &
-  istart, iend, chunk_size, compact, charlen)
+  istart, iend, stride, chunk_size, compact, charlen)
 
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 integer(HID_T), intent(in) :: dtype
 integer(HSIZE_T), dimension(:), intent(in) :: mem_dims, dset_dims
 integer(HID_T), intent(out) :: filespace_id, memspace, dset_id
 integer(HID_T), intent(out), optional :: dtype_id
-integer, intent(in), dimension(:), optional :: chunk_size, istart, iend
+integer, intent(in), dimension(:), optional :: chunk_size, istart, iend, stride
 logical, intent(in), optional :: compact
 integer, intent(in), optional :: charlen !< length of character scalar
 end subroutine
@@ -152,59 +152,59 @@ module subroutine h5write_scalar(self, dname, A, compact)
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_1d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_1d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:)
-integer, intent(in), dimension(1), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(1), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_2d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_2d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:)
-integer, intent(in), dimension(2), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(2), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_3d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_3d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:)
-integer, intent(in), dimension(3), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(3), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_4d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_4d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:,:)
-integer, intent(in), dimension(4), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(4), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_5d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_5d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:,:,:)
-integer, intent(in), dimension(5), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(5), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_6d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_6d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:,:,:,:)
-integer, intent(in), dimension(6), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(6), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_7d(self, dname, A, dset_dims, istart, iend, chunk_size, compact)
+module subroutine h5write_7d(self, dname, A, dset_dims, istart, iend, stride, chunk_size, compact)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:,:,:,:,:)
-integer, intent(in), dimension(7), optional :: istart, iend, chunk_size, dset_dims
+integer, intent(in), dimension(7), optional :: chunk_size, istart, iend, stride, dset_dims
 logical, intent(in), optional :: compact
 end subroutine
 
@@ -289,53 +289,53 @@ module subroutine h5read_scalar(self, dname, A)
 class(*), intent(inout)        :: A
 end subroutine
 
-module subroutine h5read_1d(self, dname, A, istart, iend)
+module subroutine h5read_1d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:)
-integer, intent(in), dimension(1), optional :: istart, iend
+integer, intent(in), dimension(1), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_2d(self, dname, A, istart, iend)
+module subroutine h5read_2d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:)
-integer, intent(in), dimension(2), optional :: istart, iend
+integer, intent(in), dimension(2), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_3d(self, dname, A, istart, iend)
+module subroutine h5read_3d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:,:)
-integer, intent(in), dimension(3), optional :: istart, iend
+integer, intent(in), dimension(3), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_4d(self, dname, A, istart, iend)
+module subroutine h5read_4d(self, dname, A,  istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:,:,:)
-integer, intent(in), dimension(4), optional :: istart, iend
+integer, intent(in), dimension(4), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_5d(self, dname, A, istart, iend)
+module subroutine h5read_5d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:,:,:,:)
-integer, intent(in), dimension(5), optional :: istart, iend
+integer, intent(in), dimension(5), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_6d(self, dname, A, istart, iend)
+module subroutine h5read_6d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:,:,:,:,:)
-integer, intent(in), dimension(6), optional :: istart, iend
+integer, intent(in), dimension(6), optional :: istart, iend, stride
 end subroutine
 
-module subroutine h5read_7d(self, dname, A, istart, iend)
+module subroutine h5read_7d(self, dname, A, istart, iend, stride)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout) :: A(:,:,:,:,:,:,:)
-integer, intent(in), dimension(7), optional :: istart, iend
+integer, intent(in), dimension(7), optional :: istart, iend, stride
 end subroutine
 
 end interface
@@ -538,13 +538,14 @@ module logical function is_hdf5(filename)
 character(*), intent(in) :: filename
 end function
 
-module subroutine mpi_hyperslab(mem_dims, dset_dims, dset_id, filespace, memspace, istart, iend)
+module subroutine mpi_hyperslab(mem_dims, dset_dims, dset_id, filespace, memspace, istart, iend, stride)
 !! Each process defines dataset in memory and writes it to the hyperslab in the file.
 integer(HSIZE_T), dimension(:), intent(in) :: mem_dims, dset_dims
 integer(HID_T), intent(in) :: dset_id
 integer(HID_T), intent(inout) :: filespace, memspace
 integer, dimension(:), intent(in) :: istart
 integer, dimension(size(istart)), intent(in) :: iend
+integer, dimension(size(istart)), intent(in), optional :: stride
 end subroutine
 
 module integer(HID_T) function mpi_collective(dname) result(xfer_id)

src/reader.inc

@@ -9,7 +9,7 @@ call h5open_read(self, dname, dims, dset_dims, file_space_id, mem_space_id, dset
 
 if(self%use_mpi) then
   if(present(istart) .and. present(iend)) then
-    call mpi_hyperslab(dims, dset_dims, dset_id, file_space_id, mem_space_id, istart=istart, iend=iend)
+    call mpi_hyperslab(dims, dset_dims, dset_id, file_space_id, mem_space_id, istart=istart, iend=iend, stride=stride)
   endif
   xfer_id = mpi_collective(dname)
 endif

src/utils.f90

@@ -292,7 +292,7 @@
 
 module procedure mpi_hyperslab
 
-integer(HSIZE_T), dimension(size(mem_dims)) :: c_mem_dims, i0
+integer(HSIZE_T), dimension(size(mem_dims)) :: c_mem_dims, i0, istride
 integer(HID_T) :: dcpl
 integer :: ierr
 logical :: filters_OK
@@ -332,6 +332,9 @@
 i0 = istart - 1
 c_mem_dims = iend - i0
 
+istride = 1
+if(present(stride)) istride = int(stride, HSIZE_T)
+
 if(any(c_mem_dims /= mem_dims)) then
   write(stderr,*) "ERROR:h5fortran:mpi_hyperslab: memory size /= dataset size: check variable slice (index). " // &
     " Dset_dims:", dset_dims, "C Mem_dims", c_mem_dims
@@ -344,9 +347,9 @@
 
 call h5sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, &
 start=i0, &
+stride=istride, &
 count=c_mem_dims, &
 hdferr=ierr)
-! stride=1, &  !< for now we don't stride data
 ! block=blk  !< would this help performance?
 
 if (ierr/=0) error stop "g5fortran:mpi_hyperslab:h5sselect_hyperslab: " // dset_name
@@ -387,15 +390,15 @@
 
 !> check for matching rank, else bad reads can occur--doesn't always crash without this check
 call h5ltget_dataset_ndims_f(self%file_id, dname, drank, ierr)
-if (ierr/=0) error stop 'ERROR:h5fortran:rank_check: get_dataset_ndim ' // dname // ' read ' // self%filename
+if (ierr/=0) error stop 'ERROR:h5fortran:rank_check:get_dataset_ndims: ' // dname // ' in ' // self%filename
 
 if (drank == mrank) return
 
 if (present(vector_scalar) .and. drank == 1 .and. mrank == 0) then
   !! check if vector of length 1
   call h5ltget_dataset_info_f(self%file_id, dname, dims=ddims, &
     type_class=type_class, type_size=type_size, errcode=ierr)
-  if (ierr/=0) error stop 'ERROR:h5fortran:rank_check: get_dataset_info ' // dname // ' read ' // self%filename
+  if (ierr/=0) error stop 'ERROR:h5fortran:rank_check:get_dataset_info ' // dname // ' in ' // self%filename
   if (ddims(1) == 1) then
     vector_scalar = .true.
     return

src/writer.inc

@@ -33,12 +33,12 @@ end select
 !> create or open dataset
 call hdf_create(self, dname, dtype, mem_dims=mem_dims, dset_dims=dims_dset, &
 filespace_id=file_space_id, memspace=mem_space_id, dset_id=dset_id, &
-istart=istart, iend=iend, chunk_size=chunk_size, compact=compact, &
+istart=istart, iend=iend, stride=stride, chunk_size=chunk_size, compact=compact, &
 dtype_id=dtype_id, charlen=charlen)
 
 if(self%use_mpi) then
   if(present(dset_dims)) then
-    call mpi_hyperslab(mem_dims, dims_dset, dset_id, file_space_id, mem_space_id, istart=istart, iend=iend)
+    call mpi_hyperslab(mem_dims, dims_dset, dset_id, file_space_id, mem_space_id, istart=istart, iend=iend, stride=stride)
   elseif(self%mpi_id > 0) then
     call h5sselect_none_f(file_space_id, ier)
     if(ier /= 0) error stop "ERROR:h5fortran:writer:h5sselect_none: selecting no write failed for worker. " // dname