add compact write option

add scalar shape test

Author: scivision

src/interface.f90

@@ -77,14 +77,17 @@ module h5mpi
 hdf5version, HSIZE_T
 
 interface !< write.f90
-module subroutine hdf_create(self, dname, dtype, mem_dims, dset_dims, filespace, memspace, dset_id, istart, iend, chunk_size)
+module subroutine hdf_create(self, dname, dtype, mem_dims, dset_dims, filespace, memspace, dset_id, &
+  istart, iend, chunk_size, compact)
+
 class(hdf5_file), intent(inout) :: 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), optional :: filespace, memspace, dset_id
 integer(HSIZE_T), dimension(:), intent(in), optional :: istart, iend
 integer, dimension(:), intent(in), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine hdf_create
 end interface
 
@@ -97,73 +100,81 @@ end subroutine get_hdf5_config
 
 interface !< writer.f90
 
-module subroutine h5write_scalar(self, dname, value)
+module subroutine h5write_scalar(self, dname, value, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value
+logical, intent(in), optional :: compact
 end subroutine h5write_scalar
 
-module subroutine ph5write_1d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_1d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:)
 class(*), intent(in), dimension(1), optional :: dset_dims  !< integer or integer(HSIZE_T) full disk shape (not just per worker)
 integer(HSIZE_T), intent(in), dimension(1), optional :: istart, iend
 integer, intent(in), dimension(1), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_1d
 
-module subroutine ph5write_2d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_2d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:)
 class(*), intent(in), dimension(2), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(2), optional :: istart, iend
 integer, intent(in), dimension(2), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_2d
 
-module subroutine ph5write_3d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_3d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:)
 class(*), intent(in), dimension(3), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(3), optional :: istart, iend
 integer, intent(in), dimension(3), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_3d
 
-module subroutine ph5write_4d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_4d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:)
 class(*), intent(in), dimension(4), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(4), optional :: istart, iend
 integer, intent(in), dimension(4), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_4d
 
-module subroutine ph5write_5d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_5d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:)
 class(*), intent(in), dimension(5), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(5), optional :: istart, iend
 integer, intent(in), dimension(5), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_5d
 
-module subroutine ph5write_6d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_6d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:)
 class(*), intent(in), dimension(6), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(6), optional :: istart, iend
 integer, intent(in), dimension(6), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_6d
 
-module subroutine ph5write_7d(self, dname, value, dset_dims, istart, iend, chunk_size)
+module subroutine ph5write_7d(self, dname, value, dset_dims, istart, iend, chunk_size, compact)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:,:)
 class(*), intent(in), dimension(7), optional :: dset_dims
 integer(HSIZE_T), intent(in), dimension(7), optional :: istart, iend
 integer, intent(in), dimension(7), optional :: chunk_size
+logical, intent(in), optional :: compact
 end subroutine ph5write_7d
 
 end interface
@@ -587,17 +598,16 @@ function hdf5version() result(v)
 end function hdf5version
 
 
-subroutine hdf_flush(self, ierr)
+subroutine hdf_flush(self)
 !! request operating system flush data to disk.
 !! The operating system can do this when it desires, which might be a while.
 class(hdf5_file), intent(in) :: self
-integer, intent(out), optional :: ierr
-integer :: ier
 
-call h5fflush_f(self%file_id, H5F_SCOPE_GLOBAL_F, ier)
+integer :: ierr
+
+call h5fflush_f(self%file_id, H5F_SCOPE_GLOBAL_F, ierr)
 
-if (present(ierr)) ierr = ier
-if (check(ier, 'ERROR: HDF5 flush ' // self%filename) .and. .not.present(ierr)) error stop
+if (ierr /= 0) error stop 'ERROR: HDF5 flush ' // self%filename
 
 end subroutine hdf_flush
 

src/read/reader.in.f90

@@ -7,8 +7,8 @@
 
 module procedure h5read_scalar
 
-integer(HSIZE_T) :: dims(rank(value))
-integer(hid_t) :: dset_id
+integer(HSIZE_T) :: dims(0)
+integer(HID_T) :: dset_id, xfer_id
 integer :: dclass, ier
 
 logical :: vector_scalar
@@ -44,6 +44,10 @@
 
 call get_dset_class(self, dname, dclass, dset_id)
 
+if(self%use_mpi) then
+  xfer_id = mpi_collective(dname)
+endif
+
 !> cast the dataset read from disk to the variable type presented by user h5f%read("/my_dataset", x)
 !> We only cast when needed to save memory.
 !! select case doesn't allow H5T_*

src/read/reader_template.f90

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

src/tests/unit/CMakeLists.txt

@@ -5,7 +5,7 @@ max_gcd(${MPI_MAX} ${MPIEXEC_MAX_NUMPROCS} Nmpi)
 
 message(STATUS "Unit tests using ${Nmpi} processes")
 
-set(test_names deflate_write deflate_props deflate_read scalar shape)
+set(test_names deflate_write deflate_props deflate_read layout shape)
 
 foreach(t IN LISTS test_names)
 
@@ -18,11 +18,28 @@ foreach(t IN LISTS test_names)
 
 endforeach()
 
+# --- write test data
+add_executable(test_write test_write.f90)
+target_link_libraries(test_write PRIVATE h5mpi HDF5::HDF5 MPI::MPI_Fortran)
+
+add_test(NAME write COMMAND test_write)
+set_tests_properties(write PROPERTIES
+FIXTURES_SETUP test_files
+TIMEOUT 10
+)
+
+# --- test dependencies
+
 set_tests_properties(${test_names} PROPERTIES
 TIMEOUT 10
 PROCESSORS ${Nmpi}
 )
 
+set_tests_properties(layout shape PROPERTIES
+FIXTURES_REQUIRED test_files
+REQUIRED_FILES ${CMAKE_CURRENT_BINARY_DIR}/test_write.h5
+)
+
 set_tests_properties(deflate_write PROPERTIES
 FIXTURES_SETUP deflate_files
 )

src/tests/unit/test_layout.f90

@@ -0,0 +1,87 @@
+program test_layout
+
+use, intrinsic :: iso_fortran_env, only : real32, real64, int32
+
+use h5mpi, only : hdf5_file
+
+use hdf5, only : H5D_COMPACT_F
+use mpi, only : mpi_init, MPI_COMM_WORLD, mpi_comm_rank, mpi_barrier
+
+implicit none (type, external)
+
+external :: mpi_finalize
+
+character(*), parameter :: fn = 'test_layout.h5'
+integer :: ierr, mpi_id
+
+call mpi_init(ierr)
+if (ierr /= 0) error stop "mpi_init"
+
+call mpi_comm_rank(MPI_COMM_WORLD, mpi_id, ierr)
+if (ierr /= 0) error stop "mpi_comm_rank"
+
+call test_layout_read(fn)
+if(mpi_id == 0) print *, "OK: read layout"
+
+call test_layout_props(fn)
+if(mpi_id == 0) print *, "OK: layout props"
+
+call mpi_finalize(ierr)
+
+contains
+
+
+subroutine test_layout_read(fn)
+
+character(*), intent(in) :: fn
+
+type(hdf5_file) :: h
+
+real(real32) :: r32
+real(real64) :: r64
+integer(int32) :: i32
+
+real(real32), dimension(1,1,1,1,1,1,1) :: r7_32
+real(real64), dimension(1,1,1,1,1,1,1) :: r7_64
+
+!> read casting
+call h%open(fn, action="r", mpi=.true.)
+
+call h%read("/compact_r32", r64)
+if(r64 /= 142) error stop "read real32 => real64"
+call h%read("/compact_r64", r32)
+if(r32 /= 142) error stop "read real64 => real32"
+call h%read("/compact_i32", i32)
+if(r32 /= 142) error stop "read int32 => int32"
+
+
+call h%read("/compact7d_32", r7_64)
+if (any(r7_64 /= 42)) error stop "read real32 => real64"
+
+call h%read("/compact7d_64", r7_32)
+if (any(r7_32 /= 42)) error stop "read real64 => real32"
+
+call h%close()
+
+end subroutine test_layout_read
+
+
+subroutine test_layout_props(fn)
+
+character(*), intent(in) :: fn
+
+type(hdf5_file) :: h
+
+call h%open(fn, action="r", mpi=.true.)
+
+if (h%layout("/compact1d") /= H5D_COMPACT_F) error stop "expected compact"
+if (.not. h%is_compact("/compact1d")) error stop "1d is_compact fail"
+
+if (.not. h%is_compact("/compact7d_32")) error stop "7d is_compact fail"
+if (.not. h%is_compact("/compact0d")) error stop "0d is_compact fail"
+
+call h%close()
+
+end subroutine test_layout_props
+
+end program