enhance use of chunk_size per-variable

Author: scivision

CMakeLists.txt

@@ -4,7 +4,7 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 project(hdf5iface
   LANGUAGES Fortran
-  VERSION 2.3.1
+  VERSION 2.4.0
   HOMEPAGE_URL https://github.com/scivision/h5fortran)
 enable_testing()
 

README.md

@@ -187,6 +187,11 @@ call h5f%finalize(ierr)
 
 chunk_size may optionally be set in the `%write()` method.
 
+compression and chunking are disabled if:
+
+* any element of chunk_size is less than 1
+* chunk_size is not given in the initialize() call AND not specified in %write()
+
 ### Read scalar, 3-D array of unknown size
 
 ```fortran

meson.build

@@ -1,6 +1,6 @@
 project('h5fortran', 'fortran',
   meson_version : '>=0.52.0',
-  version : '2.3.1',
+  version : '2.4.0',
   default_options : ['default_library=static', 'buildtype=release', 'warning_level=3'])
 
 subdir('meson')

src/hdf5_interface.f90

@@ -13,13 +13,14 @@ module h5fortran
 type :: hdf5_file
 
 character(:),allocatable  :: filename
-integer(HID_T) :: lid, &   !< location identifier
-                  gid, &    !< group identifier
-                  glid, &   !< group location identifier
-                  sid, did, pid
-
-integer  :: comp_lvl = 0 !< compression level (1-9)  0: disable compression
-integer(HSIZE_T) :: chunk_size(7) = [64,64,1,1,1,1,1]  !< chunk size per dimension (arbitrary)
+integer(HID_T) :: lid, &   !< location ID
+                  gid, &    !< group ID
+                  glid, &   !< group location ID
+                  sid, &   !< dataspace ID
+                  did      !< dataset ID
+
+integer :: comp_lvl = 0 !< compression level (1-9)  0: disable compression
+integer(HSIZE_T) :: chunk_size(7) = [1,1,1,1,1,1,1]  !< chunk size per dimension
 logical :: verbose=.false.
 
 contains
@@ -70,10 +71,11 @@ module subroutine hdf_wrapup(self, ierr)
 integer, intent(out) :: ierr
 end subroutine hdf_wrapup
 
-module subroutine hdf_set_deflate(self, dims, ierr)
+module subroutine hdf_set_deflate(self, dims, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 integer(HSIZE_T), intent(in) :: dims(:)
 integer, intent(out) :: ierr
+integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_set_deflate
 
 module subroutine hdf_write_scalar(self,dname,value, ierr)
@@ -94,47 +96,47 @@ module subroutine hdf_write_2d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_2d
 
 module subroutine hdf_write_3d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_3d
 
 module subroutine hdf_write_4d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_4d
 
 module subroutine hdf_write_5d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_5d
 
 module subroutine hdf_write_6d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_6d
 
 module subroutine hdf_write_7d(self,dname,value, ierr, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:,:)
-integer, intent(in), optional :: chunk_size(:)
+integer, intent(in), optional :: chunk_size(rank(value))
 integer, intent(out) :: ierr
 end subroutine hdf_write_7d
 
@@ -232,7 +234,7 @@ end subroutine writeattr
 contains
 
 
-subroutine hdf_initialize(self,filename,ierr, status,action,comp_lvl)
+subroutine hdf_initialize(self,filename,ierr, status,action,comp_lvl,chunk_size)
 !! Opens hdf5 file
 
 class(hdf5_file), intent(inout)    :: self
@@ -241,16 +243,17 @@ subroutine hdf_initialize(self,filename,ierr, status,action,comp_lvl)
 character(*), intent(in), optional :: status
 character(*), intent(in), optional :: action
 integer, intent(in), optional      :: comp_lvl
+integer, intent(in), optional      :: chunk_size(:)
 
 character(:), allocatable :: lstatus, laction
 logical :: exists
 
-self%pid = 0
 self%sid = 0
 !! arbitrary sentinel values, telling us it hasn't been used by HDF5
 self%filename = filename
 
 if (present(comp_lvl)) self%comp_lvl = comp_lvl
+if (present(chunk_size)) self%chunk_size(1:size(chunk_size)) = chunk_size
 
 !> Initialize FORTRAN interface.
 call h5open_f(ierr)

src/string_utils.f90

@@ -19,7 +19,7 @@ elemental function toLower(str)
 
 toLower = str
 
-do concurrent (i = 1:len(str))
+do i = 1,len(str)
   j = index(upper,str(i:i))
   if (j > 0) toLower(i:i) = lower(j:j)
 end do

src/write.f90

@@ -55,10 +55,8 @@
 if(exists) then
   !> open dataset
   call h5dopen_f(self%lid, dname, self%did, ierr)
-  if (ierr /= 0) then
-    write(stderr,*) 'ERROR: open ' // dname // ' ' // self%filename
-    return
-  endif
+  if (ierr /= 0) write(stderr,*) 'ERROR: open ' // dname // ' ' // self%filename
+  return
 else
   call self%write(dname, ierr)
   if (ierr /= 0) then
@@ -67,16 +65,7 @@
   endif
 endif
 
-if(size(dims) >= 2) then
-  if (present(chunk_size)) self%chunk_size(:size(dims)) = chunk_size
-
-  call hdf_set_deflate(self, dims, ierr)
-else
-  self%pid = 0
-  !! sentinel value for unused property
-endif
-
-if(exists) return
+if(size(dims) >= 2) call hdf_set_deflate(self, dims, ierr, chunk_size)
 
 if(size(dims) == 0) then
   call h5screate_f(H5S_SCALAR_F, self%sid, ierr)
@@ -89,7 +78,7 @@
 endif
 
 if(size(dims) >= 2) then
-  call h5dcreate_f(self%lid, dname, dtype, self%sid, self%did, ierr, self%pid)
+  call h5dcreate_f(self%lid, dname, dtype, self%sid, self%did, ierr)
 else
   call h5dcreate_f(self%lid, dname, dtype, self%sid, self%did, ierr)
 endif
@@ -100,42 +89,50 @@
 
 module procedure hdf_set_deflate
 
-integer :: ndims, i
-integer(HSIZE_T), allocatable :: chunk_size(:)
-
+integer :: i
+integer(HSIZE_T) :: cs(size(dims))
+integer(HID_T) :: pid
 
-ndims = size(dims)
-allocate(chunk_size(ndims))
+if (self%comp_lvl < 1 .or. self%comp_lvl > 9) return
+if (.not.present(chunk_size) .and. all(self%chunk_size == 1) .or. any(self%chunk_size < 1)) return
+if (present(chunk_size)) then
+  if (any(chunk_size < 1)) return
+endif
 
-do i=1,ndims
-  chunk_size(i) = min(self%chunk_size(i), dims(i))
-enddo
+if (present(chunk_size)) then
+  cs = chunk_size
+else
+  do i = 1,size(dims)
+    cs(i) = min(self%chunk_size(i), dims(i))
+  enddo
+endif
 
-if (self%verbose) print *,'dims: ',dims,'chunk size: ',chunk_size
+if (self%verbose) print *,'dims: ',dims,'chunk size: ', cs
 
-call h5pcreate_f(H5P_DATASET_CREATE_F, self%pid, ierr)
+call h5pcreate_f(H5P_DATASET_CREATE_F, pid, ierr)
 if (ierr /= 0) then
   write(stderr,*) 'ERROR: create property ' // self%filename
   return
 endif
 
-call h5pset_chunk_f(self%pid, ndims, chunk_size, ierr)
+call h5pset_chunk_f(pid, size(dims), cs, ierr)
 if (ierr /= 0) then
   write(stderr,*) 'ERROR: set chunk ' // self%filename
   return
 endif
 
 if (self%comp_lvl < 1 .or. self%comp_lvl > 9) return
 
-call h5pset_shuffle_f(self%pid, ierr)
-if (ierr /= 0) then
-  write(stderr,*) 'ERROR: enable Shuffle ' // self%filename
-  return
-endif
+!! let these errors continue to close property
+call h5pset_shuffle_f(pid, ierr)
+if (ierr /= 0) write(stderr,*) 'ERROR: enable Shuffle ' // self%filename
 
-call h5pset_deflate_f(self%pid, self%comp_lvl, ierr)
+call h5pset_deflate_f(pid, self%comp_lvl, ierr)
 if (ierr /= 0) write(stderr,*) 'ERROR: enable Deflate compression ' // self%filename
 
+call h5pclose_f(pid, ierr)
+if (ierr /= 0) write(stderr,*) 'ERROR: close property: ', pid, self%filename
+
 end procedure hdf_set_deflate
 
 
@@ -149,14 +146,6 @@
   endif
 endif
 
-if(self%pid /= 0) then
-  call h5pclose_f(self%pid, ierr)
-  if (ierr /= 0) then
-    write(stderr,*) 'ERROR: close property: ', self%pid, self%filename
-    return
-  endif
-endif
-
 call h5dclose_f(self%did, ierr)
 if (ierr /= 0) write(stderr,*) 'ERROR: close dataset: ',self%did, self%filename