add read/write stride= option

Author: scivision

src/interface.f90

@@ -78,10 +78,10 @@ module subroutine nc_create(self, dset_name, dtype, dims, dim_names, chunk_size,
 integer, intent(out), optional :: varid
 end subroutine
 
-module subroutine def_dims(self, dname, dimnames, dims, dimids)
+module subroutine def_dims(self, dname, dim_names, dims, dimids)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
-character(*), intent(in), optional :: dimnames(:)
+character(*), intent(in), optional :: dim_names(:)
 integer, intent(in) :: dims(:)
 integer, intent(out) :: dimids(size(dims))
 end subroutine
@@ -100,66 +100,66 @@ module subroutine nc_write_scalar(self, dname, value)
 class(*), intent(in) :: value
 end subroutine
 
-module subroutine nc_write_1d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_1d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:)
 character(*), intent(in), optional :: dims(1)
-integer, intent(in), dimension(1), optional :: istart, iend
+integer, intent(in), dimension(1), optional :: istart, iend, stride
 integer, intent(in), dimension(1), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_2d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_2d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:)
 character(*), intent(in), optional :: dims(2)
-integer, intent(in), dimension(2), optional :: istart, iend
+integer, intent(in), dimension(2), optional :: istart, iend, stride
 integer, intent(in), dimension(2), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_3d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_3d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:)
 character(*), intent(in), optional :: dims(3)
-integer, intent(in), dimension(3), optional :: istart, iend
+integer, intent(in), dimension(3), optional :: istart, iend, stride
 integer, intent(in), dimension(3), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_4d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_4d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:)
 character(*), intent(in), optional :: dims(4)
-integer, intent(in), dimension(4), optional :: istart, iend
+integer, intent(in), dimension(4), optional :: istart, iend, stride
 integer, intent(in), dimension(4), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_5d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_5d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:)
 character(*), intent(in), optional :: dims(5)
-integer, intent(in), dimension(5), optional :: istart, iend
+integer, intent(in), dimension(5), optional :: istart, iend, stride
 integer, intent(in), dimension(5), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_6d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_6d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:)
 character(*), intent(in), optional :: dims(6)
-integer, intent(in), dimension(6), optional :: istart, iend
+integer, intent(in), dimension(6), optional :: istart, iend, stride
 integer, intent(in), dimension(6), optional :: chunk_size
 end subroutine
 
-module subroutine nc_write_7d(self, dname, value, dims, istart, iend, chunk_size)
+module subroutine nc_write_7d(self, dname, value, dims, istart, iend, stride, chunk_size)
 class(netcdf_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: value(:,:,:,:,:,:,:)
 character(*), intent(in), optional :: dims(7)
-integer, intent(in), dimension(7), optional :: istart, iend
+integer, intent(in), dimension(7), optional :: istart, iend, stride
 integer, intent(in), dimension(7), optional :: chunk_size
 end subroutine
 
@@ -208,53 +208,53 @@ module subroutine nc_read_scalar(self, dname, value)
 !! inout for character
 end subroutine
 
-module subroutine nc_read_1d(self, dname, value, istart, iend)
+module subroutine nc_read_1d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:)
-integer, intent(in), dimension(1), optional :: istart, iend
+integer, intent(in), dimension(1), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_2d(self, dname, value, istart, iend)
+module subroutine nc_read_2d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:)
-integer, intent(in), dimension(2), optional :: istart, iend
+integer, intent(in), dimension(2), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_3d(self, dname, value, istart, iend)
+module subroutine nc_read_3d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:,:)
-integer, intent(in), dimension(3), optional :: istart, iend
+integer, intent(in), dimension(3), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_4d(self, dname, value, istart, iend)
+module subroutine nc_read_4d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:,:,:)
-integer, intent(in), dimension(4), optional :: istart, iend
+integer, intent(in), dimension(4), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_5d(self, dname, value, istart, iend)
+module subroutine nc_read_5d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:,:,:,:)
-integer, intent(in), dimension(5), optional :: istart, iend
+integer, intent(in), dimension(5), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_6d(self, dname, value, istart, iend)
+module subroutine nc_read_6d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:,:,:,:,:)
-integer, intent(in), dimension(6), optional :: istart, iend
+integer, intent(in), dimension(6), optional :: istart, iend, stride
 end subroutine
 
-module subroutine nc_read_7d(self, dname, value, istart, iend)
+module subroutine nc_read_7d(self, dname, value, istart, iend, stride)
 class(netcdf_file), intent(in)     :: self
 character(*), intent(in)         :: dname
 class(*), intent(inout)      :: value(:,:,:,:,:,:,:)
-integer, intent(in), dimension(7), optional :: istart, iend
+integer, intent(in), dimension(7), optional :: istart, iend, stride
 end subroutine
 
 end interface

src/reader.inc

@@ -20,13 +20,13 @@ endif
 
 select type (value)
 type is (real(real64))
-  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (real(real32))
-  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (integer(int64))
-  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (integer(int32))
-  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_get_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 class default
   ier = NF90_EBADTYPE
 end select

src/utils.f90

@@ -1,5 +1,7 @@
 submodule (nc4fortran) utils
 
+use netcdf, only : NF90_STRERROR
+
 implicit none (type, external)
 
 contains
@@ -28,7 +30,7 @@
 case('r')
   ier = nf90_open(self%filename, NF90_NOWRITE, self%file_id)
 case('r+')
-  ier = nf90_open(self%filename, NF90_NETCDF4, self%file_id)
+  ier = nf90_open(self%filename, NF90_WRITE, self%file_id)
 case('rw', 'a')
   if(is_netcdf(filename)) then
     !! NF90_WRITE is necessary to be in true read/write mode
@@ -122,47 +124,10 @@
 
 
 module procedure check_error
-character(:), allocatable :: m
-
-check_error = .true.
-
-select case (code)
-case (NF90_NOERR)
-  check_error = .false.
-case (NF90_EHDFERR)
-  m = 'ERROR: ' // dname // ' an error was reported by the HDF5 layer.'
-case (NF90_EBADNAME)
-  m = 'ERROR: ' // dname // ' Name contains illegal characters.'
-case (NF90_EBADTYPE)
-  m = 'ERROR: ' // dname // ' specified type is not a valid netCDF type'
-case (NF90_EDIMSIZE)
-  m = 'ERROR: ' // dname // ' bad dimension size'
-case (NF90_EBADDIM)
-  m = 'ERROR: ' // dname // ' invalid dimension ID or Name'
-case (NF90_EBADGRPID)
-  m = 'ERROR: ' // dname // ' bad group ID in file_id'
-case (NF90_EBADID)
-  m = 'ERROR: ' // dname // ' Bad group id or file_id invalid'
-case (NF90_ENOTVAR)
-  m = 'ERROR: ' // dname // ' variable not found'
-case (NF90_ENOTNC)
-  m = 'ERROR: ' // dname // ' not a NetCDF file'
-case (NF90_ENAMEINUSE)
-  m = 'ERROR: ' // dname // ' That name is in use. Compound type names must be unique in the data file.'
-case (NF90_ECHAR)
-  m = 'ERROR: ' // dname // ' attempt to convert between text & numbers'
-case (NF90_EEDGE)
-  m = 'ERROR: ' // dname // ' edge + start exceeds dimension bound'
-case (NF90_ESTRIDE)
-  m = 'ERROR: ' // dname // ' illegal stride'
-case (NF90_EINDEFINE)
-  m = 'ERROR: ' // dname // ' operation not allowed in define mode'
-case default
-  write(stderr,'(/,A,I8)') 'ERROR: ' // dname // ' unknown error',code
-  m = ''
-end select
 
-if(check_error) write(stderr,'(/,A)') m
+check_error = code /= NF90_NOERR
+
+if(check_error) write(stderr,'(/,A)') "ERROR:nc4fortran:" // NF90_STRERROR(code)
 
 end procedure check_error
 

src/write.f90

@@ -11,7 +11,7 @@
 
 integer :: var_id, dimids(size(dims)), ier
 
-call def_dims(self, dset_name, dimnames=dim_names, dims=dims, dimids=dimids)
+call def_dims(self, dset_name, dim_names, dims=dims, dimids=dimids)
 
 if(present(chunk_size)) then
   ier = nf90_def_var(self%file_id, dset_name, dtype, dimids=dimids, varid=var_id, &
@@ -102,19 +102,20 @@ end subroutine filler
 if(.not.self%is_open) error stop 'ERROR:nc4fortran:write:def_dims: file handle not open'
 
 do i=1,size(dims)
-  if (present(dimnames)) then
-    ierr = nf90_inq_dimid(self%file_id, dimnames(i), dimids(i))
+  if(present(dim_names)) then
+    ierr = nf90_inq_dimid(self%file_id, dim_names(i), dimids(i))
     if(ierr==NF90_NOERR) cycle
     !! dimension already exists
   endif
-  !! create new dimension
-  if(present(dimnames)) then
-    ierr = nf90_def_dim(self%file_id, dimnames(i), dims(i), dimids(i))
+
+  !> create new dimension
+  if(present(dim_names)) then
+    ierr = nf90_def_dim(self%file_id, dim_names(i), dims(i), dimids(i))
   else
     write(name,'(A,A4,I1)') dname,"_dim",i
     ierr = nf90_def_dim(self%file_id, trim(name), dims(i), dimids(i))
-    ! print *,trim(name)
   endif
+  if(self%debug) print '(a,i1,a)', "TRACE:def_dims: dimension ", i, " name: " // trim(name)
   if (check_error(ierr, dname)) error stop "ERROR:nc4fortran:write def_dim " // dname // " in " // self%filename
 end do
 

src/writer.inc

@@ -28,13 +28,13 @@ endif
 
 select type (value)
 type is (real(real32))
-  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (real(real64))
-  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (integer(int32))
-  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 type is (integer(int64))
-  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i)
+  ier = nf90_put_var(self%file_id, varid, value, start=istart, count=i, stride=stride)
 class default
   ier = NF90_EBADTYPE
 end select