Compressed state option for MITgcm_ocean NBLING

assimilation_code/modules/utilities/netcdf_utilities_mod.f90

@@ -2415,7 +2415,7 @@ function nc_create_file(filename, context)
 character(len=*), parameter :: routine = 'nc_create_file'
 integer :: ret, ncid, oldmode
 
-ret = nf90_create(filename, NF90_CLOBBER, ncid)
+ret = nf90_create(filename, ior(NF90_CLOBBER,NF90_64BIT_OFFSET), ncid)
 call nc_check(ret, routine, 'create '//trim(filename)//' read/write', context)
 
 call add_fh_to_list(ncid, filename)

assimilation_code/programs/model_mod_check/model_mod_check.f90

@@ -416,7 +416,7 @@ subroutine check_meta_data( iloc )
                                    kind_index=qty_index, &
                                    kind_string=qty_string)
 
-write(string1,'("index ",i11," is i,j,k",3(1x,i4)," and is in domain ",i2)') &
+write(string1,'("index ",i11," is i,j,k",3(1x,i10)," and is in domain ",i2)') &
                   iloc, ix, iy, iz, dom_id
 write(string2,'("is quantity ", I4,", ",A)') var_type, trim(qty_string)//' at location'
 call write_location(0,loc,charstring=string3)
@@ -556,9 +556,12 @@ subroutine check_all_meta_data()
                                    kind_string=qty_string)
 
    ! CLM has (potentially many) columns and needs i7 ish precision
-   write(string1,'(i11,1x,''i,j,k'',3(1x,i7),'' domain '',i2)') &
+!    write(string1,'(i11,1x,''i,j,k'',3(1x,i7),'' domain '',i2)') &
+!                   iloc, ix, iy, iz, dom_id
+   ! EL: integer to short for the new I/O method
+   ! Change to long int to avoid problems
+   write(string1,'(i21,1x,''i,j,k'',3(1x,i21),'' domain '',i2)') &
                   iloc, ix, iy, iz, dom_id
-
    call get_state_meta_data(iloc, loc, var_type)
    metadata_qty_string = trim(get_name_for_quantity(var_type))
 

models/MITgcm_ocean/expand_netcdf.f90

@@ -0,0 +1,149 @@
+! Uncompress a netcdf fil
+program expand_netcdf
+
+use netcdf_utilities_mod, only: nc_open_file_readonly, nc_get_dimension_size, &
+                                nc_define_dimension, nc_create_file, &
+                                nc_get_variable, nc_close_file, nc_put_variable, &
+                                nc_define_real_variable, nc_end_define_mode, &
+                                nc_add_attribute_to_variable
+
+use types_mod,        only : r4, MISSING_R4
+
+use utilities_mod,    only : initialize_utilities, finalize_utilities
+
+use netcdf
+
+implicit none
+
+integer :: ncid, ncid_comp, dimid(1), dimlen, ret
+integer :: Nx,Ny,Nz
+integer :: nvars ! total number of variables in compressed file
+integer :: id, n, c! loop variables
+integer :: i,j,k, ncomp3d, ncomp2d
+character(len=NF90_MAX_NAME) :: varname
+real(r4), allocatable :: vals3d(:,:,:), vals2d(:,:), vals_comp(:)
+integer, allocatable :: Xcomp_ind(:), Ycomp_ind(:), Zcomp_ind(:)
+
+call initialize_utilities('expand_netcdf')
+
+ncid_comp = nc_open_file_readonly('compressed.nc')
+ncid = nc_create_file('expanded.nc')
+
+! get the Nx,Ny,Nz
+Nx = nc_get_dimension_size(ncid_comp, 'XC')
+Ny = nc_get_dimension_size(ncid_comp, 'YC')
+Nz = nc_get_dimension_size(ncid_comp, 'ZC')
+
+! define Nx,Ny,Nz in the expanded file
+call nc_define_dimension(ncid, 'X', Nx)
+call nc_define_dimension(ncid, 'Y', Ny)
+call nc_define_dimension(ncid, 'Z', Nz)
+
+! get the compressed size
+ncomp2d = nc_get_dimension_size(ncid_comp, 'comp2d')
+ncomp3d = nc_get_dimension_size(ncid_comp, 'comp3d')
+
+allocate(vals_comp(ncomp3d))
+allocate(vals2d(Nx,Ny), vals3d(Nx,Ny,Nz))
+
+! read in
+allocate(Xcomp_ind(ncomp3d), Ycomp_ind(ncomp3d), Zcomp_ind(ncomp3d))
+call nc_get_variable(ncid_comp, 'Ycomp_ind', Ycomp_ind)
+call nc_get_variable(ncid_comp, 'Xcomp_ind', Xcomp_ind)
+call nc_get_variable(ncid_comp, 'Zcomp_ind', Zcomp_ind)
+
+
+! get the number of variables
+ret = nf90_inquire(ncid_comp, nVariables=nvars)
+
+! define variables
+do id = 1, nvars
+   ret = nf90_inquire_variable(ncid_comp, id, varname, dimids=dimid)
+
+   !  is a it a compressed state variable?
+   if (var_of_interest(varname)) then
+
+      ! inquire dimention length (2d or 3d)
+      ret = nf90_inquire_dimension(ncid_comp, dimid(1), len=dimlen)
+
+      ! define expanded variable
+      if (dimlen == ncomp3d) then
+         call nc_define_real_variable(ncid, varname, (/'X','Y','Z'/))
+      else
+         call nc_define_real_variable(ncid, varname, (/'X','Y'/))
+      endif
+
+      call nc_add_attribute_to_variable(ncid, varname, 'missing_value', MISSING_R4)
+
+   endif
+enddo
+
+call nc_end_define_mode(ncid)
+
+! write variables
+do id = 1, nvars
+   ret = nf90_inquire_variable(ncid_comp, id, varname, dimids=dimid)
+
+   !  is a it a compressed state variable?
+   if (var_of_interest(varname)) then
+
+      ! inquire dimention length (2d or 3d)
+      ret = nf90_inquire_dimension(ncid_comp, dimid(1), len=dimlen)
+
+      ! read in compressed variable
+      if (dimlen == ncomp3d) then
+         call nc_get_variable(ncid_comp, varname, vals_comp)
+         vals3d = MISSING_R4
+      else
+         call nc_get_variable(ncid_comp, varname, vals_comp(1:ncomp2d))
+         vals2d = MISSING_R4
+      endif
+
+      ! expand
+      c = 1
+      do n = 1, ncomp3d
+         i = Xcomp_ind(n)
+         j = Ycomp_ind(n)
+         k = Zcomp_ind(n)
+         if (k == 1 .and. dimlen == ncomp2d) then
+            vals2d(i,j) = vals_comp(c)
+            c = c + 1
+         else
+            vals3d(i,j,k) = vals_comp(n)
+         endif
+      enddo
+
+      ! write expanded variable
+      if (dimlen == ncomp3d) then
+         call nc_put_variable(ncid, varname, vals3d)
+      else
+         call nc_put_variable(ncid, varname, vals2d)
+      endif
+
+   endif
+enddo
+
+call nc_close_file(ncid_comp)
+call nc_close_file(ncid)
+
+call finalize_utilities('expand_netcdf')
+
+contains
+
+   ! logical to ignore compression variables
+   function var_of_interest(varname)
+   character(len=*), intent(in) :: varname
+   logical :: var_of_interest
+
+   select case (varname)
+      case ('XGcomp', 'XCcomp', 'YGcomp', 'YCcomp', 'ZCcomp', 'Xcomp_ind', 'Ycomp_ind', 'Zcomp_ind')
+         var_of_interest = .false.
+      case ('XC', 'YC', 'ZC', 'XG', 'YG')
+         var_of_interest = .false.
+      case default
+         var_of_interest = .true.
+    end select
+
+   end function var_of_interest
+
+end program expand_netcdf