Fix bugs found during code review (with additional test).

Author: nusbaume

src/physics/utils/pio_reader.F90

@@ -1453,7 +1453,7 @@ subroutine get_netcdf_var_real_5d(this, varname, var, errmsg, errcode, start, co
 
       !Now attempt to allocate and initialize the variable,
       !and read-in the NetCDF data:
-      allocate(var(dim_sizes(1), dim_sizes(2), dim_sizes(3), dim_sizes(4), dim_sizes(5)), &
+      allocate(var(alloc_dims(1), alloc_dims(2), alloc_dims(3), alloc_dims(4), alloc_dims(5)), &
                stat=errcode, errmsg=errmsg)
       if(errcode /= 0) then
          !Reset PIO back to original error handling method:
@@ -2600,12 +2600,12 @@ subroutine var_subset_check(varname, var_ndims, dim_sizes, do_subset, alloc_dims
 
       !Check if count indices are within bounds:
       do i = 1, file_var_dim_num
-         if ((count(i) < 1) .or. (count(i) > dim_sizes(i))) then
+         if ((count(i) < 1) .or. ((start(i)+count(i)-1) > dim_sizes(i))) then
             errcode = bad_subset_range_err
             write(errmsg, '(a,i0,3a,i0,a,i0,a)') &
                   "Element ", i, " of 'count' for variable '", &
                   trim(varname), "' is out of bounds.  Expected 1 to ", &
-                  dim_sizes(i), " but got ", count(i), "."
+                  (dim_sizes(i)-start(i)+1), " but got ", count(i), "."
             return
          end if
       end do

test/unit/fortran/src/pio_reader/test_pio_reader.pf

@@ -1920,20 +1920,28 @@ subroutine test_pio_reader_bad_count_element_range()
     ! Open file:
     call reader%open_file(fname, errmsg, errcode)
 
-    ! Attempt to read variable with negative start element:
+    ! Attempt to read variable with negative count element:
     call reader%get_var("pressure", pressure, errmsg, errcode, start=(/1/), count=(/-6/))
 
     ! Check that the correct error was raised:
     @assertNotEqual(0, errcode)
     @assertEqual(expected_err_msg_neg, trim(errmsg))
 
-    ! Next attempt to read variable with too-large start element:
+    ! Next attempt to read variable with too-large count element:
     call reader%get_var("pressure", pressure, errmsg, errcode, start=(/1/), count=(/60/))
 
     ! Check that the correct error was raised:
     @assertNotEqual(0, errcode)
     @assertEqual(expected_err_msg_huge, trim(errmsg))
 
+    ! Now attempt to read variable with too-large start+count element:
+    call reader%get_var("pressure", pressure, errmsg, errcode, start=(/3/), count=(/58/))
+
+    ! Check that the correct error was raised:
+    @assertNotEqual(0, errcode)
+    @assertEqual(expected_err_msg_huge, trim(errmsg))
+
+
     ! Perform test cleanup:
     call reader%close_file(errmsg, errcode)
     deallocate(reader)