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Enable PIO to Add Attributes to Existing NetCDF Files #1234

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Enable PIO to Add Attributes to Existing NetCDF Files #1234

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c066590
Implement try-fail method to write new attributes to NetCDF files in PIO
amstokely Sep 9, 2024
d03136a
Removed incorrect data mode/preexisting file logic in mpas_io.F
amstokely Dec 5, 2024
d5744e2
Removed commented out code block in mpas_io.F.
amstokely Dec 6, 2024
ce3c460
Wrapped new pio subroutine defs in MPAS_PIO_SUPPORT preprocessing dir…
amstokely Dec 6, 2024
dbc3933
Fixed unterminated #ifdef MPAS_PIO_SUPPORT
amstokely Dec 6, 2024
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187 changes: 142 additions & 45 deletions src/framework/mpas_io.F
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,10 @@ module mpas_io

#ifdef MPAS_PIO_SUPPORT
integer, private :: io_global_err = PIO_noerr
interface put_att_pio
module procedure put_att_0d_generic_pio
module procedure put_att_1d_generic_pio
end interface put_att_pio
#endif
#ifdef MPAS_SMIOL_SUPPORT
integer, private :: io_global_err = SMIOL_SUCCESS
Expand Down Expand Up @@ -5033,6 +5037,131 @@ subroutine MPAS_io_get_att_real1d(handle, attName, attValue, fieldname, precisio

end subroutine MPAS_io_get_att_real1d

#ifdef MPAS_PIO_SUPPORT

function handle_put_att_pio_redef(handle) result (pio_ierr)
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Why is _put_att_ in these function names? They don't do anything with attributes.

implicit none
type(MPAS_IO_Handle_type), intent(inout) :: handle
integer :: pio_ierr

pio_ierr = PIO_redef(handle % pio_file)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

end function handle_put_att_pio_redef

function handle_put_att_pio_enddef(handle) result (pio_ierr)
implicit none
type(MPAS_IO_Handle_type), intent(inout) :: handle
integer :: pio_ierr

pio_ierr = PIO_enddef(handle % pio_file)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

end function handle_put_att_pio_enddef

function put_att_0d_generic_pio(handle, varid, attName, attValue, ierr) result(pio_ierr)
implicit none
type(MPAS_IO_Handle_type), intent(inout) :: handle
integer, intent(in) :: varid
character(len=*), intent(in) :: attName
class(*), intent(in) :: attValue
integer, optional :: ierr
integer :: pio_ierr

select type(attValue)
type is (integer)
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R4KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R8KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (character(len=*))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
end select

if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND

if (handle % preexisting_file .and. .not. handle % data_mode) then
if (handle_put_att_pio_redef(handle) /= PIO_noerr) return

select type(attValue)
type is (integer)
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R4KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R8KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (character(len=*))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
end select

if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

if (handle_put_att_pio_enddef(handle) /= PIO_noerr) return

if (present(ierr)) ierr = MPAS_IO_NOERR
end if
return
end if
end function put_att_0d_generic_pio

function put_att_1d_generic_pio(handle, varid, attName, attValue, ierr) result(pio_ierr)
implicit none
type(MPAS_IO_Handle_type), intent(inout) :: handle
integer, intent(in) :: varid
character(len=*), intent(in) :: attName
class(*), dimension(:), intent(in) :: attValue
integer, optional :: ierr
integer :: pio_ierr

select type(attValue)
type is (integer)
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R4KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R8KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
end select

if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND

if (handle % preexisting_file .and. .not. handle % data_mode) then
if (handle_put_att_pio_redef(handle) /= PIO_noerr) return
select type(attValue)
type is (integer)
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R4KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
type is (real(kind=R8KIND))
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValue)
end select

if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

if (handle_put_att_pio_enddef(handle) /= PIO_noerr) return
if (present(ierr)) ierr = MPAS_IO_NOERR
end if
return
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We could remove this return statement.

end if
end function put_att_1d_generic_pio
#endif


subroutine MPAS_io_get_att_text(handle, attName, attValue, fieldname, ierr)

Expand Down Expand Up @@ -5338,7 +5467,7 @@ subroutine MPAS_io_put_att_int0d(handle, attName, attValue, fieldname, syncVal,
end if

#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValueLocal)
pio_ierr = put_att_pio(handle, varid, attName, attValueLocal, ierr=ierr)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
Expand Down Expand Up @@ -5523,7 +5652,7 @@ subroutine MPAS_io_put_att_int1d(handle, attName, attValue, fieldname, syncVal,
end if

#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValueLocal)
pio_ierr = put_att_pio(handle, varid, attName, attValueLocal, ierr=ierr)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
Expand Down Expand Up @@ -5689,7 +5818,7 @@ subroutine MPAS_io_put_att_real0d(handle, attName, attValue, fieldname, syncVal,
(MPAS_IO_NATIVE_PRECISION /= MPAS_IO_SINGLE_PRECISION)) then
singleVal = real(attValueLocal,R4KIND)
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, singleVal)
pio_ierr = put_att_pio(handle, varid, attName, singleVal, ierr=ierr)
#endif

#ifdef MPAS_SMIOL_SUPPORT
Expand All @@ -5703,7 +5832,7 @@ subroutine MPAS_io_put_att_real0d(handle, attName, attValue, fieldname, syncVal,
(MPAS_IO_NATIVE_PRECISION /= MPAS_IO_DOUBLE_PRECISION)) then
doubleVal = real(attValueLocal,R8KIND)
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, doubleVal)
pio_ierr = put_att_pio(handle, varid, attName, doubleVal, ierr=ierr)
#endif

#ifdef MPAS_SMIOL_SUPPORT
Expand All @@ -5715,7 +5844,7 @@ subroutine MPAS_io_put_att_real0d(handle, attName, attValue, fieldname, syncVal,
#endif
else
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValueLocal)
pio_ierr = put_att_pio(handle, varid, attName, attValueLocal, ierr=ierr)
#endif

#ifdef MPAS_SMIOL_SUPPORT
Expand All @@ -5734,6 +5863,7 @@ subroutine MPAS_io_put_att_real0d(handle, attName, attValue, fieldname, syncVal,
return
end if
#endif

#ifdef MPAS_SMIOL_SUPPORT
if (local_ierr /= SMIOL_SUCCESS) then
call mpas_log_write('SMIOLf_define_att failed with error $i', intArgs=[local_ierr], messageType=MPAS_LOG_ERR)
Expand Down Expand Up @@ -5919,20 +6049,20 @@ subroutine MPAS_io_put_att_real1d(handle, attName, attValue, fieldname, syncVal,
allocate(singleVal(size(attValueLocal)))
singleVal(:) = real(attValueLocal(:),R4KIND)
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, singleVal)
pio_ierr = put_att_pio(handle, varid, attName, singleVal, ierr=ierr)
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I think there may be another space of indentation that's needed here to align with other code.

#endif
deallocate(singleVal)
else if ((new_attlist_node % attHandle % precision == MPAS_IO_DOUBLE_PRECISION) .and. &
(MPAS_IO_NATIVE_PRECISION /= MPAS_IO_DOUBLE_PRECISION)) then
allocate(doubleVal(size(attValueLocal)))
doubleVal(:) = real(attValueLocal(:),R8KIND)
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, doubleVal)
pio_ierr = put_att_pio(handle, varid, attName, doubleVal, ierr=ierr)
#endif
deallocate(doubleVal)
else
#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, attValueLocal)
pio_ierr = put_att_pio(handle, varid, attName, attValueLocal, ierr=ierr)
#endif
end if
#ifdef MPAS_PIO_SUPPORT
Expand All @@ -5950,6 +6080,9 @@ subroutine MPAS_io_put_att_real1d(handle, attName, attValue, fieldname, syncVal,
end subroutine MPAS_io_put_att_real1d





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It would be preferable to not add these three blank lines.

subroutine MPAS_io_put_att_text(handle, attName, attValue, fieldname, syncVal, ierr)

implicit none
Expand Down Expand Up @@ -6100,43 +6233,7 @@ subroutine MPAS_io_put_att_text(handle, attName, attValue, fieldname, syncVal, i
end if

#ifdef MPAS_PIO_SUPPORT
pio_ierr = PIO_put_att(handle % pio_file, varid, attName, trim(attValueLocal))
if (pio_ierr /= PIO_noerr) then

io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND

!
! If we are working with a pre-existing file and the text attribute is larger than in the file, we need
! to enter define mode before writing the attribute. Note the PIO_redef documentation:
! 'Entering and leaving netcdf define mode causes a file sync operation to occur,
! these operations can be very expensive in parallel systems.'
!
if (handle % preexisting_file .and. .not. handle % data_mode) then
pio_ierr = PIO_redef(handle % pio_file)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

pio_ierr = PIO_put_att(handle % pio_file, varid, attName, trim(attValueLocal))
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

pio_ierr = PIO_enddef(handle % pio_file)
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
return
end if

if (present(ierr)) ierr = MPAS_IO_NOERR

end if

return
end if
pio_ierr = put_att_pio(handle, varid, attName, attValueLocal, ierr=ierr)
#endif

#ifdef MPAS_SMIOL_SUPPORT
Expand Down