Backward compatibility for parallel netcdf opens

[anton-seaice]

There is a corner-case bug in our build of ParallelIO 2.5.10 when built without Pnetcdf (per the cosima-spack)

If you attempt to open a netcdf3 file, with the file type flags set for netcdf4 (e.g. pio_typename = netcdf4p in nuopc.runconfig), PIO should fallback to doing a non-parallel open and open the file, however it fails with the error 'Abort with message NetCDF: Attempt to use feature that was not turned on when netCDF was built.' This was fixed in PIO 2.6.2.

There is a work around, which is to use nccopy to generate a netcdf4 file from the netcdf3 file. Otherwise the fix is to update to PIO 2.6.2 (which requires an update to the spack package, with version("2.6.2", sha256="c318894f0230197458917e932ec66301b4407a744df481e9c6a6d9d85f7e5ab1") - its in the main version now , although pins us to netcdf 4.9.2 - which is the same as our current version )

It is probably unlikely this is an issue for us. It would only come up if we wanted to use old restart / initial conditions / grid files (probably not supported?) or we wanted to switch between netcdf3 & netcdf4 part way through an experiment.

[micaeljtoliveira]

@anton-seaice I can update the PIO version used in our spack instance. That should be quite simple to do.

[anton-seaice]

Do we need to keep our own version of the PIO package? Maybe we can use the main spack package?

diff -ru repos/cosima/packages/parallelio/ spack/var/spack/repos/builtin/packages/parallelio/
diff -ru repos/cosima/packages/parallelio/package.py spack/var/spack/repos/builtin/packages/parallelio/package.py
--- repos/cosima/packages/parallelio/package.py 2024-02-16 15:40:25.000000000 +1100
+++ spack/var/spack/repos/builtin/packages/parallelio/package.py        2024-02-16 15:13:21.000000000 +1100
@@ -50,8 +50,6 @@
     # Allow argument mismatch in gfortran versions > 10 for mpi library compatibility
     patch("gfortran.patch", when="@:2.5.8 +fortran %gcc@10:")
-    flag_handler = CMakePackage.build_system_flags
-
     def cmake_args(self):
         define = self.define
         define_from_variant = self.define_from_variant
Binary files repos/cosima/packages/parallelio/__pycache__/package.cpython-311.pyc and spack/var/spack/repos/builtin/packages/parallelio/__pycache__/package.cpython-311.pyc differ

[micaeljtoliveira]

Ah, I need to submit that fix upstream. Yes, we need to keep it for now, as otherwise we can't set our own compiler flags correctly.

[anton-seaice]

Cool thanks :) (FYI @harshula )

[micaeljtoliveira]

@anton-seaice Latest spack environment uses PIO 2.6.2. Shall we close this issue?

[anton-seaice]

I will test first :)

[anton-seaice]

I made a netcdf 3 copy of grid.nc, and cice loaded that successfully using the new spack - 0.21.2 build