spack-stack@2.1.0 fails to install netcdf-c plugins when build_system = cmake

[rickgrubin-noaa]

Description

spack-stack@2.1.0 fails to install netcdf-c plugins -- used when writing compressed output files with zstandard -- when netcdf-c utilizes spack's buiild_system = cmake setting

To Reproduce

Install spack-stack@2.1.0 with

• spack @ 324bf79
• repos / builtin @ 4a3312c

Build / run code that relies on writing netcdf files with zstandard compression at a compression level > 0, e.g.

+ srun --label --distribution=block:block -n 150 ./fv3.exe
144:  file: module_write_netcdf.F90 line:          500
144:  NetCDF: Filter error: undefined filter encountered
144:  ESMF_Finalize: Error closing trace stream
144: Abort(1) on node 144 (rank 144 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 144

Expected behavior

netcdf-c plugins are built and installed so that code which relies on zstandard plugins for compression successfully create netcdf files

System, compiler, code, ...

The failure result was reproducible across all EPIC / RDHPCS hosts when running UFS WM regression tests against spack-stack@2.1.0:

• derecho / gaea-c6 / hercules / orion / ursa
  • oneapi@2025.{3,2}.1
  • gcc@{13,12}

Additional context

Referencing the above error example, in module_write_netcdf.F90:

 ncerr = nf90_def_var_zstandard(ncid, varids(i), zstandard_level(grid_id)) ; NC_ERR_STOP(ncerr)

For regression testing, the default compression level is zero (export ZSTANDARD_LEVEL=0) -- no compression, see:
https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/default_vars.sh

Each test that requires zstd compression sets it as, for example, (export ZSTANDARD_LEVEL=5), see e.g.
https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/tests/control_p8

The zstandard compression level depends on the following:

... writes NetCDF files using ParallelIO (PIO), which supports HDF5-based compression filters, including Zstandard (zstd). Zstd offers better compression ratios and faster I/O than zlib. Implementing zstd requires NetCDF-4.9.0+ and the zstd filter plugin installed in the HDF5_PLUGIN_PATH

Prior to spack-stack@2.x -- e.g. spack-stack@1.9.2, netcdf-c was built with build_system=autotools:

^netcdf-c@4.9.2%oneapi@2024.2.1+blosc~byterange+dap~fsync~hdf4~jna~logging+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared~szip+zstd build_system=autotools patches=0161eb8 arch=linux-rocky9-zen3

and the configure step reports a plugin directory:

NetCDF Version:     4.9.2
Dispatch Version:    5
Install Prefix:     /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr
Plugin Install Prefix: /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr/plugins

which is populated with plugins:

$ ls /contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/oneapi/2024.2.1/netcdf-c-4.9.2-idnwcbr/plugins
lib__nch5blosc.so    lib__nch5deflate.so.0.0.0   lib__nch5zstd.so.0
lib__nch5blosc.so.0   lib__nch5fletcher32.so    lib__nch5zstd.so.0.0.0
lib__nch5blosc.so.0.0.0 lib__nch5fletcher32.so.0   lib__nczhdf5filters.so
lib__nch5bzip2.so    lib__nch5fletcher32.so.0.0.0 lib__nczhdf5filters.so.0
lib__nch5bzip2.so.0   lib__nch5shuffle.so      lib__nczhdf5filters.so.0.0.0
lib__nch5bzip2.so.0.0.0 lib__nch5shuffle.so.0     lib__nczstdfilters.so
lib__nch5deflate.so   lib__nch5shuffle.so.0.0.0   lib__nczstdfilters.so.0
lib__nch5deflate.so.0  lib__nch5zstd.so       lib__nczstdfilters.so.0.0.0

spack-stack-2.1.0 does NOT configure with --enable-plugins or --with-plugin-dir -- those options are NOT specified during the configure step, and this results in no plugins configured / built:

NetCDF Version:     4.9.2
Dispatch Version:    5
Install Prefix:     /contrib/spack-stack/spack-stack-2.1.0/envs/ue-oneapi-2025.3.1/install/intel-oneapi-compilers/2025.3.1/netcdf-c-4.9.2-322lw3t
Plugin Install Prefix: N.A.

ls /contrib/spack-stack/spack-stack-2.1.0/envs/ue-oneapi-2025.3.1/install/intel-oneapi-compilers/2025.3.1/netcdf-c-4.9.2-322lw3t
bin include lib64 share

Note the absence of the plugins directory.

---

For the spack package.py file, netcdf-c@4.9.2 is retrieved from the same commit, so netcdf-c code is consistent.

Because shared libraries are requested to be built (variant +shared), along with zstd compression (variant +zstd), this code in package.py means that plugins are to be built / enabled:

# The plugins are not built when the shared libraries are disabled:
  with when("~shared"):
    conflicts("+szip")
    conflicts("+blosc")
    conflicts("+zstd")

and

def setup_run_environment(self, env: EnvironmentModifications) -> None:
    if self.spec.satisfies("@4.9.0:+shared"):
      # Both HDF5 and NCZarr backends honor the same environment variable:
      env.append_path("HDF5_PLUGIN_PATH", self.prefix.plugins)

For spack-stack@2.1.0, netcdf-c requires building with cmake:

netcdf-c:

      require:
      - '@4.9.2'
         [...]
      - build_system=cmake

Upstream spack-packages contains this merged PR: Logic to install plugins for cmake netcdf-c builds #2887, which solves this particular issue.

JCSDA/spack-packages netcdf_c/package.py does not yet have this upstream commit / fix for spack-stack@2.1.0