netcdf-c: reproducible Zarr reading error

This is my first attempt reading zarr from netCDF, and I have found this simple, reproducible error on both my Apple Silicon and Ubuntu 20.04 machines. It exists in both 4.9.0 and 4.8.1 in different ways. I create a simple little pure zarr data set as follows with zarr 2.11.3 or zarr 2.8.1:

from numpy import *
import zarr

store = zarr.DirectoryStore('simple.zarr')
root=zarr.group(store=store)
z = root.create('z',shape=(10, 10), dtype='f',overwrite=True)
z[:] = 42

When I read this back in with zarr in python, as expected I get an array filled with 42.0. When I use the command ncdump 'file://simple.zarr#mode=nczarr,zarr' with 4.8.1 on ubuntu 20.04 or on the Apple silicon, I get

netcdf simple {
dimensions:
        .zdim_10 = 10 ;
variables:
        float z(.zdim_10, .zdim_10) ;
data:

 z =
  2.080671e-36, 5.605194e-43, 5.605194e-43, 6.305843e-44, 2.802597e-44, 
    2.942727e-44, 9.187894e-41, 3.087947e-38, 39.82812, 1.36231e+10,
  48.5647, 9.24857e-44, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;
}

When I try to read it with 4.9.0 on the apple silicon with the same command, it hangs and never returns…

ultimately, my goal is to get my zarr files available to R users via netCDF, but figuring this out seems a logical first step. I hope this bug report is helpful, and that I am not doing something stupid.

Jamie

p.s. for 4.9.0, nc-config --all gives

This netCDF 4.9.0 has been built with the following features: 

  --cc            -> /usr/bin/clang
  --cflags        -> -I/opt/local/include
  --libs          -> -L/opt/local/lib -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lz -ldl -lm -lzstd -lbz2 -lcurl -lxml2

  --has-c++       -> no
  --cxx           -> 

  --has-c++4      -> no
  --cxx4          -> 

  --has-fortran   -> no
  --has-dap       -> yes
  --has-dap2      -> yes
  --has-dap4      -> yes
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> no
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> no
  --has-cdf5      -> no
  --has-parallel4 -> no
  --has-parallel  -> no
  --has-nczarr    -> yes

  --prefix        -> /opt/local
  --includedir    -> /opt/local/include
  --libdir        -> /opt/local/lib
  --version       -> netCDF 4.9.0

and on ubuntu netcdf 4.8.1 gives

This netCDF 4.8.1 has been built with the following features: 

  --cc            -> x86_64-conda-linux-gnu-cc
  --cflags        -> -I/home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/include
  --libs          -> -L/home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/lib -lnetcdf
  --static        -> -lmfhdf -ldf -lhdf5_hl -lhdf5 -lm -lcurl -lzip

  --has-c++       -> no
  --cxx           -> 

  --has-c++4      -> no
  --cxx4          -> 

  --has-fortran   -> yes
  --fc            -> /home/conda/feedstock_root/build_artifacts/netcdf-fortran_1642696590650/_build_env/bin/x86_64-conda-linux-gnu-gfortran
  --fflags        -> -I/home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/include -I/home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/include
  --flibs         -> -L/home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/lib -lnetcdff -lnetcdf -lnetcdf -lnetcdff_c
  --has-f90       -> TRUE
  --has-f03       -> yes

  --has-dap       -> yes
  --has-dap2      -> yes
  --has-dap4      -> yes
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> yes
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> no
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no
  --has-nczarr    -> yes

  --prefix        -> /home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022
  --includedir    -> /home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/include
  --libdir        -> /home/pringle/anaconda3/envs/py3_parcels_mpi_bleedingApr2022/lib
  --version       -> netCDF 4.8.1