Configure netcdf-4.9.2 without libzip

[vbsteph]

Attempting to configure netcdf-4.9.2 with Autotools such that -lzip does not get included as an "extra library". libzip is installed on the system in question, but due to some downstream linking issues, we specifically want to build netcdf without libzip (or zlib). Based on the docs, I thought that disabling nczarr and netcdf-4 (and therefore hdf5) would be enough, but no luck. I've been unable to come up with a combination of configure line options that eliminates the dependency; this is the most recent set I tried that still resulted in -lzip as an extra library:

--disable-shared
--disable-nczarr
--disable-hdf5
--disable-netcdf-4
--disable-netcdf4
--disable-dap
--disable-byterange
--disable-testsets
--disable-cdf5

Is there a set of options I can use to eliminate that dependency? Does the configure step always include that library when found regardless of whether it's needed?

EDIT: building with gcc 10.3.0

[WardF]

This appears to be an oversight on our end; it is very rare that libzip won't be needed to be linked against, but in situations such as yours, that should be possible. Thank you for pointing out this gap in our build system.

At current, you may be able to work around this by editing the configure.ac file; around line 781, you'll find the checks for libzip. If you comment these out and remove them, and then re-generate the configure script with the command autoreconf -if, you might be able to get past this.

Not ideal, I know, but it will be the quickest way. I'll try to get a fix for this in for the upcoming v4.9.3 release. v4.9.3 will be out as soon as possible, currently I am trying to figure out an issue in nc_test that has appeared with the latest OS update. Thanks!

[vbsteph]

Thank you for looking into it! We will keep an eye on the next release, and I will try that workaround in the meantime.

[vbsteph]

It looks like the workaround you suggested will tide us over until the next release. Thank you for your help!

[WardF]

I've opened a PR here: #2793

[edwardhartnett]

We specifically require that zlib always be present for netCDF-4.

That is, we do not cope well without zlib. So there is no built-in handling of netcdf without zlib. This is really a mistake on my part, I just never understood (until quite recently) that HDF5 could be built without zlib. But it can.

So making it work might take a little more effort than you expect...

[WardF]

@vbsteph can you actually confirm my previous statement? I inferred from your original comments that we were talking about libzip, but I see now you've also mentioned zlib. I want to make sure I'm addressing the correct thing for the environment you're working in :)

[WardF]

Insofar as zlib is used to provide the deflate functionality found in hdf4/hdf5, and libzip was checked for unconditionally, but used for ncZarr-related functionality.

[vbsteph]

Yes, my question was about libzip, not zlib. I was under the impression that libzip uses zlib under the hood, so they are linked that way in my mind, but I'm certainly not an expert and could be wrong.

[WardF]

libzip may or may not use zlib, certainly; currently, we check to see if libzip is present before we check to see if we need it for use with ncZarr. My PR changes that. If we disable ncZarr but still have hdf4 and hdf5 functionality, configure will still check for and link against zlib. Or at least, it should, and appears to in my testing. Insofar as I can tell, the PR successfully only links against libzip if ncZarr is enabled. I'll double check what is linked against when disabling things comprehensively, as you have done. But insofar as we wanted to eliminate an unnecessary linkage against libzip, I think we've got that :).

[vbsteph]

I don't think zlib dependence would cause any issues with our setup, but we require neither nczarr nor hdf5 support, so my understanding is that both libzip and zlib would get eliminated from the dependency list. (Please correct me if I'm wrong.)

That said, it sounds like your changes should do exactly what we need, and I can always come back with separate questions about zlib if anything comes up later.

[DennisHeimbigner]

But as far as I know, HDF5 does not use libzip, it only requires zlib.
I think this issue is related to this PR #2712
and this PR #2722