Seacas: undefined reference to nc_inq_dimids when building Trilinos

[ikalash]

Today, some of the Albany nightlies began failing due to the following undefined reference error:

 packages/seacas/libraries/exodus/libexodus.so.16.1.0: undefined reference to `nc_inq_dimids'
collect2: error: ld returned 1 exit status

I know there were some changes to seacas recently. Could this error be a result of that? I am attaching the full build log for Trilinos. Unfortunately it's in a build that does not post the Trilinos build output to our CDash site.

@trilinos/seacas

trilinos_make_out.txt

[cgcgcg]

@trilinos/seacas It would be good to understand why this passed the autotester but then didn't build for an application. Is the autotester somehow setting the wrong options? Is this a dependency problem in Trilinos CMake? Is the code never tested in Seacas?

[ikalash]

@cgcgcg I agree. It's curious that it doesn't happen in most of the Albany builds, only one. I wonder if it is related to how netcdf was configured on that platform?

Perhaps @gsjaardema has some ideas on what could be wrong?

[spdomin]

Since we have a complementary Seacas sync issue under: #13773 , I am communicating our set of issues through sierra-help and the Seacas team.

best,

[sebrowne]

@ikalash could you provide the version of NetCDF and HDF5 used on that build? Probably good information for context (I glanced at the log but the path doesn't indicate the versions). I can then confirm whether or not the CI tests those versions.

[gsjaardema]

I think the nc_inq_dimids is due to an unprotected section of code. It looks like that function is only present if the USE_NETCDF4 is defined and probably you don't use that option (hdf5-based file format) in your netCDF build?

I do see an unprotected use of that function, so will check when it got added. I will also verify that I have or add a seacas CI build that uses a basic netCDF build to avoid this in the future.

[ikalash]

I'm using a hand-built netcdf-4.4.1 and hdf5-1.8.17. The configure scripts for each of these can be found here: https://github.com/sandialabs/Albany/blob/master/doc/nightlyTestHarness/camobap/netcdf-4.4.1-configure.sh and https://github.com/sandialabs/Albany/blob/master/doc/nightlyTestHarness/camobap/hdf5-1.8.17-configure.sh . I'm not sure if USE_NETCDF4 is defined. The netcdf was built with the --disable-netcdf4 option, it looks like.

[gsjaardema]

Note that since you use --diable-netcdf4, you should not need to build HDF5 unless it is needed for a different dependency.

[ikalash]

@gsjaardema : I think you're right. Albany does not really need HDF5, I think it was just enabled for historic reasons.

[gsjaardema]

Did #13782 solve the issue.

[ikalash]

Yes. Thank you for fixing it @gsjaardema !