Ok, the issue, at least on my system, ended up being a libtool mismatch. I
did some things that I'm not really sure how they work or if I even envoked
them correctly, but seemed to fix the problem.
I chdir into GEMPAK5.11.4/extlibs/netCDF/v3.6.2
then run this command
libtoolize --automake --force
this rebuilds libtool for the version it's using
netCDF compiled fine at this point and so did the rest of the programs,
still running tests to see if everything else is working.
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