Re: [netcdfgroup] [non-nasa source] netcdf-C 4.6.1 build error on macOS 10.13 error with ocprint link

• To: <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] [non-nasa source] netcdf-C 4.6.1 build error on macOS 10.13 error with ocprint link
• From: "Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]" <matthew.thompson@xxxxxxxx>
• Date: Tue, 31 Jul 2018 08:24:03 -0400

Dear netCDF Gurus,

First, I mistakenly opened an issue on Github for this not realizing (after reading the README.md) that this is the preferred bug question place. Sorry!

My build of netcdf-C 4.6.1 on macOS 10.13.5 isn't quite working. I'm building with GCC 8.1.0 (built from source) and Open MPI 3.1.0. I built HDF5 with --enable-parallel so mpicc is my C compiler in this stage.

From my scan of the build log, libnetcdf.a is made, but when ocprint tries to link I get:

make[4]: Entering directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-5.1.2/src/netcdf/ncdump' /bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o ocprint ocprint.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib -lmfhdf -ldf -lsz -ljpeg -L/Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib -lcurl -lz -lm         -ldl -lm libtool: link: mpicc -o ocprint ocprint.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-8.1.0/openmpi-3.1.0/Baselibs/5.1.2/Darwin/lib/libcurl.a -lz -ldl -lm

Undefined symbols for architecture x86_64:
  "_ncrc_globalstate", referenced from:
      _createtempfile in libnetcdf.a(liboc_la-ocinternal.o)
      _ocset_curlproperties in libnetcdf.a(liboc_la-ocinternal.o)
      _NC_rcload in libnetcdf.a(libdispatch_la-drc.o)
      _NC_set_rcfile in libnetcdf.a(libdispatch_la-drc.o)
      _rccompile in libnetcdf.a(libdispatch_la-drc.o)
      _rclocate in libnetcdf.a(libdispatch_la-drc.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:1046: ocprint] Error 1

make[4]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-5.1.2/src/netcdf/ncdump'

make[3]: *** [Makefile:1265: install-recursive] Error 1

make[3]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-5.1.2/src/netcdf/ncdump'

make[2]: *** [Makefile:672: install-recursive] Error 1

make[2]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-5.1.2/src/netcdf'

make[1]: *** [GNUmakefile:898: netcdf.install] Error 2

make[1]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-5.1.2/src'

make: *** [GNUmakefile:267: install] Error 2

As a test, I took netcdf-C 4.5.0 (which had worked before on this machine) and tried building it instead (feeding in the exact same libraries that went into the build above) and ocprint, etc all built just fine. So I'm missing something in my configure or LIBS or something that ocprint, et al, now need to build. Any ideas?

# Apparently fails under cmake
#set(ocprint_FILES ocprint.c )
#ADD_EXECUTABLE(ocprint ${ocprint_FILES})
#TARGET_LINK_LIBRARIES(ocprint oc2 ${ALL_TLL_LIBS})

(which is in the oc2/CMakeLists.txt, not the ncdump/CMakeLists.txt).

Matt


--
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

• References:
  • [netcdfgroup] netcdf-C 4.6.1 build error on macOS 10.13 error with ocprint link
    • From: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]