Issue building ocprint with GCC 10.1...maybe?

[mathomp4]

Prelims

• the version of the software with which you are encountering an issue
  • netCDF-C 4.7.4
• environmental information (i.e. Operating System, compiler info, java version, python version, etc.)
  • macOS 10.15.4
  • GCC 9.3.0 and 10.1.0
  • Open MPI 4.0.3
• a description of the issue with the steps needed to reproduce it
  • see below

The Issue

This is an odd one, mainly because this might be the second or third time ocprint and I have had issues. To wit, I recently built GCC 10.1.0 and am trying to build netCDF-c with it. Now, I have also built (and usually use) GCC 9.3.0 and with it, I can build netCDF-C just fine and ocprint seems to build. I don't know what it does, but it builds.

In each case, I am compiling using Open MPI wrappers as CC, CXX, and FC as I built HDF5 with parallel support. Each compiler is using Open MPI 4.0.3.

In each case, netcdf were configured within a framework as, essentially:

  $ ./configure --prefix=/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin --includedir=/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf --enable-hdf4 --disable-dap --enable-parallel-tests --disable-shared --disable-examples --enable-netcdf-4 CC=mpicc FC=mpifort CXX=mpic++ F77=mpifort

This is actually a lot of FC=$(FC) and --prefix=$(prefix), etc. in my overarching Base Library framework make system, but the configure line for each is nigh-identical save for the changes in prefix/includedir.

I've never seen this error with GCC 9.3.0 (though I'm not saying I can't), but I occasionally see it with GCC 10.1.0...and it seems weirdly non-deterministic.

First, with GCC 9.3.0. I search the log for nc4print.o and get to:

depbase=`echo nc4print.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicc -DHAVE_CONFIG_H -I. -I..  -I../include -I../oc2 -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/szlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/udunits2    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/antlr     -MT nc4print.o -MD -MP -MF $depbase.Tpo -c -o nc4print.o nc4print.c &&\
mv -f $depbase.Tpo $depbase.Po
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o nc4print nc4print.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm        -ldl -lm
libtool: link: mpicc -o nc4print nc4print.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
depbase=`echo ocprint.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicc -DHAVE_CONFIG_H -I. -I..  -I../include -I../oc2 -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/szlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/udunits2    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/antlr     -MT ocprint.o -MD -MP -MF $depbase.Tpo -c -o ocprint.o ocprint.c &&\
mv -f $depbase.Tpo $depbase.Po
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o ocprint ocprint.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/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-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
make[5]: Entering directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
 /Users/mathomp4/.homebrew/brew/bin/gmkdir -p '/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin'
  /bin/sh ../libtool   --mode=install /Users/mathomp4/.homebrew/brew/bin/ginstall -c ncdump nccopy '/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin'
libtool: install: /Users/mathomp4/.homebrew/brew/bin/ginstall -c ncdump /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/ncdump
libtool: install: /Users/mathomp4/.homebrew/brew/bin/ginstall -c nccopy /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/nccopy
 /Users/mathomp4/.homebrew/brew/bin/gmkdir -p '/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/share/man/man1'
 /Users/mathomp4/.homebrew/brew/bin/ginstall -c -m 644 ncdump.1 nccopy.1 '/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/share/man/man1'
make[5]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[4]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[3]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
Making install in unit_test

You can see we build nc4print then ocprint and then eventually install ncdump and nccopy.

Now, sometimes with netCDF-C, using GCC 10.1, I get:

depbase=`echo nc4print.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicc -DHAVE_CONFIG_H -I. -I..  -I../include  -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/szlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/udunits2    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/antlr     -MT nc4print.o -MD -MP -MF $depbase.Tpo -c -o nc4print.o nc4print.c &&\
mv -f $depbase.Tpo $depbase.Po
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o nc4print nc4print.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -lz -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg   -ldl -lm
libtool: link: mpicc -o nc4print nc4print.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a -lz /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a -ldl -lm
make[5]: Entering directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
 /Users/mathomp4/.homebrew/brew/bin/gmkdir -p '/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin'
  /bin/sh ../libtool   --mode=install /Users/mathomp4/.homebrew/brew/bin/ginstall -c ncdump nccopy '/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin'
libtool: install: /Users/mathomp4/.homebrew/brew/bin/ginstall -c ncdump /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/ncdump
libtool: install: /Users/mathomp4/.homebrew/brew/bin/ginstall -c nccopy /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/nccopy
 /Users/mathomp4/.homebrew/brew/bin/gmkdir -p '/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/share/man/man1'
 /Users/mathomp4/.homebrew/brew/bin/ginstall -c -m 644 ncdump.1 nccopy.1 '/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/share/man/man1'
make[5]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[4]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[3]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
Making install in unit_test

Once again we make nc4print and then...skip over ocprint and go right to installing ncdump and nccopy! Thus, we avoid my possible issue. I've had this happen both with a netcdf where I've done make clean && make distclean and when I've done a complete new clone/checkout of netcdf (or my full base libraries).

But, other times, I compile with GCC 10.1 and I get:

depbase=`echo nc4print.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicc -DHAVE_CONFIG_H -I. -I..  -I../include -I../oc2 -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/    -I/Users/mathomp4/installed/
MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/sz
lib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Basel
ibs/6.0.12-Snap13/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/gcc-gf
ortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/udunits2
  -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.
0.12-Snap13/Darwin/include/antlr     -MT nc4print.o -MD -MP -MF $depbase.Tpo -c -o nc4print.o nc4print.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ocprint.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicc -DHAVE_CONFIG_H -I. -I..  -I../include -I../oc2 -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/    -I/Users/mathomp4/installed/
MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/zlib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/sz
lib    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/jpeg    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Basel
ibs/6.0.12-Snap13/Darwin/include/hdf5    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/hdf    -I/Users/mathomp4/installed/MPI/gcc-gf
ortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/netcdf    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/udunits2
  -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/gsl    -I/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/include/antlr     -MT ocprint.o -MD -MP -MF $depbase.Tpo -c -o ocprint.o ocprint.c &&\
mv -f $depbase.Tpo $depbase.Po
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o ncdump ncdump.o vardata.o dumplib.o indent.o nctime0.o utils.o nciter.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm  -ldl -lm
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o nccopy nccopy.o nciter.o chunkspec.o utils.o dimmap.o list.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm     -ldl -lm
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o ncvalidator ncvalidator.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm        -ldl -lm
libtool: link: mpicc -o ncdump ncdump.o vardata.o dumplib.o indent.o nctime0.o utils.o nciter.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
libtool: link: mpicc -o nccopy nccopy.o nciter.o chunkspec.o utils.o dimmap.o list.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
libtool: link: mpicc -o ncvalidator ncvalidator.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o nc4print nc4print.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm      -ldl -lm
/bin/sh ../libtool  --tag=CC   --mode=link mpicc     -o ocprint ocprint.o ../liblib/libnetcdf.la -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lmfhdf -ldf -lsz -ljpeg  -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm        -ldl -lm
libtool: link: mpicc -o nc4print nc4print.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
libtool: link: mpicc -o ocprint ocprint.o  ../liblib/.libs/libnetcdf.a -L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5_hl.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libhdf5.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libmfhdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libdf.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libsz.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libjpeg.a /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib/libcurl.a -lz -ldl -lm
duplicate symbol '_ocdebug' in:
    ocprint.o
    ../liblib/.libs/libnetcdf.a(liboc_la-ocdebug.o)
ld: 1 duplicate symbol for architecture x86_64
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:1106: ocprint] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[3]: *** [Makefile:1332: install-recursive] Error 1
make[3]: Leaving directory '/Users/mathomp4/Baselibs/ESMA-Baselibs-6.0.12-Snap13/src/netcdf/ncdump'
make[2]: *** [Makefile:707: install-recursive] Error 1

I am so confused. Perhaps make distclean is not enough to clean netCDF-C? Why do I sometimes get ocprint building and other times I don't?

I also thought this is perhaps a race condition as I usually build make -j3 or make -j8. But, I hacked my build scripts to force make -j1 install when building netcdf, so it should be serial.

Are there any thoughts on what I might be doing wrong? As I said before, I did have ocprint issues on macOS before, but 4.6.2 solved it for me and I've never had issues since.

[DennisHeimbigner]

First, WRT not building ocprint. This is conditional on enabling DAP.
This in turn requires access to libcurl. So my speculation is that
libcurl is not always being found. If you look at the ouput
from ./configure, it should have a line something like:

checking for curl_easy_setopt in -lcurl .. yes
If it says no, then libcurl was not found (or was misconfigured)
and DAP will be disabled.

[DennisHeimbigner]

Second, the duplicate symbol error is actually correct.
My surmise is that gcc 9 either recognizes that the two
declarations are the same, or issues a warning --
but since I do not see it in the output you sent, it is probably
the former. In any case, gcc 9 and gcc 10 are handling this
different.
I will issue a patch, but in the meantime, you can try the following:

1. FInd the following line in ncdump/ocprint,c (about line 59)

int ocdebug;

2. Change that line to this:

extern int ocdebug;

[mathomp4]

First, WRT not building ocprint. This is conditional on enabling DAP.
This in turn requires access to libcurl. So my speculation is that
libcurl is not always being found. If you look at the ouput
from ./configure, it should have a line something like:

checking for curl_easy_setopt in -lcurl .. yes
If it says no, then libcurl was not found (or was misconfigured)
and DAP will be disabled.

@DennisHeimbigner Ah! Indeed. I do see it saying yes and no on and off in my log files, which isn't good.

As far as I know, curl is building with GCC 10.1 just fine. My GNUmakefile requires a good cURL build to proceed to netcdf (along with hdf5). And I can see it there. curl the executable is built and curl-config between GCC 9.3 and 10.1 are identical (save for directory names). Do you know if:

./configure --prefix=foo --includedir=foo --libdir=foo
 --with-zlib=/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin
 --disable-ldap --enable-manual 
--disable-shared --enable-static 
--without-libidn --without-libidn2 CFLAGS= CC=gcc CXX=g++ FC=gfortran

Is enough to build curl_easy_setopt or perhaps I need more/less? Very baffling...

[DennisHeimbigner]

Can you post the output of config.log for the case when
ocprint is not being compiled?

[DennisHeimbigner]

Ah! Indeed. I do see it saying yes and no on and off in my log files, which isn't good.

So you are saying that for gcc 9, that sometimes curl_easy_setopt
is found and other times it is not? Is there any pattern connecting
this behavior to something else like a change in the
./configure options?

[mathomp4]

@DennisHeimbigner

As far as I can tell, GCC 9 is always "curl good" if you were. I just looked at my logs and compared the curl configure output from my builds and the only substantive difference in how it configured was:

❯ diff curl.930.log curl.1010.log
31d30
< parallel-tests: installing './test-driver'
726c725
<   Install prefix:   /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin
---
>   Install prefix:   /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin

I can't imagine "parallel-tests" would cause a fundamental difference.

What I usually do is if I see curl in my libraries, I assume we want to build with DAP support so I then do:

BUILD_DAP = --enable-dap
LIB_CURL = $(shell $(prefix)/bin/curl-config --libs)
netcdf.config : netcdf/configure
        @echo "Configuring netcdf $*"
        @(cd netcdf; \
          export PATH="$(prefix)/bin:$(PATH)" ;\
          export CPPFLAGS="$(CPPFLAGS) $(NC_CPPFLAGS) $(INC_SUPP)";\
          export CFLAGS="$(CFLAGS) $(NC_CFLAGS) $(PTHREAD_FLAG)";\
          export LIBS="-L$(prefix)/lib -lmfhdf -ldf -lsz -ljpeg $(LINK_GPFS) $(LIB_CURL) -ldl -lm $(LIB_EXTRA)" ;\
          ./configure --prefix=$(prefix) \
                      --includedir=$(prefix)/include/netcdf \
                      --enable-hdf4 \
                      $(BUILD_DAP) \
                      $(NC_PAR_TESTS) \
                      --disable-shared \
                      --disable-examples \
                      --enable-netcdf-4 \
                      CC=$(NC_CC) FC=$(NC_FC) CXX=$(NC_CXX) F77=$(NC_F77) )
        @touch $@

There's a lot of extra cruft that in many cases is blank nowadays, but I rely on curl-config to provide what it wants to netcdf. And for GCC 9:

❯ /Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/curl-config --libs
-L/Users/mathomp4/installed/MPI/gcc-gfortran-9.3.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm

and for GCC 10:

❯ /Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/bin/curl-config --libs
-L/Users/mathomp4/installed/MPI/gcc-gfortran-10.1.0/openmpi-4.0.3/Baselibs/6.0.12-Snap13/Darwin/lib -lcurl -lz -lm

Honestly, the curl-config is a bit overboard, but I use nc-config and nf-config so much (with GNUmake), if I see something like it, I use it.

[mathomp4]

I think I might have to move over to cURL and see if they have ideas...

[DennisHeimbigner]

You probably do not have to do the --enable-dap option
because it is on by default unless it cannot find the curl library.
Using curl-config is ok; I do it myself.
At this point, I am baffled. There must be difference somewhere.
Can you post the following information:

1. the exact ./configure command for the case where curl is found
   and the case where curl is not found.
2. the config.log file for when curl is found and the file when curl is not found.

[mathomp4]

Oooh. You might have twigged it... Something weird is happening in make land. For some reason my make verify command (which prints out a lot of the variables in my GNUmakefile) seems to say I'll be passing in --enable-dap but when it builds netcdf suddenly that is --disable-dap.

Time to make a much more bulletproof "am I building with curl" test...even though my current one has worked for at least 5 years. (Grah. GNU Make!)

[mathomp4]

Well, if I hardcode --enable-dap I can have it fail consistently. Yay! (Yay?)

Then, if I try your change to ocprint.c in #1726, all works and ocprint is happy.

Thank you @DennisHeimbigner for figuring this out. (Next philosophical question: why is it always ocprint when I come here... 😄 )

Now time to figure out how to dynamically patch code in GNU Make since my base library repo just has netcdf as a submodule checkout out at v4.7.4...

[DennisHeimbigner]

I guess ocprint is your white whale :-)