Name collision with new UTF8 library, pnetcdf 1.6.1

[WardF]

I have not tested this with a newer version of pnetcdf; the latest support is 1.6.1, until we're able to resolve the issues around #319 .

In trying to move our regression testing to newer versions of Ubuntu and the openmpi/mpich libraries, I've encountered a couple issues. The first, we have name collisions between libnetcdf and libpnetcdf, as shown below. These functions are utf8 related and I'm sure come from the adoption of the new utf8 library. I didn't think to check before merging into master, and I will refactor the netcdf functions to avoid this collision in the future. It first arose with netCDF but could have occurred in any application which uses the same open-source utf8 implementation.

[WardF]

[ 20%] Linking C shared library libnetcdf.so
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_errmsg':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:110: multiple definition of `utf8proc_errmsg'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:95: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_iterate':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:133: multiple definition of `utf8proc_iterate'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:115: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_errmsg':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:110: multiple definition of `utf8proc_utf8class'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:(.rodata+0x44600): first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_codepoint_valid':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:169: multiple definition of `utf8proc_codepoint_valid'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:161: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_encode_char':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:174: multiple definition of `utf8proc_encode_char'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:165: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_get_property':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:207: multiple definition of `utf8proc_get_property'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:232: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o):(.rodata+0x216c0): multiple definition of `utf8proc_stage1table'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:(.rodata+0x4980): first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o):(.rodata+0x160c0): multiple definition of `utf8proc_stage2table'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:(.rodata+0x6b80): first defined here
/usr/bin/ld: Warning: size of symbol `utf8proc_stage2table' changed from 77824 in ../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o to 46592 in /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_errmsg':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:110: multiple definition of `utf8proc_properties'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:(.rodata+0x19b80): first defined here
/usr/bin/ld: Warning: size of symbol `utf8proc_properties' changed from 163848 in ../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o to 314608 in /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_decompose_char':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:217: multiple definition of `utf8proc_decompose_char'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:398: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_decompose':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:364: multiple definition of `utf8proc_decompose'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:486: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_reencode':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:423: multiple definition of `utf8proc_reencode'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:669: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_iterate':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:156: multiple definition of `utf8proc_combinations'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:(.rodata+0x41ba0): first defined here
/usr/bin/ld: Warning: size of symbol `utf8proc_combinations' changed from 10820 in ../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o to 90000 in /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_map':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:540: multiple definition of `utf8proc_map'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:695: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_NFD':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:567: multiple definition of `utf8proc_NFD'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:729: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_NFC':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:574: multiple definition of `utf8proc_NFC'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:736: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_NFKD':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:581: multiple definition of `utf8proc_NFKD'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:743: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o): In function `utf8proc_NFKC':
/home/tester/parallel-netcdf-1.6.1/src/lib/utf8proc.c:588: multiple definition of `utf8proc_NFKC'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:750: first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o):(.rodata+0x238c0): multiple definition of `utf8proc_sequences'
../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o:/home/tester/netcdf-c/libdispatch/utf8proc.c:91: first defined here
/usr/bin/ld: Warning: size of symbol `utf8proc_sequences' changed from 18808 in ../libdispatch/CMakeFiles/dispatch.dir/utf8proc.c.o to 46016 in /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libpnetcdf.a(utf8proc.o)
collect2: error: ld returned 1 exit status
liblib/CMakeFiles/netcdf.dir/build.make:302: recipe for target 'liblib/libnetcdf.so.11.4.0' failed
make[2]: *** [liblib/libnetcdf.so.11.4.0] Error 1
CMakeFiles/Makefile2:1533: recipe for target 'liblib/CMakeFiles/netcdf.dir/all' failed
make[1]: *** [liblib/CMakeFiles/netcdf.dir/all] Error 2

[DennisHeimbigner]

If pnetcdf is using utf8proc, then it needs to upgrade to the same versions we are using
in netcdf. As I mentioned elsewhere, we can make everything in utf8proc.c be static
except the 2 or 3 functions I mentioned. We could rename those functions by prepending
them with e.g. nc_.

[WardF]

That was my thought; I have my hands full tonight but will pretend the relevant functions with nc_ tomorrow before turning back to unravel the issues with #319 on ARM.

[wkliao]

I found this problem as well.
Starting from PnetCDF 1.8.0, I added the prefix "ncmpi_" to those functions in utf8 related files.
The problem should go away if using 1.8.0 and later.

[WardF]

I was going to drop you a note this morning @wkliao but I'm glad to see you've already addressed this :). Once I get this taken care of I will return to resolving the issues on #319 so that we can finally get that taken care of and start using the latest parallel netcdf! Updating our regression test docker images to the latest Ubuntu has uncovered a handful of issues that needed to be resolved, so it's taken a little bit longer than expected.