I need to recompile netcdf-fortran-4.2 with intel-fortran in order to move it. I have successfully rebuilt its dependencies hdf5-1.8.11 and netcdf-4.3.0. I am compiling this in an HPC environment, using modules to load dependencies. Source is extracted from github. The build steps are as follows (ansible script)
source /etc/profile.d/modules.sh
export MODULEPATH={{ modulefiles_dir }}:$MODULEPATH
module load netcdf-4.3.0
autoreconf -i
./configure --prefix={{ install_dir }})/intel18/intelmpi2018/netcdf-4.3.0 CC=mpiicc CFLAGS=-march=core-avx2 FC=mpiifort FCFLAGS=-march=core-avx2
Although it compiles without any issues, when I compare the content of libnetcdff.so with the existing build using nm I see the following difference:
...
000000000006dec0 T netcdf_mp_nf90_var_par_access_
U nf_abort_
0000000000012470 T nf_abort__
U nf_close_
0000000000011fc0 T nf_close__
U nf_copy_att_
0000000000013090 T nf_copy_att__
0000000000013d50 T nf_copy_var__
U nf__create_
0000000000011c00 T nf__create__
U nf_create_
0000000000011b00 T nf_create__
U nf__create_mp_
00000000000120d0 T nf__create_mp__
U nf_create_par_
0000000000019c20 T nf_create_par__
U nf_def_compound_
...
Existing libnetcdff.so library:
...
000000000006c0e0 T netcdf_mp_nf90_var_par_access_
0000000000010690 T nf_abort_
00000000000101e0 T nf_close_
00000000000112b0 T nf_copy_att_
0000000000011f70 T nf_copy_var_
000000000000fe20 T nf__create_
000000000000fd20 T nf_create_
00000000000102f0 T nf__create_mp_
0000000000017e40 T nf_create_par_
0000000000018920 T nf_def_compound_
...
What clued me in to this is that next I have to rebuild an old version XIOS (1.0_rel660) which fails with unresoved symbols errors all over the place, as it is looking for symbols ending with '_' and not '__'.
I cannot for the life of me figure out why I am ending up with this. The only difference I can tell between my build and the existing build is the version of autoconf (2.69 vs. 2.66) and its associated tools. Otherwise I am using the same compiler versions (ifort 18.0.5 20180823, icc 18.0.5 20180823, gcc 4.8.5 20150623) which I also used to build the dependencies. Any ideas highly appreciated.
Double-underscore is something that the old g77 did. A convention on Linux and Unix is for Fortran global names to have a single underscore at the end, but g77 would sometimes use two underscores if the name itself contained an underscore.
By default, Intel Fortran doesn't do that, but you can ask it to by adding the option -assume 2underscores. However, I don't think you want to do that. Rebuild everything with the same compiler and options.