On Tue, Jul 5, 2016 at 12:25 PM, gmail <a.mesgarne...@gmail.com> wrote:
> Dear developers, > > (I appologize if you are getting multiple copies of this, I sent this > email previously using my other email address that I don’t think is in the > list.) > > I’m getting a NetCDF symbol error when I try to compile libMesh (commit > a58bb96d07c20eb541b557b0053269e6d8c92f15) vs PETSc 3.7.2 (commit > 6d2c40479446d0366a4edb124b2d1250692ca322): > > make[1]: Entering directory > `/home/mesgarnejad/Packages/libmesh/build/Linux-gnu-O' > CXXLD fparser_parse-opt > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libpetsc.so: undefined > reference to `nc_def_var_deflate' > collect2: error: ld returned 1 exit status > make[1]: *** [fparser_parse-opt] Error 1 > make[1]: Leaving directory > `/home/mesgarnejad/Packages/libmesh/build/Linux-gnu-O' > make: *** [all-recursive] Error 1 > > It’s confusing since the libpetsc.so knows where to find the correct > libnetcdf.so: > > > linux-vdso.so.1 => (0x00007ffce6388000) > libsuperlu_dist.so.5 => > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libsuperlu_dist.so.5 > (0x00007f24966f4000) > libparmetis.so => > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libparmetis.so > (0x00007f24964b6000) > libmetis.so => > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libmetis.so > (0x00007f2496240000) > libsuperlu.so.5 => > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib64/libsuperlu.so.5 > (0x00007f2495fc0000) > libmpi_cxx.so.1 => > /shared/opt/openmpi/gcc-5.4.0/lib/libmpi_cxx.so.1 (0x00007f2495da6000) > libstdc++.so.6 => /shared/opt/gcc/lib64/libstdc++.so.6 > (0x00007f2495a18000) > libhwloc.so.5 => /usr/lib64/libhwloc.so.5 (0x00007f24957d9000) > libnetcdf.so.7 => > /home/mesgarnejad/Packages/petsc/Linux-gnu-O/lib/libnetcdf.so.7 > (0x00007f24954cf000) > I'm not clear on exactly what you've done here. You built NetCDF as an external package in PETSc? Did you somehow tell libmesh to use this NetCDF rather than the NetCDF that is bundled with libmesh? I'm looking at our netcdf.m4, it does not look like we intended this to be possible (there is not --with-netcdf= flag) so I'm not surprised that it doesn't quite work... I attached my config.log from libMesh + you can get my configure.log < > https://www.dropbox.com/s/82yp61eequjr0p3/configure.log?dl=0>from PETSc. Unfortunately dropbox links are blocked at my office, so I can't see this link at the moment. -- John ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
