Looks like an issue with how you compiled Mumps / PETSc. Try compiling PETSc without Mumps support and see if it goes through...
Derek On Thu, Aug 16, 2012 at 8:53 AM, Kyunghoon Lee <[email protected]>wrote: > Thank you for the tip. > > Now I got link problems related to mpi: > > ---------------------------------------------- > ----- Done Building Contributed Packages ----- > ---------------------------------------------- > Linking bin/compare-dbg > Linking bin/grid2grid-dbg > Linking bin/amr-dbg > clang: warning: argument unused during compilation: '-ansi' > clang: warning: argument unused during compilation: '-ansi' > clang: warning: argument unused during compilation: '-ansi' > Undefined symbols for architecture x86_64: > "_mpi_abort__", referenced from: > Undefined symbols for architecture x86_64: > "_mpi_abort__", referenced from: > _mumps_abort__ in libmumps_common.a(mumps_part9.o) > Undefined symbols for architecture x86_64: > "_mpi_abort__", referenced from: > _mumps_abort__ in libmumps_common.a(mumps_part9.o) > _mumps_abort__ in libmumps_common.a(mumps_part9.o) > > I'm afraid this has something to do with two mpich2 libraries I installed > --- one by macports and the other one by petsc. I'm not sure whether I > should remove mpich2 installed by macports to avoid this kind of problem or > not. > > K. Lee. > > On Thu, Aug 16, 2012 at 8:50 PM, Cody Permann <[email protected]> > wrote: > > > We are seeing this too on OS X "Mountain Lion" with the latest XCode. We > > haven't figured this one out either. As a work-around, you can build and > > run successfully in static mode: > > ./configure --disable-shared > > > > Cody > > > > On Wed, Aug 15, 2012 at 10:44 PM, Kyunghoon Lee < > > [email protected]> wrote: > > > >> Hi all, > >> > >> I'd like to report a build error occurred during compiling metis: > >> > >> Compiling C (in debug mode) wspace.c... > >> Linking > >> > >> > /Users/aeronova/Development/local/lib/libmesh/svn-real/contrib/lib/x86_64-apple-darwin12.0.0_dbg/libmetis.dylib > >> ld: illegal thread local variable reference to regular symbol > >> _gk_cur_jbufs > >> for architecture x86_64 > >> clang: error: linker command failed with exit code 1 (use -v to see > >> invocation) > >> make[2]: *** > >> > >> > [/Users/aeronova/Development/local/lib/libmesh/svn-real/contrib/lib/x86_64-apple-darwin12.0.0_dbg/libmetis.dylib] > >> Error 1 > >> make[1]: *** [all] Error 2 > >> make: *** > >> > >> > [/Users/aeronova/Development/local/lib/libmesh/svn-real/lib/x86_64-apple-darwin12.0.0_dbg/libmesh.dylib] > >> Error 2 > >> > >> My configure options for libmesh are > >> > >> ./configure > >> --prefix=/Users/aeronova/Development/local/lib/libmesh/svn-real > >> --enable-petsc --enable-slepc --enable-glpk > >> > >> > --with-glpk-include=/Users/aeronova/Development/local/lib/glpk/4.35/include > >> --with-glpk-lib=/Users/aeronova/Development/local/lib/glpk/4.35/lib > >> --enable-ifem --enable-eigen > >> > >> > --with-eigen-include=/Users/aeronova/Development/local/lib/eigen/3.1.1/include/eigen3 > >> --disable-fparser > >> > >> , and those for petsc are > >> > >> ./configure > >> --prefix=/Users/aeronova/Development/local/lib/petsc/3.3-p2-real > >> --download-blacs=1 --download-metis=1 --download-parmetis=1 > >> --download-scalapack=1 --download-mumps=1 --download-umfpack=1 > >> --with-clanguage=C++ --download-mpich=1 > >> > >> I'd appreciate it if someone would take a look at the problem. > >> > >> Regards, > >> K. Lee. > >> > >> > ------------------------------------------------------------------------------ > >> Live Security Virtual Conference > >> Exclusive live event will cover all the ways today's security and > >> threat landscape has changed and how IT managers can respond. > Discussions > >> will include endpoint security, mobile security and the latest in > malware > >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > >> _______________________________________________ > >> Libmesh-users mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/libmesh-users > >> > > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
