That's interesting: link_all_deplibs is set to "no" on this Ubuntu 14.04 machine. However, it is set to "unknown" on a machine running Ubuntu 13.04, where everything works fine.
FYI, uninstalling the system netcdf and starting from a fresh clone didn't work, but Miguel's workaround did. Dana On Fri, Oct 3, 2014 at 5:46 PM, Roy Stogner <royst...@ices.utexas.edu> wrote: > > Hey, here's a question - what does link_all_deplibs get set to in your > ./libtool script? Debian+Ubuntu disable that, but we depend on it. I > *thought* that our practice of distributing the output of bootstrap > was enough to avoid requiring deb users to build their own autotools, > but perhaps that's not the case. > --- > Roy > > > On Fri, 3 Oct 2014, Dana Christen wrote: > > Hi Roy, >> >> Thanks for your reply. Uninstalling the system netcdf doesn't help. >> Running make -n shows that the problematic command is the following: >> >> /bin/bash ./libtool --silent --tag=CXX --mode=link mpicxx -std=gnu++11 >> -O2 -felide-constructors -funroll-loops -fstrict-aliasing >> -Wdisabled-optimization -fopenmp -std=gnu++11 -o meshid-opt >> src/apps/meshid_opt-meshid.o libmesh_opt.la -L/lib -lhdf5 >> -Wl,-rpath,/lib -lz >> -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/slepc///lib >> -L/home/dana/software/libmesh_install/opt_real/slepc///lib -lslepc >> -L/home/dana/software/libmesh_install/opt_real/petsc/lib >> -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.7 >> -L/usr/lib/x86_64-linux-gnu >> -L/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lpetsc >> -lX11 -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/petsc/lib >> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis >> -lmetis -lscalapack -lblacs -lHYPRE -Wl,-rpath,/usr/lib/openmpi/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.7 >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >> -Wl,-rpath,/lib/x86_64-linux-gnu >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -lumfpack -lamd -llapack >> -lblas -lmpi_f90 -lmpi_f77 -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ >> -lmpi -lhwloc -lgcc_s -lpthread -ldl >> >> I can work around the problem by manually adding the path to the compiled >> netcdf library (in my case >> /mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7). >> Note that simply adding -lnetcdf to that command >> works too (in this case the system library is used if it's installed). >> >> I'm going to try Miguel's workaround. I'll keep you posted. >> >> Dana >> >> On Fri, Oct 3, 2014 at 3:51 PM, Roy Stogner <royst...@ices.utexas.edu> >> wrote: >> >> On Fri, 3 Oct 2014, Dana Christen wrote: >> >> Just realized there was a typo in my original message: I >> updated to Ubuntu >> 14.04 (latest long-term-support version). This error occurs >> with GCC 4.7.3, >> GCC 4.8.2, with and without the system netcdf libraries. >> >> >> You're not the first person to run into this: >> >> http://comments.gmane.org/gmane.comp.mathematics.libmesh.user/6345 >> >> But I'm running on Ubuntu 14.04 and have never managed to replicate >> the problem. I've never had the system netcdf installed, though; if >> you can uninstall that and try building from a fresh directory >> hopefully your system will work like mine. >> >> If that doesn't work (and please let us know either way), you can >> try >> the workaround Miguel had success with: configure >> --enable-netcdf=old --enable-exodus=old --enable-nemesis=old >> --- >> Roy >> >> On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen < >> dana.chris...@akselos.com> >> wrote: >> >> Hello, >> >> I updated my workstation to Ubuntu 10.04 and libMesh >> now fails to compile. >> I'm getting the following error while compiling the >> latest revision of a >> fresh libmesh clone: >> >> (...) >> CXXLD meshid-opt >> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined >> reference to symbol >> 'nc_close' >> //mnt/DATA/dana/software/libmesh_build/opt_real/ >> contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: >> error adding symbols: DSO missing from command line >> collect2: error: ld returned 1 exit status >> make[1]: *** [meshid-opt] Error 1 >> make[1]: Leaving directory `/mnt/DATA/dana/software/ >> libmesh_build/opt_real' >> make: *** [all-recursive] Error 1 >> >> The libnetcdf package is not installed on my system and >> I'm doing an >> out-of-tree build. Here's my configure line: >> >> /mnt/DATA/dana/software/libmesh-src/configure >> --enable-everything >> --enable-slepc --with-metis=PETSc >> --with-subdomain-id-bytes=4 >> --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/ >> software/libmesh_install >> --with-methods=opt --enable-shared >> >> The new version of GCC that was installed is the >> following: gcc (Ubuntu >> 4.8.2-19ubuntu1) 4.8.2 >> >> Any help would be greatly appreciated. >> >> Thanks, >> Dana >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? 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