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 <[email protected]> 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 <[email protected] >> > >> 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? Download White paper >> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer >> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&; >> iu=/4140/ostg.clktrk >> _______________________________________________ >> Libmesh-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> >> >> ------------------------------------------------------------------------------ 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? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
