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
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