Hi all,
I am trying to install libmesh with petsc and openmpi on OS X 10.6.
libmesh configuration (exact petsc and libmesh configure options are given
below) and compilation worked fine but compiling the examples gives the warnings
ld: warning: directory
'-L/Users/agerner/Software/slepc-3.0.0-p7/x86_64-apple-darwin10.0/lib'
following -L not found
ld: warning: duplicate dylib /opt/local/lib/libz.1.dylib
and running ex 9 shows the following error:
***************************************************************
* Running Example ./ex9-opt
***************************************************************
Mesh Information:
mesh_dimension()=2
spatial_dimension()=3
n_nodes()=6273
n_local_nodes()=6273
n_elem()=13650
n_local_elem()=13650
n_active_elem()=10240
n_subdomains()=1
n_processors()=1
processor_id()=0
ERROR: cannot convert system "Convection-Diffusion" to requested type!
[0] /Users/agerner/Software/libmesh/include/systems/equation_systems.h, line
668, compiled Jun 9 2010 at 17:17:04
terminate called after throwing an instance of 'libMesh::LogicError'
what(): Error in libMesh internal logic
[93-024:47101] *** Process received signal ***
[93-024:47101] Signal: Abort trap (6)
[93-024:47101] Signal code: (0)
[93-024:47101] [ 0] 2 libSystem.B.dylib 0x00007fff85dc480a
_sigtramp + 26
[93-024:47101] [ 1] 3 ??? 0x00007fff5fbfdae0
0x0 + 140734799796960
[93-024:47101] [ 2] 4 libstdc++.6.dylib 0x00007fff839b65d2
__tcf_0 + 0
[93-024:47101] [ 3] 5 libobjc.A.dylib 0x00007fff84356d3d
_objc_terminate + 120
[93-024:47101] [ 4] 6 libstdc++.6.dylib 0x00007fff839b4ae1
_ZN10__cxxabiv111__terminateEPFvvE + 11
[93-024:47101] [ 5] 7 libstdc++.6.dylib 0x00007fff839b4b16
_ZN10__cxxabiv112__unexpectedEPFvvE + 0
[93-024:47101] [ 6] 8 libstdc++.6.dylib 0x00007fff839b4bfc
_ZL23__gxx_exception_cleanup19_Unwind_Reason_CodeP17_Unwind_Exception + 0
[93-024:47101] [ 7] 9 ex9-opt 0x000000010000b89e
_ZN15EquationSystems10get_systemI15TransientSystemI20LinearImplicitSystemEEERT_RKSs
+ 1422
[93-024:47101] [ 8] 10 ex9-opt 0x0000000100001999
_Z7init_cdR15EquationSystemsRKSs + 57
[93-024:47101] [ 9] 11 libmesh.dylib 0x000000010137945d
_ZN15EquationSystems4initEv + 781
[93-024:47101] [10] 12 ex9-opt 0x000000010000208c
main + 684
[93-024:47101] [11] 13 ex9-opt 0x0000000100001958
start + 52
[93-024:47101] *** End of error message ***
make[2]: *** [run] Abort trap
make[1]: *** [run] Error 1
make: *** [run_examples] Error 2
Concerning the latter, David Maxwell et al. already provided some information
on or about 2010-04-27 (indeed, building libmesh as a static library solves the
issue...) but still, I do not exactly understand what is happening there.
I would be very grateful for any further explanations on this.
-Anna
petsc configure options:
./config/configure.py --with-fc=0 --with-mpi=1 --download-openmpi=1
--with-x11=1 --with-umfpack=1
--with-umfpack-include=/opt/local/include/ufsparse
--with-umfpack-lib=[/opt/local/lib/libamd.a,/opt/local/lib/libcamd.a,/opt/local/lib/libccolamd.a,/opt/local/lib/libcholmod.a,/opt/local/lib/libcolamd.a,/opt/local/lib/libumfpack.a]
libmesh configuration:
CC=mpicc CXX=mpicxx ./configure LIBS="-L/opt/local/lib -lgsl -lgslcblas -lglpk"
--enable-everything=yes --enable-slepc=yes
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