I am trying to build a rpm for libmesh from svn on FC7. I have compiled libmesh with the following option with openmpi (openmpi-1.1-8.fc7) :
./configure --prefix=/usr/local/%{name}-openmpi-%{version} \
--enable-everything \
--enable-amr \
--enable-periodic \
--enable-pfem \
--enable-ifem \
--enable-complex \
--enable-second \
--enable-xdr \
--enable-reference-counting \
--enable-optional \
--enable-mpi \
--enable-petsc \
--enable-slepc \
--enable-tbb \
--enable-laspack \
--enable-sfc \
--enable-gzstreams \
--enable-tecplot \
--enable-metis \
--enable-parmetis \
--enable-tetgen \
--enable-triangle \
--enable-gmv \
--enable-vtk \
--enable-netcdf \
--enable-exodus \
--enable-libHilbert \
--with-vtk-lib=%{_libdir} \
CC=mpicc CXX=mpic++
The examples ex17 ends up with a seg fault :
***************************************************************
* Running Example ./ex17-opt -n 5
***************************************************************
Running ./ex17-opt -n 5
Mesh Information:
mesh_dimension()=2
spatial_dimension()=3
n_nodes()=441
n_local_nodes()=441
n_elem()=400
n_local_elem()=400
n_active_elem()=400
n_subdomains()=1
n_processors()=1
processor_id()=0
EquationSystems
n_systems()=1
System "Eigensystem"
Type "Eigen"
Variables="p"
Finite Element Types="LAGRANGE", "JACOBI_20_00"
Infinite Element Mapping="CARTESIAN"
Approximation Orders="FIRST", "THIRD"
n_dofs()=441
n_local_dofs()=441
n_constrained_dofs()=0
n_vectors()=0
Number of converged eigenpairs: 5
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 8, Fri Nov 16
17:03:40 CST 2007 HG revision: 414581156e67e55c761739b0deb119f7590d0f4b
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./ex17-opt on a linux-gnu named calcul8.lcmi.local by
trophime Tue Feb 26 09:43:19 2008
[0]PETSC ERROR: Libraries linked
from /usr/local/petsc/lib/linux-gnu-cxx-opt-openmpi
[0]PETSC ERROR: Configure run at Fri Feb 15 14:16:50 2008
[0]PETSC ERROR: Configure options --CFLAGS=-O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic --CXXFLAGS=-O2 -g -pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic --with-debugging=no
--PETSC_DIR=/home/trophime/rpmbuild/BUILD/petsc-2.3.3-p8
--PETSC_ARCH=linux-gnu-cxx-opt-openmpi --prefix=/usr/local/petsc
--with-shared --with-x=1 --download-hypre=1 --download-blopex=1
--with-clanguage=C++ --with-c-support
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[calcul8.lcmi.local:11513] [0,0,0] ORTE_ERROR_LOG: Not found in file
base/pls_base_proxy.c at line 189
-------------------------------------------------------------------
| Time: Tue Feb 26 09:43:19 2008 |
| OS: Linux |
| HostName: calcul8.lcmi.local |
| OS Release: 2.6.23.14-64.fc7 |
| OS Version: #1 SMP Sun Jan 20 22:20:19 EST 2008 |
| Machine: x86_64 |
| Username: trophime |
| Configuration: ./configure run on Tue Feb 26 09:33:39 CET 2008 |
-------------------------------------------------------------------
-------------------------------------------------------------------------------
| libMesh Performance: Alive time=0.211647, Active time=0.173877
|
-------------------------------------------------------------------------------
| Event nCalls Total Avg
Percent of |
| Time Time
Active Time |
|-------------------------------------------------------------------------------|
|
|
|
|
| DofMap
|
| add_neighbors_to_send_list() 1 0.0001 0.000145 0.08
|
| compute_sparsity() 1 0.0022 0.002247 1.29
|
| create_dof_constraints() 1 0.0001 0.000105 0.06
|
| distribute_dofs() 1 0.0016 0.001587 0.91
|
| dof_indices() 1200 0.0022 0.000002 1.25
|
| reinit() 1 0.0011 0.001084 0.62
|
| sort_send_list() 1 0.0000 0.000014 0.01
|
|
|
| FE
|
| compute_affine_map() 400 0.0010 0.000002 0.57
|
| compute_shape_functions() 400 0.0008 0.000002 0.45
|
| init_shape_functions() 1 0.0001 0.000091 0.05
|
|
|
| Mesh
|
| find_neighbors() 1 0.0015 0.001524 0.88
|
| renumber_nodes_and_elem() 1 0.0000 0.000029 0.02
|
|
|
| MeshTools::Generation
|
| build_cube() 1 0.0004 0.000410 0.24
|
|
|
| SlepcEigenSolver
|
| solve_generalized() 1 0.1568 0.156846 90.21
|
|
|
| System
|
| assemble() 1 0.0058 0.005832 3.35
|
-------------------------------------------------------------------------------
| Totals: 2012 0.1739
100.00 |
-------------------------------------------------------------------------------
make[2]: *** [run] Error 59
smime.p7s
Description: S/MIME cryptographic signature
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