On Tue, May 17, 2016 at 12:17 PM, Kathrin Smetana <ksmet...@mit.edu> wrote:
> Hi all, > > I have just installed and configured libmesh (version 0.9.4) using PETSC > 3.4.5. During making check I got the following error in introduction_ex3: > > [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/documentation/faq.html#valgrind[0]PETSC > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] VecMAXPY line 1246 > /home/kathrin/Implementations/petsc-3.4.5/src/vec/vec/interface/rvector.c > [0]PETSC ERROR: [0] KSPGMRESClassicalGramSchmidtOrthogonalization line 45 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/borthog2.c > [0]PETSC ERROR: [0] KSPGMRESCycle line 131 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve_GMRES line 229 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve line 356 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.4.5, Jun, 29, 2014 > [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: > /home/kathrin/Implementations/libmesh/examples/introduction/introduction_ex3/.libs/lt-example-dbg > on a arch-linux2-cxx-debug named kathrin-920W-PS by kathrin Tue May 17 > 12:03:44 2016 > [0]PETSC ERROR: Libraries linked from > /home/kathrin/Implementations/petsc-3.4.5/arch-linux2-cxx-debug/lib > [0]PETSC ERROR: Configure run at Tue May 17 10:52:34 2016 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/kathrin/Implementations/mpich-install > --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 > --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 > --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 > --download-metis --with-scalar-type=complex --with-clanguage=cxx > PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > However, if I just run example-opt of the same example I do not observe > any problems. Most likely because you didn't run with the same number of refinement steps that 'make check' uses? Try libtool --mode=execute ./example-opt refinement_type=matchedhp max_r_steps=5 instead? > I have configured libmesh with the following options: > > ./configure --enable-eigen --enable-shared --enable-everything > --enable-complex --prefix=/home/kathrin/Implementations/libmesh-install/ > --with-metis=PETSc > CXX=/home/kathrin/Implementations/mpich-install/bin/mpicxx > CC=/home/kathrin/Implementations/mpich-install/bin/mpicc > PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > > Does anyone of you has any idea how to fix this? > Your best bet is probably to update to a newer version of PETSc. Since the segfault originates there, and none of us can reproduce the problem using newer PETScs, that may just fix your problem. You could also ignore the issue and see if your build just works OK for your current project... -- John ------------------------------------------------------------------------------ Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
