Hi Roy and Cody,
Sorry for the delay in answering… I had some problems with my HD and I needed
to reinstall the system.
I can’t say if any other example fails since I’m still stuck with this problem.
I have tried Clang and I can’t even build the library. I receive the following
error:
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
make[3]: Nothing to be done for `all-am'.
make[2]: Nothing to be done for `all-am'.
CXX src/base/libmesh_dbg_la-dof_map.lo
CXX src/base/libmesh_dbg_la-dof_map_constraints.lo
CXX src/base/libmesh_dbg_la-dof_object.lo
CXX src/base/libmesh_dbg_la-libmesh.lo
src/base/libmesh.C:40:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
make[1]: *** [src/base/libmesh_dbg_la-libmesh.lo] Error 1
make: *** [all-recursive] Error 1
I will try to make the other examples and see what happens. I will also try
MPICH2 instead of Open-MPI.
Currently I can’t paste the gdb output here because I am not able to build the
code neither with gcc or clang.
Best regards,
Daniel.
> On Jan 26, 2015, at 13:23, Cody Permann <[email protected]> wrote:
>
> Are there any other examples that are crashing? Just last week I found a
> repeatable problem that crashes or hangs everytime I run it on OS X Yosemite.
> Unfortunately it's a relatively complex problem with lots of different pieces
> of code including the use of SuperLU. We tried the same problem on a stack
> using MPICH2 instead of Open-MPI and I haven't gotten the problem to crash
> since! Since your issue is a serial run, it may be unrelated. Have you tried
> using Clang? It's a much better compiler on OS X, no need for Mac Ports.
>
> Cody
>
> On Sun Jan 25 2015 at 6:56:36 PM Daniel Vasconcelos <[email protected]
> <mailto:[email protected]>> wrote:
> Hi,
>
> I have recently upgraded from Mac OS X Maverick to Yosemite but so far I have
> had a lot of trouble to build libMesh on the system. I am using MacPorts to
> install the packages I need such as GCC, Open-MPI, PETSc and VTK.
>
> I configured the master version of libMesh with the following command (in
> attachment is the config log):
>
> ./configure \
> --prefix=/Users/dmva/Development/lib/libmesh-0.9.4 \
> --with-tbb=/opt/local \
> --with-eigen-include=/opt/local/include/eigen3 \
> --with-glpk-include=/opt/local/include \
> --with-glpk-lib=/opt/local/lib \
> --with-vtk-include=/opt/local/include/vtk-6.1 \
> --with-vtk-lib=/opt/local/lib \
> --with-slpec-include=/opt/local/include \
> --with-slepc-lib=/opt/local/lib/slepc/lib \
> --enable-mpi \
> --enable-perflog \
> --enable-dirichlet \
> --enable-periodic \
> --enable-nodeconstraint \
> --enable-blocked-storage \
> --enable-petsc \
> --enable-slepc \
> --enable-parmesh \
> --enable-vtk \
> --enable-examples \
> --disable-trilinos \
> --disable-hdf5 \
> --disable-netcdf-4 \
> --disable-netcdf \
> --disable-tecplot \
> --disable-tecio \
> METHOD=dbg
>
> When I run make check I receive an error on the example adjoints_ex1. See
> below:
>
> [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
> <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC> ERROR:
> or try http://valgrind.org <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: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.5.2, unknown
> [0]PETSC ERROR:
> /Users/dmva/Development/lib/libmesh/examples/adjoints/adjoints_ex1/.libs/example-opt
> on a arch-macports named MacBook-Pro-de-Daniel.local by dmva Sun Jan 25
> 20:51:29 2015
> [0]PETSC ERROR: Configure options --prefix=/opt/local
> --prefix=/opt/local/lib/petsc --with-valgrind=0 --with-shared-libraries
> --with-c2html-dir=/opt/local --with-x=0
> --with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate
> --with-hwloc-dir=/opt/local --with-debugging=1
> CC=/opt/local/bin/mpicc-openmpi-mp CXX=/opt/local/bin/mpicxx-openmpi-mp
> FC=/opt/local/bin/mpif90-openmpi-mp F77=/opt/local/bin/mpif90-openmpi-mp
> F90=/opt/local/bin/mpif90-openmpi-mp COPTFLAGS=-Os CXXOPTFLAGS=-Os
> FOPTFLAGS=-Os LDFLAGS="-L/opt/local/lib -Wl,-headerpad_max_install_names"
> CPPFLAGS=-I/opt/local/include CFLAGS="-Os -arch x86_64" CXXFLAGS=-Os
> FFLAGS=-Os FCFLAGS=-Os F90FLAGS=-Os PETSC_ARCH=arch-macports
> --with-mpiexec=mpiexec-openmpi-mp
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Any idea of what is going on? I have used the same setup on a Linux machine
> and it is working perfectly.
>
> Best Regards,
>
> Daniel.
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look and join the conversation now. http://goparallel.sourceforge.net/
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