Here is the error messages when I run the systems_of_equation ex1:
Memory out of range......
but this doesn't happen for PETSc examples.
Xujun
***************************************************************
* Running Example systems_of_equations_ex1:
* example-opt
***************************************************************
Mesh Information:
mesh_dimension()=2
spatial_dimension()=3
n_nodes()=961
n_local_nodes()=961
n_elem()=225
n_local_elem()=225
n_active_elem()=225
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
EquationSystems
n_systems()=1
System #0, "Stokes"
Type "LinearImplicit"
Variables={ "u" "v" } "p"
Finite Element Types="LAGRANGE", "JACOBI_20_00" "LAGRANGE",
"JACOBI_20_00"
Infinite Element Mapping="CARTESIAN" "CARTESIAN"
Approximation Orders="SECOND", "THIRD" "FIRST", "THIRD"
n_dofs()=2178
n_local_dofs()=2178
n_constrained_dofs()=0
n_local_constrained_dofs()=0
n_vectors()=1
n_matrices()=1
DofMap Sparsity
Average On-Processor Bandwidth <= 38.4683
Average Off-Processor Bandwidth <= 0
Maximum On-Processor Bandwidth <= 59
Maximum Off-Processor Bandwidth <= 0
DofMap Constraints
Number of DoF Constraints = 0
Number of Node Constraints = 0
[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: --------------------- Error Message
--------------------------------------------------------------*
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See 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: ./example-opt on a arch-darwin-c-debug named inl424641 by
xzhao Sat Jan 17 13:40:22 2015
[0]PETSC ERROR: Configure options --download-fblaslapack --download-mpich
--download-mumps --download-scalapack --download-hypre
-download-superlu_dist --download-parmetis --download-metis
--with-debugging --with-opencl=0
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
------------------------------------------------------------------------------------------------------------------
| Time: Sat Jan 17 13:40:22 2015
|
| OS: Darwin
|
| HostName: inl424641
|
| OS Release: 14.0.0
|
| OS Version: Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT
2014; root:xnu-2782.1.97~2/RELEASE_X86_64 |
| Machine: x86_64
|
| Username: xzhao
|
| Configuration: ./configure '-prefix=/Users/xzhao/software/libmesh_dbg'
|
| '--enable-everything'
|
| '--disable-strict-lgpl'
|
| 'PETSC_DIR=/Users/xzhao/software/petsc/petsc_352_dbg_gcc49'
|
| 'PETSC_ARCH=arch-darwin-c-debug'
|
------------------------------------------------------------------------------------------------------------------
On Sat, Jan 17, 2015 at 11:59 AM, Dmitry Karpeyev <[email protected]>
wrote:
> Sounds like something went wrong during configure/build.
> Can you send the complete PETSc error messages you get when running
> libMesh examples?
> Can you build with METHOD=dbg and see if the problem persists and whether
> this gives more information
> to work with? This is also required if you end up having to go after this
> with a debugger, but
> this behavior is most likely due to some build incompatibility. Could you
> capture the output of
> libMesh configure (and/or the resulting config.log) and send that?
>
> Thanks.
> Dmitry.
>
> On Sat Jan 17 2015 at 11:13:56 AM Xujun Zhao <[email protected]> wrote:
>
>> Hi folks,
>>
>> I have a strange situation. The PETSc and libmesh are installed
>> successfully, and I didn't see anything wrong during installation. when I
>> run libmesh examples, they pass the 'make', but some errors came out
>> immediately during run, like this:
>>
>> inl424641:ex1 xzhao$ make
>>
>> Compiling C++ (in optimized mode) introduction_ex1.C...
>>
>> mpicxx -DNDEBUG -std=gnu++11 -O2 -felide-constructors -funroll-loops
>> -fstrict-aliasing -Wdisabled-optimization -fopenmp
>> -I/Users/xzhao/software/libmesh_xzhao/include -D_THREAD_SAFE -pthread
>> -I/Users/xzhao/software/petsc/petsc_352_opt_gcc49/include
>> -I/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/include
>> -I./contrib/boost/include -c introduction_ex1.C -o
>> introduction_ex1.x86_64-apple-darwin14.0.0.opt.o
>>
>> Linking example-opt...
>>
>> libtool: link: mpicxx -std=gnu++11 -O2 -felide-constructors -funroll-loops
>> -fstrict-aliasing -Wdisabled-optimization -fopenmp
>> introduction_ex1.x86_64-apple-darwin14.0.0.opt.o -o example-opt
>> -Wl,-rpath
>> -Wl,/Users/xzhao/software/libmesh_xzhao/lib -Wl,-bind_at_load
>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-darwin-c-opt/lib
>> -L/usr/local/Cellar/gcc/4.9.2/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2
>> -L/usr/local/Cellar/gcc/4.9.2/lib
>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/externalpackages/mpich-3.1/src/mpl
>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/externalpackages/mpich-3.1/src/openpa/src
>> -L/Users/xzhao/software/libmesh_xzhao/lib
>> /Users/xzhao/software/libmesh_xzhao/lib/libmesh_opt.dylib
>> /Users/xzhao/software/libmesh_xzhao/lib/libnetcdf.dylib -lcurl -lz
>> -lpetsc
>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
>> -lsuperlu_dist_3.3 -lHYPRE -lflapack -lfblas -lparmetis -lmetis -lssl
>> -lcrypto
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libmpichf90.dylib
>> -lgfortran -lquadmath -lm
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libmpichcxx.dylib
>> -lstdc++
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libpmpich.dylib
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libmpich.dylib
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libopa.dylib
>> -lpthread
>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-
>> darwin-c-opt/lib/libmpl.dylib
>> -lSystem -lgcc_ext.10.5 -ldl -fopenmp
>>
>> inl424641:ex1 xzhao$ sh run.sh
>>
>> ***************************************************************
>>
>> * Running Example introduction_ex1:
>>
>> * example-opt -d 3
>> /Users/xzhao/software/libmesh_xzhao/reference_elements/3D/one_hex27.xda
>>
>> ***************************************************************
>>
>>
>>
>> Stack frames: 2
>>
>> 0: 0 libmesh_opt.0.dylib 0x0000000109843730
>> libMesh::print_trace(std::ostream&) + 1520
>>
>> 1: 1 libmesh_opt.0.dylib 0x0000000109841b0c
>> libMesh::MacroFunctions::report_error(char const*, int, char const*, char
>> const*) + 124
>>
>> [0] src/utils/xdr_cxx.C, line 227, compiled Jan 17 2015 at 10:13:44
>>
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>
>> [unset]: aborting job:
>>
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>
>>
>>
>> I also tried some other examples, unfortunately, all failed! For some of
>> them, it showed PETSc errors, although there were no problems when I run
>> several PETSc examples. Can anyone help me figure out why?
>>
>> thanks a lot.
>>
>> Xujun
>> ------------------------------------------------------------
>> ------------------
>> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
>> GigeNET is offering a free month of service with a new server in Ashburn.
>> Choose from 2 high performing configs, both with 100TB of bandwidth.
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>> _______________________________________________
>> Libmesh-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>
------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
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