Dear libmesh users,
I am trying to link matlab and libmesh. I wrote a very stupide mex file
"mex_loadlibmesh.cxx" (see below) to test the inital call of libmesh
from matlab. The problem is that my mex file never stop ! I suspect of
course a problem related to MPI but I have no idea how to fix this. Some
additional informations : I am using a standard libmesh installation
(+MPICH2+PETSC+SLEPC) on linux 64b. Every libmesh examples run very well
with one or more processors. You will find below the console ouput with
some details on my installation.
I compiled this file on the command line (outside of matlab) by the
following instructions (which are the standard instructions to build mex
files) :
Any suggestions are welcome,
best regards,
Edouard.
#-----------------------------------------------------------------------------
# Compile
#-----------------------------------------------------------------------------
HOMEMATLAB=/usr/local/matlab
MATLABCOMPILE="-I${HOMEMATLAB}/extern/include -DMATLAB_MEX_FILE -ansi
-D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -DTETLIBRARY
-DMX_COMPAT_32 -DNDEBUG -O -w"
MATLABLINK="-O -pthread -shared
--version-script,${HOMEMATLAB}/extern/lib/glnxa64/mexFunction.map
-Wl,--no-undefined -o mexversion.o
-Wl,-rpath-link,${HOMEMATLAB}/bin/glnxa64 -L${HOMEMATLAB}/bin/glnxa64
-lmx -lmex -lmat -lm"
FILETOCOMPILE=mex_loadlibmesh
${LIBMESH_CXX} -c ${HOMEMATLAB}/extern/src/mexversion.c ${MATLABCOMPILE}
${LIBMESH_CXX} -c ${FILETOCOMPILE}.cxx ${MATLABCOMPILE}
${LIBMESH_CXXFLAGS} ${LIBMESH_INCLUDEPERSO}
${LIBMESH_CXX} ${FILETOCOMPILE}.o ${MATLABLINK}
${LIBMESH_CXXFLAGS} ${LIBMESH_LIBS} ${LIBMESH_LDFLAGS}
${LIBMESH_INCLUDEPERSO} -o ${FILETOCOMPILE}.mexa64
#-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// mex_loadlibmesh.cxx
//-----------------------------------------------------------------------------
#include <iostream>
// Functions to initialize the library.
#include "libmesh.h"
// Matlab include
#include "mex.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
int argc;char **argv;
// Initialize libMesh and the dependent libraries.
argc = 2;
argv = new char*[argc];
argv[0] = new char[20];
argv[0] = "test";
argv[1] = new char[20];
argv[1] = "-log_summary";
LibMeshInit init(argc, argv);
std::cout << "LibMeshInit done " << std::endl;
return;
}
//-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
# OUTPUT
#-----------------------------------------------------------------------------
>> mex_loadlibmesh
LibMeshInit done
************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r
-fCourier9' to print this document ***
************************************************************************************************************************
---------------------------------------------- PETSc Performance Summary:
----------------------------------------------
test on a linux-gnu named lama.univ-savoie.fr with 1 processor, by oudet Tue
Mar 16 11:55:07 2010
Using Petsc Release Version 3.0.0, Patch 11, Mon Feb 1 11:01:51 CST 2010
Max Max/Min Avg Total
Time (sec): 2.091e-04 1.00000 2.091e-04
Objects: 0.000e+00 0.00000 0.000e+00
Flops: 0.000e+00 0.00000 0.000e+00 0.000e+00
Flops/sec: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00
MPI Reductions: 0.000e+00 0.00000
Flop counting convention: 1 flop = 1 real number operation of type
(multiply/divide/add/subtract)
e.g., VecAXPY() for real vectors of length N --> 2N
flops
and VecAXPY() for complex vectors of length N -->
8N flops
Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- --
Message Lengths -- -- Reductions --
Avg %Total Avg %Total counts %Total
Avg %Total counts %Total
0: Main Stage: 2.0695e-04 99.0% 0.0000e+00 0.0% 0.000e+00 0.0%
0.000e+00 0.0% 0.000e+00 0.0%
------------------------------------------------------------------------------------------------------------------------
See the 'Profiling' chapter of the users' manual for details on interpreting
output.
Phase summary info:
Count: number of times phase was executed
Time and Flops: Max - maximum over all processors
Ratio - ratio of maximum to minimum over all processors
Mess: number of messages sent
Avg. len: average message length
Reduct: number of global reductions
Global: entire computation
Stage: stages of a computation. Set stages with PetscLogStagePush() and
PetscLogStagePop().
%T - percent time in this phase %F - percent flops in this phase
%M - percent messages in this phase %L - percent message lengths in
this phase
%R - percent reductions in this phase
Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all
processors)
------------------------------------------------------------------------------------------------------------------------
Event Count Time (sec) Flops
--- Global --- --- Stage --- Total
Max Ratio Max Ratio Max Ratio Mess Avg len Reduct
%T %F %M %L %R %T %F %M %L %R Mflop/s
------------------------------------------------------------------------------------------------------------------------
--- Event Stage 0: Main Stage
------------------------------------------------------------------------------------------------------------------------
Memory usage is given in bytes:
Object Type Creations Destructions Memory Descendants' Mem.
--- Event Stage 0: Main Stage
========================================================================================================================
Average time to get PetscTime(): 0
#PETSc Option Table entries:
-log_summary
#End o PETSc Option Table entries
Compiled without FORTRAN kernels
Compiled with full precision matrices (default)
sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8
sizeof(PetscScalar) 8
Configure run at: Mon Mar 15 08:51:22 2010
Configure options: --with-cc=gcc --with-fc=gfortran --with-mpi-compilers=0
--with-shared=1 --with-debugging=0 --with-superlu=1 --download-superlu=1
--with-superlu_dist=1 --download-superlu_dist=1 --with-umfpack=1
--download-umfpack=1 --with-spooles=1 --download-spooles=1 --with-mpi
--download-mpich=1 --download-f-blas-lapack=yes --with-parmetis
--download-parmetis=1 --with-hypre --download-hypre=1
-----------------------------------------
Libraries compiled on Mon Mar 15 08:51:23 CET 2010 on lama.univ-savoie.fr
Machine characteristics: Linux lama.univ-savoie.fr 2.6.31-20-generic #57-Ubuntu
SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux
Using PETSc directory: ~/C++/Petsc/petsc-3.0.0-p11
Using PETSc arch: linux-gnu-opt
-----------------------------------------
Using C compiler: ~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/bin/mpicc -fPIC
-Wall -Wwrite-strings -Wno-strict-aliasing -O
Using Fortran compiler: ~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/bin/mpif90
-fPIC -Wall -Wno-unused-variable -O
-----------------------------------------
Using include paths: -I/~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/include
-I~/C++/Petsc/petsc-3.0.0-p11/include
-I~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/include
------------------------------------------
Using C linker: ~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/bin/mpicc -fPIC -Wall
-Wwrite-strings -Wno-strict-aliasing -O
Using Fortran linker: ~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/bin/mpif90
-fPIC -Wall -Wno-unused-variable -O
Using libraries: -Wl,-rpath,~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib
-L~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib -lpetscts -lpetscsnes
-lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lX11
-Wl,-rpath,~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib
-L~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib -lspooles -lHYPRE
-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.1
-Wl,-rpath,/usr/lib/x86_64-linux-gnu -lmpichcxx -lstdc++ -lsuperlu_dist_2.3
-lsuperlu_3.1 -lumfpack -lamd -lflapack -lfblas -lparmetis -lmetis -lnsl -lrt
-Wl,-rpath,~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib
-L~/C++/Petsc/petsc-3.0.0-p11/linux-gnu-opt/lib
-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.1
-L/usr/lib/gcc/x86_64-linux-gnu/4.4.1 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -lmpichf90
-lgfortranbegin -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu
-L/usr/lib/gcc/x86_64-linux-gnu -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++
-ldl -lmpich -lpthread -lrt -lgcc_s -ldl
------------------------------------------
--
Edouard Oudet : http://www.lama.univ-savoie.fr/~oudet/
Université de Savoie
Laboratoire de Mathématiques (LAMA) UMR 5127
Campus Scientifique
73 376 Le-Bourget-Du-Lac
+33 (0)4 79 75 87 65 (office)
+33 (0)4 79 68 82 06 (home)
------------------------------------------------------------------------------
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