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Re: [Libmesh-users] segmentation fault error for testing examples on a Mac
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From: Kyunghoon L. <gt...@gm...> - 2011-06-01 03:44:54
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>> On Tue, May 31, 2011 at 1:08 PM, Kyunghoon Lee <gt...@gm...> wrote: >>> Hello, >>> >>> I'm trying to install libmesh on a MacOS X 10.6.7, which has a gcc-4.2 compiler from Xcode 3.2.6. I had no trouble with compiling libmesh, but I got a seg fault error for the examples. >>> >>> First, I source-compiled petsc with the following configuration option: >>> >>> export PETSC_DIR=$PWD >>> ./config/configure.py --prefix=/usr/local/share/petsc/petsc-3.1-p8 --with-cc=gcc --with-cxx=g++ --with-fc=0 —download-c-blas-lapack=1 --download-mpich=1 >>> make >>> sudo make install PETSC_DIR=$PWD >>> make PETSC_DIR=/usr/local/share/petsc/petsc-3.1-p8 test >>> >>> and test results were good. After petsc, I source-compiled an svn version of libmesh with the following configuration option: >>> >>> export METHOD=dbg >>> ./configure PETSC_DIR=/usr/local/share/petsc/petsc-3.1-p8 --enable-petsc > On May 31, 2011, at 1:22 PM, John Peterson wrote: >> >> It's possible libmesh is using the wrong mpicc/mpicxx compilers when >> you use this configuration line. It will use the first one it finds >> in your path, *not* the one you downloaded with PETSc. >> >> So could you try: >> >> CXX=/path/to/petsc/mpich/bin/mpicxx CC=/path/to/petsc/mpich/bin/mpicc >> ./configure >> >> and see if you have any better luck with the executables? >> >> -- >> John >> >> ------------------------------------------------------------------------------ >> Simplify data backup and recovery for your virtual environment with vRanger. >> Installation's a snap, and flexible recovery options mean your data is safe, >> secure and there when you need it. Data protection magic? >> Nope - It's vRanger. Get your free trial download today. >> http://p.sf.net/sfu/quest-sfdev2dev >> _______________________________________________ >> Libmesh-users mailing list >> Lib...@li... >> https://lists.sourceforge.net/lists/listinfo/libmesh-users On May 31, 2011, at 3:28 PM, Derek Gaston wrote: > To avoid this... if you are not needing to compile any fortran then you can just use the MPI that comes with OSX (OpenMP). Just set CC, CXX, etc to mpicc, mpicxx etc for both PetsC and libMesh... and don't tell PetsC to download mpich. > > Note that we don't typically work this way. We usually download a third party MPI (like MPICH2)... compile it and install it somewhere on our system... then set our path and compiler environment variables to point to this location and compile both PetsC and libMesh with it. This has the nice property that it is a bit more reusable across multiple packages you might be compiling on your system. > > So there are lots of options.... > > Derek Thanks to John, Derek, and David's help, I was able to compile petsc and libmesh successfully on my Mac. As they pointed out, the main problem was caused by inconsistent compilers used in building petsc and libmesh. So I tried to use the same mpicc and mpicxx compilers. First, I used "--download-mpich=1" option in configuring petsc. This way I can get mpicc from petsc-3.1-p8/externalpackages/ when petsc was compiled. However, somehow I could not get mpicxx. Second, I used mpicc and mpicxx that come with Apple's Xcode. I set export CXX=/usr/bin/mpicxx export CC=/usr/bin/mpicc , but I got seg fault errors when I tested the compiled petsc with examples. Last, I installed mpich2 separately using MacPorts such that sudo port -v install mpich2 +default_mpi , and then used mpicc and mpicxx from the MacPorts' mpich2 as follows: export CXX=/opt/local/bin/mpicxx export CC=/opt/local/bin/mpicc After that, I compiled petsc using the following commands. export PETSC_DIR=$PWD export CXX=/opt/local/bin/mpicxx export CC=/opt/local/bin/mpicc ./config/configure.py --prefix=/usr/local/share/petsc/petsc-3.1-p8 --with-fc=0 --download-c-blas-lapack=1 make sudo make install PETSC_DIR=$PWD make PETSC_DIR=/usr/local/share/petsc/petsc-3.1-p8 test (Note that I don't need Fortran, and I put the compiled petsc under /usr/local/share) I had no errors in testing the compiled petsc. Finally, I compiled libmesh with the following commands. export METHOD=dbg export CXX=/opt/local/bin/mpicxx export CC=/opt/local/bin/mpicc ./configure PETSC_DIR=/usr/local/share/petsc/petsc-3.1-p8 --enable-petsc make make run_examples Although I got the same warnings repetitively (plz see the below) for building libmesh and testing examples, all examples worked fine. I really appreciate all the help from the nice guys! Best regards, K. Lee. p.s. The below is the warning messages I got for building libmesh and examples: /opt/local/include/mpicxx.h:386: warning: unused parameter ‘oldtype’ /opt/local/include/mpicxx.h:386: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:386: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:386: warning: unused parameter ‘attr_in’ /opt/local/include/mpicxx.h:386: warning: unused parameter ‘attr_out’ /opt/local/include/mpicxx.h:388: warning: unused parameter ‘type’ /opt/local/include/mpicxx.h:388: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:388: warning: unused parameter ‘attr’ /opt/local/include/mpicxx.h:388: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:390: warning: unused parameter ‘oldtype’ /opt/local/include/mpicxx.h:390: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:390: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1453: warning: unused parameter ‘oldcomm’ /opt/local/include/mpicxx.h:1453: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1453: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1453: warning: unused parameter ‘attr_in’ /opt/local/include/mpicxx.h:1453: warning: unused parameter ‘attr_out’ /opt/local/include/mpicxx.h:1454: warning: unused parameter ‘comm’ /opt/local/include/mpicxx.h:1454: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1454: warning: unused parameter ‘attr’ /opt/local/include/mpicxx.h:1454: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1457: warning: unused parameter ‘oldcomm’ /opt/local/include/mpicxx.h:1457: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1457: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1886: warning: unused parameter ‘oldwin’ /opt/local/include/mpicxx.h:1886: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1886: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1886: warning: unused parameter ‘attr_in’ /opt/local/include/mpicxx.h:1886: warning: unused parameter ‘attr_out’ /opt/local/include/mpicxx.h:1888: warning: unused parameter ‘win’ /opt/local/include/mpicxx.h:1888: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1888: warning: unused parameter ‘attr’ /opt/local/include/mpicxx.h:1888: warning: unused parameter ‘ex’ /opt/local/include/mpicxx.h:1890: warning: unused parameter ‘oldwin’ /opt/local/include/mpicxx.h:1890: warning: unused parameter ‘keyval’ /opt/local/include/mpicxx.h:1890: warning: unused parameter ‘ex’ |
