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Re: Mac-Intel math performance libraries


From: Ben Abbott
Subject: Re: Mac-Intel math performance libraries
Date: Thu, 02 Oct 2008 03:43:36 -0400


On Oct 1, 2008, at 3:01 PM, Samir Sharshar wrote:

Hello,

Don't know if you've receive my last post concerning Intel Math Kernel Library and SuiteSparse compilation on MacIntel. I send it again with a copy the help-octave mailing list.

Regards,

Samir Sharshar MD

Début du message réexpédié :

De : Samir Sharshar <address@hidden>
Date : 30 septembre 2008 21:03:31 HAEC
À : Jaroslav Hajek <address@hidden>
Objet : Rép : Mac-Intel math performance libraries

Hello,

Thanks for your help.

Here are more details :

1. I'm using i686-apple-darwin9-gcc4.0.1 (gcc -version at the command line) 2. GNU Fortran 4.4.0 20080801 (gfortran --version at the command line) 3. Installing m_mkl_p_10.0.4.022.dmg as Intel Math Kernel Library : Intel site claims its compatibility with gcc and gfortran compilers, 4. As I said in my previous mail, XCode 3.1 and a 10.5.5 system (last updates)

Compiling FFTW :

1. Download fresh sources of fftw-3.1.2,
2. Running ./configure --prefix=/usr/local --enable-shared
3. make && make check && sudo make install running smoothly without errors/warnings

but I guess I miss some extra configuration to tell fftw to use the Intel MKL...

Compiling UMFPACK (SuiteSparse) :

1. Download SuiteSparse-3.2.0
2. Download metis-4.0
3. mv the metis.tar.gz to the SuiteSparse directory, untar it, then make, 4. change the UFconfig/UFconfig.mk file : only uncomment the lines concerning Macintosh configuration, run make && make check without errors/warnings,
5. execute the following script (from wiki.octave.org) as superuser :

    INSTALL_DIR=/usr/local
    # Make sure the install directories exist
    if !(test -d $INSTALL_DIR/include);
    then
echo $INSTALL_DIR/include did not exist, creating $INSTALL_DIR/ include
    mkdir $INSTALL_DIR/include
    fi;
    if !(test -d $INSTALL_DIR/include/suitesparse);
    then
echo $INSTALL_DIR/include/suitesparse did not exist, creating $INSTALL_DIR/include/suitesparse
    mkdir $INSTALL_DIR/include/suitesparse
    fi;
    if !(test -d $INSTALL_DIR/lib);
    then
    echo $INSTALL_DIR/lib did not exist, creating $INSTALL_DIR/lib
    mkdir $INSTALL_DIR/lib
    fi;
    # Copy all the files to the new directories
    echo Copying UMFPACK files into $INSTALL_DIR...
    cp UFconfig/UFconfig.h $INSTALL_DIR/include/suitesparse
    cp UMFPACK/Include/*.h $INSTALL_DIR/include/suitesparse
    cp UMFPACK/Lib/libumfpack.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libumfpack.a
    echo Copying AMD files into $INSTALL_DIR/...
    cp AMD/Include/*.h $INSTALL_DIR/include/suitesparse
    cp AMD/Lib/libamd.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libamd.a
    echo Copying CAMD files into $INSTALL_DIR/...
    cp CAMD/Include/*.h $INSTALL_DIR/include/suitesparse
    cp CAMD/Lib/libcamd.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libcamd.a
    echo Copying COLAMD files into $INSTALL_DIR/...
    cp COLAMD/*.h $INSTALL_DIR/include/suitesparse
    cp COLAMD/libcolamd.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libcolamd.a
    echo Copying CCOLAMD files into $INSTALL_DIR/...
    cp CCOLAMD/*.h $INSTALL_DIR/include/suitesparse
    cp CCOLAMD/libccolamd.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libccolamd.a
    echo Copying CXSPARSE files into $INSTALL_DIR/...
    cp CHOLMOD/Source/*.h $INSTALL_DIR/include/suitesparse
    cp CHOLMOD/Lib/libcholmod.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libcholmod.a
    echo Copying CHOLMOD files into $INSTALL_DIR/...
    cp CXSparse/Include/*h $INSTALL_DIR/include/suitesparse
    cp CXSparse/Source/libcxsparse.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libcxsparse.a
    echo Copying METIS files into $INSTALL_DIR/...
    cp metis-4.0/Lib/*.h $INSTALL_DIR/include/suitesparse
    cp metis-4.0/libmetis.a $INSTALL_DIR/lib
    ranlib $INSTALL_DIR/lib/libmetis.a

6. and get the following errors :

Copying UMFPACK files into /usr/local...
ranlib: file: /usr/local/lib/libumfpack.a(umf_di_dump.o) has no symbols ranlib: file: /usr/local/lib/libumfpack.a(umf_dl_dump.o) has no symbols ranlib: file: /usr/local/lib/libumfpack.a(umf_zi_dump.o) has no symbols ranlib: file: /usr/local/lib/libumfpack.a(umf_zl_dump.o) has no symbols
Copying AMD files into /usr/local/...
ranlib: file: /usr/local/lib/libamd.a(amd_i_dump.o) has no symbols
ranlib: file: /usr/local/lib/libamd.a(amd_l_dump.o) has no symbols
Copying CAMD files into /usr/local/...
ranlib: file: /usr/local/lib/libcamd.a(camd_i_dump.o) has no symbols
ranlib: file: /usr/local/lib/libcamd.a(camd_l_dump.o) has no symbols
Copying COLAMD files into /usr/local/...
cp: COLAMD/*.h: No such file or directory
cp: COLAMD/libcolamd.a: No such file or directory
ranlib: can't open file: /usr/local/lib/libcolamd.a (No such file or directory)
Copying CCOLAMD files into /usr/local/...
cp: CCOLAMD/*.h: No such file or directory
cp: CCOLAMD/libccolamd.a: No such file or directory
ranlib: can't open file: /usr/local/lib/libccolamd.a (No such file or directory)
Copying CXSPARSE files into /usr/local/...
cp: CHOLMOD/Source/*.h: No such file or directory
Copying CHOLMOD files into /usr/local/...
cp: CXSparse/Source/libcxsparse.a: No such file or directory
ranlib: can't open file: /usr/local/lib/libcxsparse.a (No such file or directory)
Copying METIS files into /usr/local/...

and here I'm stuck :)

Perharps I need to use the Intel compilers instead of the ones I have. But think I miss to set some FLAGS.
Sorry for my ignorance of the compilation process.
So if you drive me on the right way in order to compile octave with the Intel MKL, it would be great !

Regards,

Samir.

Your errors each originate from suitesparse. As a reference you can take a look at the patch and package information used by Fink. The links below are for patching and building version 3.1. I haven't looked at building 3.2.

http://fink.cvs.sourceforge.net/fink/dists/10.4/stable/main/finkinfo/sci/suitesparse.patch?view=markup

http://fink.cvs.sourceforge.net/fink/dists/10.4/stable/main/finkinfo/sci/suitesparse.info?view=markup

I don't recall the details, but do remember encountering the "has no symbols" error when working to create my first Fink package for suitesparse.

Ben


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