Re: octave, arpack, umfpack

[John W. Eaton]

On 17-Nov-2010, sibu xolo wrote:

| On Wednesday 17 November 2010 06:54:28 Ananda Murthy R S wrote:
| > Can you please mention on which distribution of Linux are you trying to
| > compile?
| 
| I am using cblfs compiled from sources  and 64-bit non multilib.  Here is an 
| update  I had prepared to post   to the maintner list I hoped to join:-
| 
| I am compiling   on a machine with the following:-
| ----cpu  amd64 2cores
| ----o/s cblfs linux 64-bit  non-multilib kernel-2.6.32, gcc-4.4.2
| ----BLAS: atlas3.9.32  SuiteSparse-3.4.0 lapack-3.2.2 arpac-0.92 (autoconf'ed)
| 
| AND this is what happens:-
| Both SuiteSparse and arpac are  compiled to give  shared and statc libs and 
| linked to  atlas and lapack libraries.  They are available at the locations 
| shown below:-
| 
| ---------------- arpack and umfpack locations:-
| rt [ ~ ]# ls -l /home/rt/ArpackTEST3/lib
| total 1000
| -rw-r--r-- 1 rt users 662720 Nov 16 23:46 libarpack.a
| lrwxrwxrwx 1 rt users     14 Nov 16 23:46 libarpack.so -> libarpack.so.9
| -rwxr-xr-x 1 rt users 350904 Nov 16 23:46 libarpack.so.0.9.2
| lrwxrwxrwx 1 rt users     18 Nov 16 23:46 libarpack.so.9 -> libarpack.so.0.9.2
| rt [ ~ ]# 
| 
| 
| rt [ ~ ]# ls -l  /usr/local/algebra/lib/libumfpack*
| lrwxrwxrwx 1 root root     15 Nov 17 12:49 
usr/local/algebra/lib/libumfpack.so 
| -> libumfpack.so.5
| lrwxrwxrwx 1 root root     19 Nov 17 12:49 
| usr/local/algebra/lib/libumfpack.so.5 -> libumfpack.so.5.2.0
| -rwxr-xr-x 1 root root 708862 Nov 17 12:44 
| usr/local/algebra/lib/libumfpack.so.5.2.0
| rt [ ~ ]# 
| rt [ ~ ]# ls -l  /usr/local/algebra/static_lib/libumfpack*
| -rw-r--r-- 1 root root 1328178 Nov 17 12:45 
| usr/local/algebra/static_lib/libumfpack.a
| rt [ ~ ]# 
| --------------------------
| 
| I  then   ran the configure script  for octave-3.3.53 with the folowing 
| switches:-
| 
| --with-umfpack-includedir=/usr/local/algebra/include \
| --with-umfpack-libdir=/usr/local/algebra/static_lib \
| --with-arpack-libdir=/home/rt/ArpackTEST3/lib \
| --with-arpack-includedir=/home/rt/ArpackTEST3/include
| 
| 
| -------------it responds as shown below:-
| configure: WARNING: UMFPACK not found.  This will result in some lack of 
| functionality for sparse matrices.
| configure: WARNING: ARPACK not found.  The eigs function will be disabled.
| ------------------
| 
| The rest of the SparseSuite components including libcholmod are found  but 
not 
| umfpack.  Also if arpac is compiled and not linked to atlas   it is  'found'.
|   I am wondering if there is a problem  octave-3.3.53 has with libraries 
| already linked to atlas and lapack (compiled with gfortan) and if there is 
| whether a fix upstream exists or otherwise.
| 
| I very much want to have  octave   compiled with umfpack and arpack 
| functionality  and linked to BLAS and LAPACK libraries so advice would be 
| appreciasted.

The following works for me:

ARPACK (http://www.caam.rice.edu/software/ARPACK)

  In ARmake.inc set the following variables:

    home=path to directory ARPACK
    FC=gfortran 
    FFLAGS=-fPIC -O
    MAKE=make 
    ARPACKLIB=$(home)/libarpack.a
    DIRS=$(UTILdir) $(SRCdir)

  Edit the file UTIL/second.f and change the line

    EXTERNAL           ETIME

  to

    INTRINSIC          ETIME

  After building .a library, you can make a shared version with

    mkdir tmp
    cd tmp
    ar x ../libarpack.a
    gcc -shared -o ../libarpack.so *.o -L$prefix64/lib -llapack -lblas 
    cd ..
    rm -rf tmp

  Copy the library libarpack.so to $prefix/lib/libarpack.a.

SUITESPARSE (http://www.cise.ufl.edu/research/sparse/SuiteSparse)

  In UFconfig/UFconfig.mk use the following options for CFLAGS and F77FLAGS:

    CC = gcc
    CFLAGS = -fPIC -O
    F77 = gfortran
    F77FLAGS = -fPIC -O
    BLAS = -lblas -lgfortran
    LAPACK = -llapack

  Disable the GPL-incompatible METIS library:

    CHOLMOD_CONFIG = -DNPARTITION
    SPQR_CONFIG = -DNPARTITION
    METIS_PATH =
    METIS =

  Run make to build the libraries.

  The SuiteSparse Makefile does not have an install target so you must
  install the files by hand:

    cp {AMD,BTF,CAMD,CCOLAMD,CHOLMOD,COLAMD,CXSparse,UMFPACK}/Lib/lib*a 
$prefix/lib
    mkdir $prefix/include/suitesparse
    cp {AMD,BTF,CAMD,CCOLAMD,CHOLMOD,COLAMD,CXSparse,UMFPACK}/Include/*h 
UFconfig/UFconfig.h $prefix64/include/suitesparse

  You can generate shared versions of these libraries by doing the
  following in the $prefix64/lib directory:

    top=$(pwd)
    for f in *.a; do
      mkdir tmp
      cd tmp
      ar vx ../$f
      gcc -shared -o ../${f%%.a}.so *.o
      cd $top
      rm -rf tmp
    done

I did the above and put the suitesparse libraries in
/tmp/suitesparse/lib and the suitesparse include files in
/tmp/suitesparse/include/suitesparse and the arpack library in
/tmp/arpack.  Then I configured Octave with

  ./configure CPPFLAGS=-I/tmp/suitesparse/include \
              LDFLAGS="-L/tmp/suitesparse/lib -L/tmp/arpack"
  

and it worked for me.  I also tried

  ./configure --with-amd-includedir=/tmp/suitesparse/include \
              --with-amd-libdir=/tmp/suitesparse/lib \
              --with-camd-includedir=/tmp/suitesparse/include \
              --with-camd-libdir=/tmp/suitesparse/lib \
              --with-colamd-includedir=/tmp/suitesparse/include \
              --with-colamd-libdir=/tmp/suitesparse/lib \
              --with-ccolamd-includedir=/tmp/suitesparse/include \
              --with-ccolamd-libdir=/tmp/suitesparse/lib \
              --with-cholmod-includedir=/tmp/suitesparse/include \
              --with-cholmod-libdir=/tmp/suitesparse/lib \
              --with-cxsparse-includedir=/tmp/suitesparse/include \
              --with-cxsparse-libdir=/tmp/suitesparse/lib \
              --with-umfpack-includedir=/tmp/suitesparse/include \
              --with-umfpack-libdir=/tmp/suitesparse/lib \
              --with-arpack-libdir=/tmp/arpack

and it also worked for me.

Note that if you use the --with-X-libdir and --with-X-includedir
options and you installed the suitesparse libraries and header files
in a location where the compiler will not find them by default, then
you must specify all the --with options for all the libraries since
some of them depend on others.  Currently there are no options like
--with-suitesparse-{include,lib}dir options that will set all the
other variables.

jwe