Enable large arrays: Build octave such that it can use arrays larger than 2Gb.

From Octave
Revision as of 13:02, 22 November 2011 by KaKiLa (talk | contribs) (First version, copy paste)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

By default, the size of a single Octave array cannot exceed 2 GB of memory. Trying to create one will produce the following error:

octave:1> a = zeros(1024,1024,512);
error: memory exhausted or requested size too large for range of Octave's index type -- trying to return to prompt

You will obtain this error even if your system has enough RAM to create this array (4 GB in the above case).

To use arrays larger than 2 GB, Octave has to be configured with the option --enable-64. This option is experimental and you are (as always) encouraged to submit bug reports if you find a problem. With this option, Octave will use internally 64-bit integers for array dimensions and indexing. However, all numerical libraries used by Octave will need to use also 64-bit integers for array dimensions and indexing, and in most cases they need to be compiled from source.

The following instructions are tested with Octave 3.2.0 and gcc/gfortran 4.2.4 on a 64-bit CPU. They might also be useful on a 32-bit CPU as long as you have more than 2 GB of memory.


BLAS

Various implementations of the BLAS library exist. Once you compiled this library make sure that you use this library for compiling LAPACK, SuiteSparse, ARPACK and Octave. In the following we assume that you installed the BLAS library as $BLAS/lib/libblas.a.

Reference BLAS

To compile this library use the gfortran compiler options -fdefault-integer-8 and -fPIC (for 64-bit CPUs). Either add those options to the variable OPTS in make.inc, or use the following make command:

make FORTRAN=gfortran OPTS="-fPIC -O3 -fdefault-integer-8" BLASLIB=libblas.a

ATLAS

Not yet tested.

GotoBLAS

In Makefile.rule, set your Fortran compiler (F_COMPILER) to GFORTRAN, uncomment the line with INTERFACE64 = 1 and BINARY64 = 1 (if you have a 64-bit CPU) or use the command:

make F_COMPILER=GFORTRAN BINARY64=1 INTERFACE64=1

Note that GotoBLAS is available free of charge for research but it is not free software.


LAPACK

Copy the file make.inc.example and name it make.inc. The options -fdefault-integer-8 and -fPIC (on 64-bit CPU) have to be added to the variable OPTS and NOOPT. Alternatively, the following command can be used (with some additional optimizations):

 cp make.inc.example  make.inc
 make FORTRAN=gfortran LOADER=gfortran OPTS="-funroll-all-loops -O3 -fPIC -fdefault-integer-8" NOOPT="-fPIC -fdefault-integer-8" PLAT=  \
  LAPACKLIB=liblapack.a  BLASLIB=$BLAS/lib/libblas.a TIMER=INT_ETIME  lapacklib

Once you compiled this library make sure that you use this library for compiling Suite Sparse and Octave. In the following we assume that you installed the LAPACK library as $LAPACK/lib/liblapack.a.


ARPACK

With gfortran 4.2.4 I had to apply the patch from: https://cvs.fedoraproject.org/viewvc/rpms/arpack/F-9/arpack-etime.patch?revision=1.1&view=markup&pathrev=arpack-2_1-10_fc9

In ARmake.inc set the following variables:

home=path to directory ARPACK
FC=gfortran 
FFLAGS=-fPIC -fdefault-integer-8
MAKE=/usr/bin/make 
ARPACKLIB=$(home)/libarpack.a
DIRS=$(UTILdir) $(SRCdir)

Alternatively, they can be defined as arguments of make:

make FC=gfortran FFLAGS="-fPIC -fdefault-integer-8" MAKE=/usr/bin/make ARPACKLIB=$PWD/libarpack.a home=$PWD DIRS="$PWD/UTIL $PWD/SRC" lib

Copy the library libarpack.a to $ARPACK/lib/libarpack.a.

SuiteSparse

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

CFLAGS=-fPIC -O -DLP64 -D'LONGBLAS=long int' -D'LONG=long int'
F77FLAGS=-fPIC -O -fdefault-integer-8
BLAS=-L$BLAS/lib -lblas -lgfortran -lpthread"
LAPACK=-L$LAPACK/lib -llapack"

The library -lpthread for BLAS is only needed is you used the multithreaded GotoBLAS library. Optionally, Suite Sparse needs metis. In metis-4.0/Makefile.in the following options have to be defined:

OPTFLAGS = -O2 -fPIC

In the following we assume that you installed all SuiteSparse libraries (and metis) in $SUITESPARSE/lib and all header files in $SUITESPARSE/include/suitesparse. Since SuiteSparse makefile does not have an install target, you might use:

cp {AMD,BTF,CAMD,CCOLAMD,CHOLMOD,COLAMD,CXSparse,UMFPACK}/Lib/lib*a metis-4.0/libmetis.a $SUITESPARSE/lib/
cp {AMD,BTF,CAMD,CCOLAMD,CHOLMOD,COLAMD,CXSparse,UMFPACK}/Include/*h UFconfig/UFconfig.h  $SUITESPARSE/include/suitesparse


QHull

Suggestions on how to compile qhull will be most welcome.

Octave

Octave's 64-bit index support is activated with the configure option --enable-64.

./configure \
  CPPFLAGS="-I$SUITESPARSE/include -I$QHULL/include " \
  LIBS="-L$SUITESPARSE/lib -lmetis -L$QHULL/lib  -L$ARPACK -larpack -L$LAPACK/lib -L$BLAS/lib -lblas -lgfortran -lm -lpthread" \
  FFLAGS=-fdefault-integer-8 \
  F77=gfortran --enable-64