Editing Enable large arrays: Build octave such that it can use arrays larger than 2Gb.
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'''Note: the following only applies to systems that have 64-bit pointers (64bit architecture)''' | |||
By default, the size of a single Octave array cannot exceed 2 GB of memory. Trying to create one will produce the following error: | |||
However, | <pre> | ||
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 | |||
</pre> | |||
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. | |||
For details about how to compile these libraries please read the [http://adf.ly/4hRa0 GNU Octave manual]. | |||
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== BLAS == | |||
Various implementations of the BLAS library exist. Once you compiled this library make sure that you use this library for compiling LAPACK, <nowiki>SuiteSparse</nowiki>, ARPACK and Octave. In the following we assume that you installed the BLAS library as $BLAS/lib/libblas.a. | |||
=== Reference BLAS === | |||
To compile this library use the gfortran compiler options -fdefault-integer-8 and -fPIC (for 64-bit CPUs). Either add those options to the variable OPTS in make.inc, or use the following make command: | |||
<pre> | |||
make FORTRAN=gfortran OPTS="-fPIC -O3 -fdefault-integer-8" BLASLIB=libblas.a | |||
</pre> | |||
=== ATLAS === | |||
<i>Not yet tested.</i> | |||
=== GotoBLAS === | |||
In Makefile.rule, set your Fortran compiler (F_COMPILER) to GFORTRAN, uncomment the line with INTERFACE64 = 1 and BINARY64 = 1 (if you have a 64-bit CPU) or use the command: | |||
<pre> | |||
make F_COMPILER=GFORTRAN BINARY64=1 INTERFACE64=1 | |||
</pre> | |||
Note that <nowiki>GotoBLAS</nowiki> is available free of charge for research but it is not free software. | |||
== LAPACK == | |||
Copy the file make.inc.example and name it make.inc. The options -fdefault-integer-8 and -fPIC (on 64-bit CPU) have to be added to the variable OPTS and NOOPT. Alternatively, the following command can be used (with some additional optimizations): | |||
<pre> | |||
cp make.inc.example make.inc | |||
make FORTRAN=gfortran LOADER=gfortran OPTS="-funroll-all-loops -O3 -fPIC -fdefault-integer-8" NOOPT="-fPIC -fdefault-integer-8" PLAT= \ | |||
LAPACKLIB=liblapack.a BLASLIB=$BLAS/lib/libblas.a TIMER=INT_ETIME lapacklib | |||
</pre> | |||
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 $LAPACK/lib/liblapack.a. | |||
== ARPACK == | |||
With gfortran 4.2.4 I had to apply the patch from: https://cvs.fedoraproject.org/viewvc/rpms/arpack/F-9/arpack-etime.patch?revision=1.1&view=markup&pathrev=arpack-2_1-10_fc9 | |||
In ARmake.inc set the following variables: | |||
<pre> | |||
home=path to directory ARPACK | |||
FC=gfortran | |||
FFLAGS=-fPIC -fdefault-integer-8 | |||
MAKE=/usr/bin/make | |||
ARPACKLIB=$(home)/libarpack.a | |||
DIRS=$(UTILdir) $(SRCdir) | |||
</pre> | |||
Alternatively, they can be defined as arguments of make: | |||
<pre> | |||
make FC=gfortran FFLAGS="-fPIC -fdefault-integer-8" MAKE=/usr/bin/make ARPACKLIB=$PWD/libarpack.a home=$PWD DIRS="$PWD/UTIL $PWD/SRC" lib | |||
</pre> | |||
Copy the library libarpack.a to $ARPACK/lib/libarpack.a. | |||
a | |||
== SuiteSparse == | |||
In UFconfig/UFconfig.mk use the following options for CFLAGS and F77FLAGS: | |||
<pre> | |||
CFLAGS=-fPIC -O -DLP64 -D'LONGBLAS=long int' -D'LONG=long int' | |||
F77FLAGS=-fPIC -O -fdefault-integer-8 | |||
BLAS=-L$BLAS/lib -lblas -lgfortran -lpthread" | |||
LAPACK=-L$LAPACK/lib -llapack" | |||
</pre> | |||
The library -lpthread for BLAS is only needed is you used the multithreaded <nowiki>GotoBLAS</nowiki> library. | |||
Optionally, Suite Sparse needs metis. In metis-4.0/Makefile.in the following options have to be defined: | |||
<pre> | |||
OPTFLAGS = -O2 -fPIC | |||
</pre> | |||
In the following we assume that you installed all <nowiki>SuiteSparse</nowiki> libraries (and metis) in $SUITESPARSE/lib and all header files in $SUITESPARSE/include/suitesparse. Since <nowiki>SuiteSparse</nowiki> makefile does not have an install target, you might use: | |||
<pre> | <pre> | ||
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 $SUITESPARSE/include/suitesparse | |||
</pre> | </pre> | ||
== QHull == | |||
<i>Suggestions on how to compile qhull will be most welcome.</i> | |||
== | == Octave == | ||
Octave's 64-bit index support is activated with the configure option --enable-64. | |||
<pre> | |||
./configure \ | |||
CPPFLAGS="-I$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 | |||
</pre> | |||
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