Editing Octave and separate toolchain

{{Warning|This page is outdated (October 2019).  For a simpler approach on building GNU Octave using a separate toolchain, see [[MXE]].}}

Building of octave together with a separate toolchain (custom built gcc/binutils/...).

This is required mainly when the base linux distribution ships too old a version of gcc.
Unexperienced users should upgrade their distribution, though. Or use [[MXE]].

The main build directory will be called {{Path|/usr/local/build}}. 
It was first created by root, and then changed to be owned by the user who will perform compilations.
You might want change this to another directory in your {{Path|$HOME}} for instance.

 export buildroot=/usr/local/build

We will need a directory to hold downloaded files

 export downloads=$buildroot/downloads

 mkdir -p $buildroot/downloads


== gcc toolchain ==

This part is largely inspired by [http://stackoverflow.com/a/6228588/3565696 this answer]

 cd $buildroot
 # work in a subshell, to isolate mistakes
 bash
 # check that PATH and LD_RUN_PATH are normal
 echo $PATH
 echo $LD_RUN_PATH

 cd $downloads
 wget ftp://ftp.gnu.org/gnu/binutils/binutils-2.27.tar.bz2
 wget ftp://ftp.gnu.org/gnu/gcc/gcc-6.2.0/gcc-6.2.0.tar.bz2
 wget ftp://ftp.gnu.org/gnu/mpfr/mpfr-3.1.5.tar.xz
 wget ftp://ftp.gnu.org/gnu/mpc/mpc-1.0.3.tar.gz
 wget ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.1.tar.xz
 wget http://isl.gforge.inria.fr/isl-0.17.tar.xz

 cd $buildroot
 tar --no-same-owner -xvf $downloads/binutils-2.27.tar.bz2
 tar --no-same-owner -xvf $downloads/gcc-6.2.0.tar.bz2
 tar --no-same-owner -xvf $downloads/mpfr-3.1.5.tar.xz
 tar --no-same-owner -xvf $downloads/mpc-1.0.3.tar.gz
 tar --no-same-owner -xvf $downloads/gmp-6.1.1.tar.xz
 tar --no-same-owner -xvf $downloads/isl-0.17.tar.xz

 cd $buildroot/gcc-6.2.0
 ln -s ../mpfr-3.1.5 mpfr
 ln -s ../mpc-1.0.3 mpc
 ln -s ../gmp-6.1.1 gmp
 ln -s ../isl-0.17/ isl
 # Now symlink everything from the binutils dir which doesn't exist in the gcc dir,
 # so anything which already exists will take priority but the
 # binutils tools will look be visible to the build:
 for file in ../binutils-2.27/* ; do ln -s "${file}" ; done
 # errors ending with "File exists" are normal

Now we are ready to build the toolchain

 cd $buildroot
 mkdir gcc-6.2.0_isl_build; cd $_
 ../gcc-6.2.0/configure --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl --disable-nls --enable-languages=c,c++,fortran,java --disable-multilib
 make -j 6 bootstrap
 sudo make install
 # see what has been installed
 ls /usr/local/gcc-6.2.0_binutils-2.27_isl/bin


== OpenBLAS ==

We need an optimized BLAS library, such as [http://www.openblas.net/ OpenBLAS]

 cd $downloads
 wget -O OpenBLAS-0.2.19.tar.gz http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz

 cd $buildroot
 tar --no-same-owner -xvf $downloads/OpenBLAS-0.2.19.tar.gz
 cd OpenBLAS-0.2.19/
 
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 # check
 which gcc
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gcc
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran
 
 # do not use threads 
 # (because I use pararrayfun from the parallel package)
 make USE_THREAD=0 CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native" CXXFLAGS="-O2 -march=native" FFLAGS="-O2 -march=native" LDFLAGS="-L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 -Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64"

One should get

 OpenBLAS build complete. (BLAS CBLAS LAPACK LAPACKE)
 
  OS               ... Linux             
  Architecture     ... x86_64               
  BINARY           ... 64bit                 
  C compiler       ... GCC  (command line : gcc)
  Fortran compiler ... GFORTRAN  (command line : gfortran)
  Library Name     ... libopenblas_haswell-r0.2.19.a (Single threaded)  

Checking the runpath:

 ldd libopenblas.so
        linux-vdso.so.1 (0x00007fff961fc000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f3ee88cb000)
        libgfortran.so.3 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libgfortran.so.3 (0x00007f3ee85a3000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f3ee81f9000)
        libquadmath.so.0 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/../lib64/libquadmath.so.0 (0x00007f3ee7fb9000)
        libgcc_s.so.1 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/../lib64/libgcc_s.so.1 (0x00007f3ee7da2000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f3ee9ad6000)

Manual installation
 sudo cp libopenblas.a libopenblas_haswell-r0.2.19.a libopenblas_haswell-r0.2.19.so /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64
 cd /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/
 sudo ln -s libopenblas_haswell-r0.2.19.so libopenblas.so.0
 sudo ln -s libopenblas.so.0 libopenblas.so

== qrupdate ==
download the latest version (1.1.2 as of this writing) to $downloads 

https://sourceforge.net/projects/qrupdate/files/latest/download?source=typ_redirect

Start from a clean state

 exit
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran

 cd $buildroot
 tar --no-same-owner -xvf $downloads/qrupdate-1.1.2.tar.gz
 cd qrupdate-1.1.2/

Save the following to $downloads/qrupdate-1.1.2_Makeconf.patch

{{Code|qrupdate-1.1.2_Makeconf.patch|<pre>
--- Makeconf.orig	2016-09-20 16:33:23.061756020 +0200
+++ Makeconf	2016-09-20 16:39:47.385547117 +0200
@@ -1,26 +1,26 @@
 # set this to your compiler's executable name (e.g. gfortran, g77)
 FC=gfortran
 # requested flags
-FFLAGS=-fimplicit-none -O3 -funroll-loops 
+FFLAGS=-fimplicit-none -march=native -O3 -funroll-loops -lgfortran
 # set if you need shared library
 FPICFLAGS=-fPIC
 
 # BLAS library (only required for tests)
-BLAS=-lblas
+BLAS=-lopenblas
 # LAPACK library (only required for tests)
-LAPACK=-llapack
+LAPACK=
 
 # Library version
 VERSION=1.1
 MAJOR=1
 
 # The default library dir
-LIBDIR=lib
+LIBDIR=lib64
 
 # Destination installation offset
 DESTDIR=
 
 # set default prefix to /usr/local
 ifeq ($(strip $(PREFIX)),)
-  PREFIX=/usr/local
+  PREFIX=/usr/local/gcc-6.2.0_binutils-2.27_isl
 endif
</pre>
}}

 patch -p0 < $downloads/qrupdate-1.1.2_Makeconf.patch
 make solib

as root ({{codeline|su}}, not {{codeline|sudo}},  because we want PATH to contain {{Path|/usr/local/gcc-6.2.0_binutils-2.27_isl/bin}})
 make install-shlib

{{codeline|exit}} root session, then {{codeline|exit}} current bash, to return to a clean state

== arpack-ng ==

https://github.com/opencollab/arpack-ng/releases

 cd $downloads
 wget -O arpack-ng-3.4.0.tar.gz https://github.com/opencollab/arpack-ng/archive/3.4.0.tar.gz
 
Start from a clean state

 exit
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran

 cd $buildroot
 tar --no-same-owner -xvf $downloads/arpack-ng-3.4.0.tar.gz
 cd arpack-ng-3.4.0
 ./bootstrap
 ./configure CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native" CXXFLAGS="-O2 -march=native" FFLAGS="-O2 -march=native" LDFLAGS="-L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 -Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl
 
 make -j 6
 make check
  # TOTAL: 12
  # PASS:  12

 # check libraries
 ldd ./SRC/.libs/libarpack.so
        linux-vdso.so.1 (0x00007fff1f38c000)
        libopenblas.so.0 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libopenblas.so.0 (0x00007f80c79d8000)
        libgfortran.so.3 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libgfortran.so.3 (0x00007f80c76b0000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f80c7368000)
        libgcc_s.so.1 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libgcc_s.so.1 (0x00007f80c7151000)
        libquadmath.so.0 => /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libquadmath.so.0 (0x00007f80c6f11000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f80c6b67000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f80c892e000)
 
as root ({{codeline|su}}, not {{codeline|sudo}},  because we want PATH to contain {{Path|/usr/local/gcc-6.2.0_binutils-2.27_isl/bin}})
 make install

{{codeline|exit}} root session, then {{codeline|exit}} current bash, to return to a clean state

== SuiteSparse ==

http://faculty.cse.tamu.edu/davis/suitesparse.html

 cd $downloads
 wget http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.3.tar.gz

Save the code below to $downloads/UMFPACK_Demo_Makefile-4.5.3.patch

{{Code|UMFPACK_Demo_Makefile-4.5.3.patch|<pre>
--- UMFPACK/Demo/Makefile.orig	2016-09-19 16:20:46.317044240 +0200
+++ UMFPACK/Demo/Makefile	2016-09-19 16:30:15.079302070 +0200
@@ -27,9 +27,9 @@
 C = $(CC) $(CF) $(UMFPACK_CONFIG) $(CONFIG_PARTITION) \
     -I../../include
 
-LIBS = $(LDLIBS) -L../../lib -lumfpack -lamd -lsuitesparseconfig \
+LIBS = $(LDFLAGS) $(LDLIBS) -L../../lib -lumfpack -lamd -lsuitesparseconfig \
 	$(LIB_WITH_CHOLMOD) $(LAPACK) $(BLAS)
 
 libs: metis
 	( cd ../../SuiteSparse_config ; $(MAKE) )
 	( cd ../../AMD ; $(MAKE) library )

</pre>
}}


 cd $buildroot
 tar --no-same-owner -xvf $downloads/SuiteSparse-4.5.3.tar.gz
 mv SuiteSparse SuiteSparse-4.5.3
 cd SuiteSparse-4.5.3/
 
 patch -p0 < $downloads/UMFPACK_Demo_Makefile-4.5.3.patch
 # should get: "patching file UMFPACK/Demo/Makefile"

If the following command

 find . -name Makefile -exec grep "LDLIBS +=" {} \; -print

yields {{codeline|LDLIBS}} lines not starting with {{codeline|override}}, 
then the patch sent upstream has not been applied,
and we should do it here:

 find . -name Makefile -exec sed -i 's/LDLIBS +=/override LDLIBS +=/g' {} \;

Now we are ready to build SuiteSparse

 make -j6 LAPACK= CF="-march=native -O3 -fexceptions -fPIC -fopenmp" F77FLAGS="-march=native -O3" LDFLAGS="-L/usr/local/build/SuiteSparse-4.5.3/lib -L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" LDLIBS="-lm -lrt -Wl,-rpath=/usr/local/build/SuiteSparse-4.5.3/lib:/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64"

fix RUN_PATH and install

 cp -Rdp lib lib_chrpath
 patchelf --set-rpath /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 lib_chrpath/*
 sudo cp lib_chrpath/* /usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/
 sudo mkdir /usr/local/gcc-6.2.0_binutils-2.27_isl/include/suitesparse/
 sudo cp include/* /usr/local/gcc-6.2.0_binutils-2.27_isl/include/suitesparse/



== FFTW ==

http://www.fftw.org/

 cd $downloads
 wget http://www.fftw.org/fftw-3.3.5.tar.gz

Start from a clean state

 exit
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran

 cd $buildroot
 tar --no-same-owner -xvf $downloads/fftw-3.3.5.tar.gz
 cd fftw-3.3.5/

=== Single precision ===
 ./configure --enable-shared --enable-sse2 --enable-avx --enable-openmp --enable-threads --enable-float CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native" CXXFLAGS="-O2 -march=native" FFLAGS="-O2 -march=native" LDFLAGS="-L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 -Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" PKG_CONFIG_PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/pkgconfig --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl
 make -j6
 make check

as root ({{codeline|su}}, not {{codeline|sudo}},  because we want PATH to contain {{Path|/usr/local/gcc-6.2.0_binutils-2.27_isl/bin}})

 make install
 exit

=== Double precision ===

 ./configure --enable-shared --enable-sse2 --enable-avx --enable-openmp --enable-threads CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native" CXXFLAGS="-O2 -march=native" FFLAGS="-O2 -march=native" LDFLAGS="-L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 -Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" PKG_CONFIG_PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/pkgconfig --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl
 make -j6
 make check

as root ({{codeline|su}}, not {{codeline|sudo}},  because we want PATH to contain {{Path|/usr/local/gcc-6.2.0_binutils-2.27_isl/bin}})

 make install
 exit

== GraphicsMagick ==

download GraphicsMagick (here, GraphicsMagick-1.3.25.tar.xz) to $downloads

https://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/

Start from a clean state

 exit
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran

 cd $buildroot
 tar --no-same-owner -xvf $downloads/GraphicsMagick-1.3.25.tar.xz
 cd GraphicsMagick-1.3.25

Disable ''webp'' and ''jbig'' that fail tests with gcc-6.2.0

 ./configure --without-webp --without-jbig --enable-static=no --enable-shared=yes --with-quantum-depth=16 CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native" CXXFLAGS="-O2 -march=native" FFLAGS="-O2 -march=native" LDFLAGS="-L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 -Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" PKG_CONFIG_PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/pkgconfig --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl

The summary should be fine. As comparison and source of relevant informations: [[GraphicsMagick]]

 make -j 6

 make -j6 check
 ============================================================================
 Testsuite summary for GraphicsMagick 1.3.25
 ============================================================================
 # TOTAL: 1215
 # PASS:  1169
 # SKIP:  46
 # XFAIL: 0
 # FAIL:  0
 # XPASS: 0
 # ERROR: 0


as root ({{codeline|su}}, not {{codeline|sudo}},  because we want PATH to contain {{Path|/usr/local/gcc-6.2.0_binutils-2.27_isl/bin}})

 make install

{{codeline|exit}} root session, then {{codeline|exit}} current bash, to return to a clean state

== Octave itself ==

The following - facultative - command avoids warnings like {{codeline|libtool: warning: '/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libgomp.la' seems to be moved}}

 sudo find /usr/local/gcc-6.2.0_binutils-2.27_isl -name "*.la" -exec sed -i 's:/lib64/../lib64:/lib64:g' {} \; -print

which will replace all unnecessary {{codeline|/lib64/../lib64}} by {{codeline|/lib64}}.

 cd $downloads
 wget ftp://alpha.gnu.org/gnu/octave/octave-4.2.0-rc4.tar.lz

Start from a clean state

 exit
 bash
 export PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/bin:$PATH
 which gfortran
 # should be /usr/local/gcc-6.2.0_binutils-2.27_isl/bin/gfortran

 cd $buildroot
 tar --no-same-owner -xvf $downloads/octave-4.2.0-rc4.tar.lz
 cd octave-4.2.0-rc4

 mkdir build-; cd $_
 ../configure --with-blas="/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/libopenblas.so" CPPFLAGS="-I/usr/local/gcc-6.2.0_binutils-2.27_isl/include" CFLAGS="-O2 -march=native -L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" CXXFLAGS="-O2 -march=native -L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" FFLAGS="-O2 -march=native -L/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64" LDFLAGS=-Wl,-rpath,/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64 PKG_CONFIG_PATH=/usr/local/gcc-6.2.0_binutils-2.27_isl/lib64/pkgconfig JAVA_HOME=/usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/ --prefix=/usr/local/gcc-6.2.0_binutils-2.27_isl
 
 make -j 6

 make check
 # or, for nvidia users,
 xvfb-run -s "-screen 0 640x480x24" make check LD_PRELOAD=/usr/lib64/libGL.so

To be continued...

[[Category:Outdated pages]]