mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-11-27 01:13:05 +00:00
Merge pull request #8182 from ttuegel/openblas
Numerical computing overhaul
This commit is contained in:
Thomas Tuegel
commit
2a2448bcb7
@ -153,6 +153,19 @@ nix-env -f "<nixpkgs>" -iA haskellPackages.cabal-install
|
||||
</para>
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</listitem>
|
||||
|
||||
<listitem>
|
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<para>
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||||
The OpenBLAS library has been updated to version
|
||||
<literal>0.2.14</literal>. Support for the
|
||||
<literal>x86_64-darwin</literal> platform was added. Dynamic
|
||||
architecture detection was enabled; OpenBLAS now selects
|
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microarchitecture-optimized routines at runtime, so optimal
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performance is achieved without the need to rebuild OpenBLAS
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locally. OpenBLAS has replaced ATLAS in most packages which use an
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optimized BLAS or LAPACK implementation.
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</para>
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</listitem>
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|
||||
</itemizedlist>
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</para>
|
||||
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|
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@ -1,7 +1,7 @@
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{ stdenv, fetchurl, blas, bzip2, gfortran, liblapack, libX11, libXmu, libXt
|
||||
{ stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt
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, libjpeg, libpng, libtiff, ncurses, pango, pcre, perl, readline, tcl
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, texLive, tk, xz, zlib, less, texinfo, graphviz, icu, pkgconfig, bison
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, imake, which, jdk, atlas
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, imake, which, jdk, openblas
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, withRecommendedPackages ? true
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}:
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@ -13,10 +13,10 @@ stdenv.mkDerivation rec {
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sha256 = "0dagyqgvi8i3nw158qi2zpwm04s4ffzvnmk5niaksvxs30zrbbpm";
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};
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||||
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buildInputs = [ blas bzip2 gfortran liblapack libX11 libXmu libXt
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buildInputs = [ bzip2 gfortran libX11 libXmu libXt
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libXt libjpeg libpng libtiff ncurses pango pcre perl readline tcl
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texLive tk xz zlib less texinfo graphviz icu pkgconfig bison imake
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which jdk atlas
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which jdk openblas
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];
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||||
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patches = [ ./no-usr-local-search-paths.patch ];
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@ -25,8 +25,8 @@ stdenv.mkDerivation rec {
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configureFlagsArray=(
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--disable-lto
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--with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
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--with-blas="-L${atlas}/lib -lf77blas -latlas"
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--with-lapack="-L${liblapack}/lib -llapack"
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--with-blas="-L${openblas}/lib -lopenblas"
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--with-lapack="-L${openblas}/lib -lopenblas"
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--with-readline
|
||||
--with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
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||||
--with-cairo
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||||
|
||||
@ -1,4 +1,4 @@
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||||
{stdenv, fetchurl, gfortran, liblapack, blas}:
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||||
{stdenv, fetchurl, gfortran, openblas}:
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||||
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stdenv.mkDerivation rec {
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||||
name = "JAGS-3.4.0";
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||||
@ -6,7 +6,8 @@ stdenv.mkDerivation rec {
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||||
url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz";
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||||
sha256 = "0ayqsz9kkmbss7mxlwr34ch2z1vsb65lryjzqpprab1ccyiaksib";
|
||||
};
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||||
buildInputs = [gfortran liblapack blas];
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buildInputs = [gfortran openblas];
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configureFlags = [ "--with-blas=-lopenblas" "--with-lapack=-lopenblas" ];
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|
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meta = {
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description = "Just Another Gibbs Sampler";
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|
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@ -1,6 +1,6 @@
|
||||
{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, zlib
|
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, readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl
|
||||
, ncurses, libunistring, lighttpd, patchelf, openblas, liblapack
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, ncurses, libunistring, lighttpd, patchelf, openblas
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, tcl, tk, xproto, libX11, git, mpfr
|
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} :
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let
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@ -71,7 +71,7 @@ stdenv.mkDerivation rec {
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||||
|
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buildInputs = [ gfortran perl m4 gmp pcre llvm readline zlib
|
||||
fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf
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openblas liblapack tcl tk xproto libX11 git mpfr
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openblas tcl tk xproto libX11 git mpfr
|
||||
];
|
||||
|
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configurePhase = ''
|
||||
@ -91,14 +91,13 @@ stdenv.mkDerivation rec {
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||||
copy_kill_hash "${dsfmt_src}" deps/random
|
||||
|
||||
${if realGcc ==null then "" else
|
||||
''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -llapack -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr"''}
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''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -lopenblas -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr"''}
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export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -fPIC "
|
||||
|
||||
export LDFLAGS="-L${suitesparse}/lib -L$out/lib/julia -Wl,-rpath,$out/lib/julia"
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||||
|
||||
export GLPK_PREFIX="${glpk}/include"
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||||
|
||||
mkdir -p "$out/lib"
|
||||
sed -e "s@/usr/local/lib@$out/lib@g" -i deps/Makefile
|
||||
sed -e "s@/usr/lib@$out/lib@g" -i deps/Makefile
|
||||
|
||||
@ -112,8 +111,11 @@ stdenv.mkDerivation rec {
|
||||
preBuild = ''
|
||||
mkdir -p usr/lib
|
||||
|
||||
echo "$out"
|
||||
mkdir -p "$out/lib"
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||||
ln -s "${openblas}/lib/libopenblas.so" "$out/lib/libblas.so"
|
||||
ln -s "${openblas}/lib/libopenblas.so" "$out/lib/liblapack.so"
|
||||
|
||||
echo "$out"
|
||||
(
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cd "$(mktemp -d)"
|
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for i in "${suitesparse}"/lib/lib*.a; do
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|
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@ -1,142 +1,138 @@
|
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{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, zlib
|
||||
, readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl
|
||||
, ncurses, libunistring, patchelf, openblas, liblapack
|
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, tcl, tk, xproto, libX11, git, mpfr, which, wget
|
||||
{ stdenv, fetchgit, fetchurl
|
||||
# build tools
|
||||
, gfortran, git, m4, patchelf, perl, which
|
||||
# libjulia dependencies
|
||||
, libunwind, llvm, readline, utf8proc, zlib
|
||||
# standard library dependencies
|
||||
, double_conversion, fftwSinglePrec, fftw, glpk, gmp, mpfr, pcre
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||||
, openblas, arpack, suitesparse
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}:
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||||
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||||
assert stdenv.isLinux;
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||||
with stdenv.lib;
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||||
|
||||
let
|
||||
realGcc = stdenv.cc.cc;
|
||||
in
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||||
stdenv.mkDerivation rec {
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||||
pname = "julia";
|
||||
version = "0.3.6";
|
||||
version = "0.3.9";
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||||
name = "${pname}-${version}";
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||||
|
||||
src = fetchgit {
|
||||
url = "git://github.com/JuliaLang/julia.git";
|
||||
rev = "refs/tags/v${version}";
|
||||
sha256 = "ad0820affefd04eb6fba7deb2603756974711846a251900a9202b8d2665a37cf";
|
||||
name = "julia-git-v${version}";
|
||||
};
|
||||
|
||||
patches = [ ./0001-work-around-buggy-wcwidth.patch ];
|
||||
|
||||
extraSrcs =
|
||||
let
|
||||
dsfmt_ver = "2.2";
|
||||
grisu_ver = "1.1.1";
|
||||
openblas_ver = "v0.2.13";
|
||||
lapack_ver = "3.5.0";
|
||||
arpack_ver = "3.1.5";
|
||||
patchelf_ver = "0.8";
|
||||
pcre_ver = "8.36";
|
||||
utf8proc_ver = "1.1.6";
|
||||
|
||||
dsfmt_src = fetchurl {
|
||||
url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmt_ver}.tar.gz";
|
||||
name = "dsfmt-${dsfmt_ver}.tar.gz";
|
||||
md5 = "cb61be3be7254eae39684612c524740d";
|
||||
};
|
||||
grisu_src = fetchurl {
|
||||
url = "http://double-conversion.googlecode.com/files/double-conversion-${grisu_ver}.tar.gz";
|
||||
md5 = "29b533ed4311161267bff1a9a97e2953";
|
||||
};
|
||||
openblas_src = fetchurl {
|
||||
url = "https://github.com/xianyi/OpenBLAS/tarball/${openblas_ver}";
|
||||
name = "openblas-${openblas_ver}.tar.gz";
|
||||
md5 = "74adf4c0d0d82bff4774be5bf2134183";
|
||||
};
|
||||
arpack_src = fetchurl rec {
|
||||
url = "https://github.com/opencollab/arpack-ng/archive/${arpack_ver}.tar.gz";
|
||||
md5 = "d84e1b6108d9ee67c0d21aba7099e953";
|
||||
name = "arpack-ng-${arpack_ver}.tar.gz";
|
||||
};
|
||||
lapack_src = fetchurl {
|
||||
url = "http://www.netlib.org/lapack/lapack-${lapack_ver}.tgz";
|
||||
name = "lapack-${lapack_ver}.tgz";
|
||||
md5 = "b1d3e3e425b2e44a06760ff173104bdf";
|
||||
};
|
||||
patchelf_src = fetchurl {
|
||||
url = "http://hydra.nixos.org/build/1524660/download/2/patchelf-${patchelf_ver}.tar.bz2";
|
||||
md5 = "5087261514b4b5814a39c3d3a36eb6ef";
|
||||
};
|
||||
pcre_src = fetchurl {
|
||||
url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-${pcre_ver}.tar.bz2";
|
||||
md5 = "b767bc9af0c20bc9c1fe403b0d41ad97";
|
||||
};
|
||||
utf8proc_src = fetchurl {
|
||||
url = "http://www.public-software-group.org/pub/projects/utf8proc/v${utf8proc_ver}/utf8proc-v${utf8proc_ver}.tar.gz";
|
||||
md5 = "2462346301fac2994c34f5574d6c3ca7";
|
||||
};
|
||||
|
||||
src = fetchgit {
|
||||
url = "git://github.com/JuliaLang/julia.git";
|
||||
rev = "refs/tags/v${version}";
|
||||
md5 = "d28e8f428485219f756d80c011d5dd32";
|
||||
name = "julia-git-v${version}";
|
||||
};
|
||||
|
||||
buildInputs = [ gfortran perl m4 gmp pcre llvm readline zlib
|
||||
fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf
|
||||
openblas liblapack tcl tk xproto libX11 git mpfr which wget
|
||||
];
|
||||
|
||||
configurePhase = ''
|
||||
for i in GMP LLVM PCRE READLINE FFTW LIBUNWIND SUITESPARSE GLPK ZLIB MPFR;
|
||||
do
|
||||
makeFlags="$makeFlags USE_SYSTEM_$i=1 "
|
||||
done
|
||||
makeFlags="$makeFlags JULIA_CPU_TARGET=core2";
|
||||
in [ dsfmt_src ];
|
||||
|
||||
prePatch = ''
|
||||
copy_kill_hash(){
|
||||
cp "$1" "$2/$(basename "$1" | sed -e 's/^[a-z0-9]*-//')"
|
||||
}
|
||||
|
||||
for i in "${grisu_src}" "${dsfmt_src}" "${arpack_src}" "${patchelf_src}" \
|
||||
"${pcre_src}" "${utf8proc_src}" "${lapack_src}" "${openblas_src}"; do
|
||||
for i in $extraSrcs; do
|
||||
copy_kill_hash "$i" deps
|
||||
done
|
||||
'';
|
||||
|
||||
${if realGcc ==null then "" else
|
||||
''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -llapack -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr -lblas -lopenblas -L$out/lib"''}
|
||||
export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -fPIC "
|
||||
|
||||
export LDFLAGS="-L${suitesparse}/lib -L$out/lib/julia -Wl,-rpath,$out/lib/julia"
|
||||
|
||||
export GLPK_PREFIX="${glpk}/include"
|
||||
|
||||
mkdir -p "$out/lib"
|
||||
sed -e "s@/usr/local/lib@$out/lib@g" -i deps/Makefile
|
||||
sed -e "s@/usr/lib@$out/lib@g" -i deps/Makefile
|
||||
|
||||
export makeFlags="$makeFlags PREFIX=$out SHELL=${stdenv.shell} prefix=$out"
|
||||
|
||||
export dontPatchELF=1
|
||||
|
||||
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PWD/usr/lib:$PWD/usr/lib/julia"
|
||||
postPatch = ''
|
||||
sed -i deps/Makefile \
|
||||
-e "s@/usr/local/lib@$out/lib@g" \
|
||||
-e "s@/usr/lib@$out/lib@g" \
|
||||
-e "s@/usr/include/double-conversion@${double_conversion}/include/double-conversion@g"
|
||||
|
||||
patchShebangs . contrib
|
||||
|
||||
export PATH="$PATH:${stdenv.cc.libc}/sbin"
|
||||
|
||||
# ldconfig doesn't seem to ever work on NixOS; system-wide ldconfig cache
|
||||
# is probably not what we want anyway on non-NixOS
|
||||
sed -e "s@/sbin/ldconfig@true@" -i src/ccall.*
|
||||
|
||||
ln -s "${openblas}/lib/libopenblas.so" "$out/lib/libblas.so"
|
||||
'';
|
||||
|
||||
preBuild = ''
|
||||
mkdir -p usr/lib
|
||||
buildInputs =
|
||||
[ libunwind llvm readline utf8proc zlib
|
||||
double_conversion fftw fftwSinglePrec glpk gmp mpfr pcre
|
||||
openblas arpack suitesparse
|
||||
];
|
||||
|
||||
echo "$out"
|
||||
mkdir -p "$out/lib"
|
||||
(
|
||||
cd "$(mktemp -d)"
|
||||
for i in "${suitesparse}"/lib/lib*.a; do
|
||||
ar -x $i
|
||||
done
|
||||
gcc *.o --shared -o "$out/lib/libsuitesparse.so"
|
||||
)
|
||||
cp "$out/lib/libsuitesparse.so" usr/lib
|
||||
for i in umfpack cholmod amd camd colamd spqr; do
|
||||
ln -s libsuitesparse.so "$out"/lib/lib$i.so;
|
||||
ln -s libsuitesparse.so "usr"/lib/lib$i.so;
|
||||
done
|
||||
nativeBuildInputs = [ gfortran git m4 patchelf perl which ];
|
||||
|
||||
makeFlags =
|
||||
let
|
||||
arch = head (splitString "-" stdenv.system);
|
||||
march =
|
||||
{ "x86_64-linux" = "x86-64";
|
||||
"x86_64-darwin" = "x86-64";
|
||||
"i686-linux" = "i686";
|
||||
}."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
|
||||
in [
|
||||
"ARCH=${arch}"
|
||||
"MARCH=${march}"
|
||||
"JULIA_CPU_TARGET=${march}"
|
||||
"PREFIX=$(out)"
|
||||
"prefix=$(out)"
|
||||
"SHELL=${stdenv.shell}"
|
||||
|
||||
"USE_SYSTEM_BLAS=1"
|
||||
"LIBBLAS=-lopenblas"
|
||||
"LIBBLASNAME=libopenblas"
|
||||
|
||||
"USE_SYSTEM_LAPACK=1"
|
||||
"LIBLAPACK=-lopenblas"
|
||||
"LIBLAPACKNAME=libopenblas"
|
||||
|
||||
"USE_SYSTEM_ARPACK=1"
|
||||
"USE_SYSTEM_FFTW=1"
|
||||
"USE_SYSTEM_GLPK=1"
|
||||
"USE_SYSTEM_GMP=1"
|
||||
"USE_SYSTEM_GRISU=1"
|
||||
"USE_SYSTEM_LIBUNWIND=1"
|
||||
"USE_SYSTEM_LLVM=1"
|
||||
"USE_SYSTEM_MPFR=1"
|
||||
"USE_SYSTEM_PATCHELF=1"
|
||||
"USE_SYSTEM_PCRE=1"
|
||||
"USE_SYSTEM_READLINE=1"
|
||||
"USE_SYSTEM_SUITESPARSE=1"
|
||||
"USE_SYSTEM_UTF8PROC=1"
|
||||
"USE_SYSTEM_ZLIB=1"
|
||||
];
|
||||
|
||||
GLPK_PREFIX = "${glpk}/include";
|
||||
|
||||
NIX_CFLAGS_COMPILE = [ "-fPIC" ];
|
||||
|
||||
# Julia tries to load these libraries dynamically at runtime, but they can't be found.
|
||||
# Easier by far to link against them as usual.
|
||||
# These go in LDFLAGS, where they affect only Julia itself, and not NIX_LDFLAGS,
|
||||
# where they would also be used for all the private libraries Julia builds.
|
||||
LDFLAGS = [
|
||||
"-larpack"
|
||||
"-lfftw3_threads"
|
||||
"-lfftw3f_threads"
|
||||
"-lglpk"
|
||||
"-lgmp"
|
||||
"-lmpfr"
|
||||
"-lopenblas"
|
||||
"-lpcre"
|
||||
"-lsuitesparse"
|
||||
"-lz"
|
||||
];
|
||||
|
||||
preConfigure = ''
|
||||
export PATH="$PATH:${stdenv.cc.libc}/sbin"
|
||||
'';
|
||||
|
||||
dontStrip = true;
|
||||
dontPatchELF = true;
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
@ -147,8 +143,8 @@ stdenv.mkDerivation rec {
|
||||
description = "High-level performance-oriented dynamical language for technical computing";
|
||||
homepage = "http://julialang.org/";
|
||||
license = stdenv.lib.licenses.mit;
|
||||
maintainers = [ stdenv.lib.maintainers.raskin ];
|
||||
platforms = with stdenv.lib.platforms; linux;
|
||||
maintainers = with stdenv.lib.maintainers; [ raskin ttuegel ];
|
||||
platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
|
||||
broken = false;
|
||||
};
|
||||
}
|
||||
|
||||
@ -0,0 +1,24 @@
|
||||
From b9070aeab0ab672ffe321089631f9afe263b0caa Mon Sep 17 00:00:00 2001
|
||||
From: Thomas Tuegel <ttuegel@gmail.com>
|
||||
Date: Thu, 4 Jun 2015 12:03:32 -0500
|
||||
Subject: [PATCH] work around buggy wcwidth
|
||||
|
||||
---
|
||||
test/unicode.jl | 3 ++-
|
||||
1 file changed, 2 insertions(+), 1 deletion(-)
|
||||
|
||||
diff --git a/test/unicode.jl b/test/unicode.jl
|
||||
index 52c3e6a..f1ef698 100644
|
||||
--- a/test/unicode.jl
|
||||
+++ b/test/unicode.jl
|
||||
@@ -103,5 +103,6 @@ end
|
||||
|
||||
# handling of embedded NUL chars (#10958)
|
||||
@test length("\0w") == length("\0α") == 2
|
||||
-@test strwidth("\0w") == strwidth("\0α") == 1
|
||||
+@test strwidth("\0w") == charwidth('\0') + charwidth('w')
|
||||
+@test strwidth("\0α") == charwidth('\0') + charwidth('α')
|
||||
@test normalize_string("\0W", casefold=true) == "\0w"
|
||||
--
|
||||
2.4.1
|
||||
|
||||
@ -119,6 +119,22 @@ self: super: {
|
||||
# Help libconfig find it's C language counterpart.
|
||||
libconfig = (dontCheck super.libconfig).override { config = pkgs.libconfig; };
|
||||
|
||||
hmatrix = overrideCabal super.hmatrix (drv: {
|
||||
configureFlags = (drv.configureFlags or []) ++ [ "-fopenblas" ];
|
||||
extraLibraries = [ pkgs.openblasCompat ];
|
||||
preConfigure = ''
|
||||
sed -i hmatrix.cabal -e 's@/usr/lib/openblas/lib@${pkgs.openblasCompat}/lib@'
|
||||
'';
|
||||
});
|
||||
|
||||
bindings-levmar = overrideCabal super.bindings-levmar (drv: {
|
||||
preConfigure = ''
|
||||
sed -i bindings-levmar.cabal \
|
||||
-e 's,extra-libraries: lapack blas,extra-libraries: openblas,'
|
||||
'';
|
||||
extraLibraries = [ pkgs.openblas ];
|
||||
});
|
||||
|
||||
# The Haddock phase fails for one reason or another.
|
||||
attoparsec-conduit = dontHaddock super.attoparsec-conduit;
|
||||
base-noprelude = dontHaddock super.base-noprelude;
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
{ stdenv, fetchurl, liblapack, readline, gettext, ncurses }:
|
||||
{ stdenv, fetchurl, readline, gettext, ncurses }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
name = "gnu-apl-${version}";
|
||||
@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
|
||||
sha256 = "0h4diq3wfbdwxp5nm0z4b0p1zq13lwip0y7v28r9v0mbbk8xsfh1";
|
||||
};
|
||||
|
||||
buildInputs = [ liblapack readline gettext ncurses ];
|
||||
buildInputs = [ readline gettext ncurses ];
|
||||
|
||||
postInstall = ''
|
||||
cp -r support-files/ $out/share/doc/
|
||||
|
||||
@ -1,10 +1,22 @@
|
||||
{ stdenv, fetchurl, gfortran, readline, ncurses, perl, flex, texinfo, qhull
|
||||
, libX11, graphicsmagick, pcre, liblapack, pkgconfig, mesa, fltk
|
||||
, fftw, fftwSinglePrec, zlib, curl, qrupdate
|
||||
, libX11, graphicsmagick, pcre, pkgconfig, mesa, fltk
|
||||
, fftw, fftwSinglePrec, zlib, curl, qrupdate, openblas
|
||||
, qt ? null, qscintilla ? null, ghostscript ? null, llvm ? null, hdf5 ? null,glpk ? null
|
||||
, suitesparse ? null, gnuplot ? null, jdk ? null, python ? null
|
||||
}:
|
||||
|
||||
let
|
||||
suitesparseOrig = suitesparse;
|
||||
qrupdateOrig = qrupdate;
|
||||
in
|
||||
# integer width is determined by openblas, so all dependencies must be built
|
||||
# with exactly the same openblas
|
||||
let
|
||||
suitesparse =
|
||||
if suitesparseOrig != null then suitesparseOrig.override { inherit openblas; } else null;
|
||||
qrupdate = if qrupdateOrig != null then qrupdateOrig.override { inherit openblas; } else null;
|
||||
in
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = "4.0.0";
|
||||
name = "octave-${version}";
|
||||
@ -14,7 +26,7 @@ stdenv.mkDerivation rec {
|
||||
};
|
||||
|
||||
buildInputs = [ gfortran readline ncurses perl flex texinfo qhull libX11
|
||||
graphicsmagick pcre liblapack pkgconfig mesa fltk zlib curl
|
||||
graphicsmagick pcre pkgconfig mesa fltk zlib curl openblas
|
||||
fftw fftwSinglePrec qrupdate ]
|
||||
++ (stdenv.lib.optional (qt != null) qt)
|
||||
++ (stdenv.lib.optional (qscintilla != null) qscintilla)
|
||||
@ -34,7 +46,13 @@ stdenv.mkDerivation rec {
|
||||
# problems on Hydra
|
||||
enableParallelBuilding = false;
|
||||
|
||||
configureFlags = [ "--enable-readline" "--enable-dl" ];
|
||||
configureFlags =
|
||||
[ "--enable-readline"
|
||||
"--enable-dl"
|
||||
"--with-blas=openblas"
|
||||
"--with-lapack=openblas"
|
||||
]
|
||||
++ stdenv.lib.optional openblas.blas64 "--enable-64";
|
||||
|
||||
# Keep a copy of the octave tests detailed results in the output
|
||||
# derivation, because someone may care
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
{ stdenv
|
||||
, fetchurl
|
||||
, gfortran
|
||||
, liblapack
|
||||
, openblas
|
||||
}:
|
||||
stdenv.mkDerivation {
|
||||
name = "qrupdate-1.1.2";
|
||||
@ -10,20 +10,25 @@ stdenv.mkDerivation {
|
||||
sha256 = "024f601685phcm1pg8lhif3lpy5j9j0k6n0r46743g4fvh8wg8g2";
|
||||
};
|
||||
|
||||
configurePhase = ''
|
||||
configurePhase =
|
||||
''
|
||||
export PREFIX=$out
|
||||
sed -i -e 's,^BLAS=.*,BLAS=-L${liblapack}/lib -L${liblapack.blas} -lcblas -lf77blas -latlas,' \
|
||||
-e 's,^LAPACK=.*,LAPACK=-L${liblapack}/lib -llapack -lcblas -lf77blas -latlas,' \
|
||||
sed -i -e 's,^BLAS=.*,BLAS=-L${openblas}/lib -lopenblas,' \
|
||||
-e 's,^LAPACK=.*,LAPACK=-L${openblas}/lib -lopenblas,' \
|
||||
Makeconf
|
||||
''
|
||||
+ stdenv.lib.optionalString openblas.blas64
|
||||
''
|
||||
sed -i Makeconf -e '/^FFLAGS=.*/ s/$/-fdefault-integer-8/'
|
||||
'';
|
||||
|
||||
doCheck = true;
|
||||
|
||||
checkTarget = "test";
|
||||
|
||||
buildTarget = "lib";
|
||||
buildFlags = [ "lib" "solib" ];
|
||||
|
||||
installTarget = "install-staticlib";
|
||||
installTargets = "install";
|
||||
|
||||
buildInputs = [ gfortran liblapack ];
|
||||
buildInputs = [ gfortran openblas ];
|
||||
}
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
{ stdenv, fetchurl, gfortran, atlasWithLapack }:
|
||||
{ stdenv, fetchurl, gfortran, openblas }:
|
||||
|
||||
with stdenv.lib;
|
||||
|
||||
let
|
||||
version = "3.2.0";
|
||||
@ -10,10 +12,15 @@ stdenv.mkDerivation {
|
||||
sha256 = "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff";
|
||||
};
|
||||
|
||||
buildInputs = [ gfortran atlasWithLapack ];
|
||||
buildInputs = [ gfortran openblas ];
|
||||
|
||||
# Auto-detection fails because gfortran brings in BLAS by default
|
||||
configureFlags="--with-blas=-latlas --with-lapack=-latlas";
|
||||
configureFlags = [
|
||||
"--with-blas=-lopenblas"
|
||||
"--with-lapack=-lopenblas"
|
||||
];
|
||||
|
||||
FFLAGS = optional openblas.blas64 "-fdefault-integer-8";
|
||||
|
||||
meta = {
|
||||
homepage = "http://forge.scilab.org/index.php/p/arpack-ng/";
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
{ stdenv, fetchurl, unzip, blas, liblapack, gfortran }:
|
||||
{ stdenv, fetchurl, unzip, openblas, gfortran }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = "3.12.3";
|
||||
@ -13,9 +13,14 @@ stdenv.mkDerivation rec {
|
||||
export CXXDEFS="-DHAVE_RAND -DHAVE_CSTRING -DHAVE_CSTDIO"
|
||||
'';
|
||||
|
||||
configureFlags = [
|
||||
"--with-blas-lib=-lopenblas"
|
||||
"--with-lapack-lib=-lopenblas"
|
||||
];
|
||||
|
||||
nativeBuildInputs = [ unzip ];
|
||||
|
||||
buildInputs = [ gfortran blas liblapack ];
|
||||
buildInputs = [ gfortran openblas ];
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
|
||||
@ -1,37 +0,0 @@
|
||||
{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
|
||||
|
||||
let local = config.openblas.preferLocalBuild or false;
|
||||
localTarget = config.openblas.target or "";
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = "0.2.10";
|
||||
|
||||
name = "openblas-${version}";
|
||||
src = fetchurl {
|
||||
url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
|
||||
sha256 = "06i0q4qnd5q5xljzrgvda0gjsczc6l2pl9hw6dn2qjpw38al73za";
|
||||
name = "openblas-${version}.tar.gz";
|
||||
};
|
||||
|
||||
preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
|
||||
|
||||
buildInputs = [gfortran perl];
|
||||
|
||||
cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
|
||||
|
||||
target = if local then localTarget else
|
||||
if cpu == "i686" then "P2" else
|
||||
if cpu == "x86_64" then "CORE2" else
|
||||
# allow autodetect
|
||||
"";
|
||||
|
||||
makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\" INTERFACE64=1";
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Basic Linear Algebra Subprograms";
|
||||
license = licenses.bsd3;
|
||||
homepage = "https://github.com/xianyi/OpenBLAS";
|
||||
platforms = [ "x86_64-linux" ];
|
||||
maintainers = with maintainers; [ ttuegel ];
|
||||
};
|
||||
}
|
||||
@ -1,37 +0,0 @@
|
||||
{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
|
||||
|
||||
let local = config.openblas.preferLocalBuild or false;
|
||||
localTarget = config.openblas.target or "";
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = "0.2.2";
|
||||
|
||||
name = "openblas-${version}";
|
||||
src = fetchurl {
|
||||
url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
|
||||
sha256 = "13kdx3knff5ajnmgn419g0dnh83plin07p7akwamr3v7z5qfrzqr";
|
||||
name = "openblas-${version}.tar.gz";
|
||||
};
|
||||
|
||||
preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
|
||||
|
||||
buildInputs = [gfortran perl];
|
||||
|
||||
cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
|
||||
|
||||
target = if local then localTarget else
|
||||
if cpu == "i686" then "P2" else
|
||||
if cpu == "x86_64" then "CORE2" else
|
||||
# allow autodetect
|
||||
"";
|
||||
|
||||
makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\"";
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Basic Linear Algebra Subprograms";
|
||||
license = licenses.bsd3;
|
||||
homepage = "https://github.com/xianyi/OpenBLAS";
|
||||
platforms = [ "x86_64-linux" ];
|
||||
maintainers = with maintainers; [ ttuegel ];
|
||||
};
|
||||
}
|
||||
@ -1,22 +1,24 @@
|
||||
{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils }:
|
||||
{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils
|
||||
# Most packages depending on openblas expect integer width to match pointer width,
|
||||
# but some expect to use 32-bit integers always (for compatibility with reference BLAS).
|
||||
, blas64 ? null
|
||||
}:
|
||||
|
||||
with stdenv.lib;
|
||||
|
||||
let local = config.openblas.preferLocalBuild or false;
|
||||
binary =
|
||||
{
|
||||
i686-linux = "32";
|
||||
{ i686-linux = "32";
|
||||
x86_64-linux = "64";
|
||||
x86_64-darwin = "64";
|
||||
}."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
|
||||
genericFlags =
|
||||
[
|
||||
"DYNAMIC_ARCH=1"
|
||||
[ "DYNAMIC_ARCH=1"
|
||||
"NUM_THREADS=64"
|
||||
"BINARY=${binary}"
|
||||
];
|
||||
localFlags = config.openblas.flags or
|
||||
optionals (hasAttr "target" config.openblas) [ "TARGET=${config.openblas.target}" ];
|
||||
blas64Orig = blas64;
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = "0.2.14";
|
||||
@ -43,9 +45,13 @@ stdenv.mkDerivation rec {
|
||||
# thus is not an explicit dependency.
|
||||
"CC=${if stdenv.isDarwin then "clang" else "gcc"}"
|
||||
''PREFIX="''$(out)"''
|
||||
"INTERFACE64=1"
|
||||
"BINARY=${binary}"
|
||||
"USE_OPENMP=${if stdenv.isDarwin then "0" else "1"}"
|
||||
"INTERFACE64=${if blas64 then "1" else "0"}"
|
||||
];
|
||||
|
||||
blas64 = if blas64Orig != null then blas64Orig else hasPrefix "x86_64" stdenv.system;
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Basic Linear Algebra Subprograms";
|
||||
license = licenses.bsd3;
|
||||
|
||||
@ -1,36 +0,0 @@
|
||||
From 456b26d0c9101adaa5876954baac0ca0e872dab6 Mon Sep 17 00:00:00 2001
|
||||
From: Thomas Tuegel <ttuegel@gmail.com>
|
||||
Date: Mon, 15 Dec 2014 10:18:01 -0600
|
||||
Subject: [PATCH 1/3] disable metis
|
||||
|
||||
---
|
||||
SuiteSparse_config/SuiteSparse_config.mk | 6 +++---
|
||||
1 file changed, 3 insertions(+), 3 deletions(-)
|
||||
|
||||
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
index ba2da23..e1514bf 100644
|
||||
--- a/SuiteSparse_config/SuiteSparse_config.mk
|
||||
+++ b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
@@ -212,8 +212,8 @@ XERBLA =
|
||||
# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
|
||||
# You may wish to use an absolute path. METIS is optional. Compile
|
||||
# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
|
||||
-METIS_PATH = ../../metis-4.0
|
||||
-METIS = ../../metis-4.0/libmetis.a
|
||||
+# METIS_PATH = ../../metis-4.0
|
||||
+# METIS = ../../metis-4.0/libmetis.a
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# UMFPACK configuration:
|
||||
@@ -273,7 +273,7 @@ UMFPACK_CONFIG =
|
||||
# -DNSUNPERF for Solaris only. If defined, do not use the Sun
|
||||
# Performance Library
|
||||
|
||||
-CHOLMOD_CONFIG = $(GPU_CONFIG)
|
||||
+CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
|
||||
|
||||
# uncomment this line to compile CHOLMOD without METIS:
|
||||
# CHOLMOD_CONFIG = -DNPARTITION
|
||||
--
|
||||
2.1.3
|
||||
|
||||
@ -1,27 +0,0 @@
|
||||
From e0fee492a315ce1ef8697b056af210beb1465334 Mon Sep 17 00:00:00 2001
|
||||
From: Thomas Tuegel <ttuegel@gmail.com>
|
||||
Date: Mon, 15 Dec 2014 10:18:12 -0600
|
||||
Subject: [PATCH 2/3] set install dir
|
||||
|
||||
---
|
||||
SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
|
||||
1 file changed, 2 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
index e1514bf..f1046a6 100644
|
||||
--- a/SuiteSparse_config/SuiteSparse_config.mk
|
||||
+++ b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
@@ -95,8 +95,8 @@ F77LIB =
|
||||
# LIB = -lm
|
||||
|
||||
# For "make install"
|
||||
-INSTALL_LIB = /usr/local/lib
|
||||
-INSTALL_INCLUDE = /usr/local/include
|
||||
+INSTALL_LIB = @out@/lib
|
||||
+INSTALL_INCLUDE = @out@/include
|
||||
|
||||
# Which version of MAKE you are using (default is "make")
|
||||
# MAKE = make
|
||||
--
|
||||
2.1.3
|
||||
|
||||
@ -1,27 +0,0 @@
|
||||
From a99cca30cfd965683564ae024e8ecc615c61697a Mon Sep 17 00:00:00 2001
|
||||
From: Thomas Tuegel <ttuegel@gmail.com>
|
||||
Date: Mon, 15 Dec 2014 10:24:08 -0600
|
||||
Subject: [PATCH 3/3] blas lapack flags
|
||||
|
||||
---
|
||||
SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
|
||||
1 file changed, 2 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
index f1046a6..1710162 100644
|
||||
--- a/SuiteSparse_config/SuiteSparse_config.mk
|
||||
+++ b/SuiteSparse_config/SuiteSparse_config.mk
|
||||
@@ -119,8 +119,8 @@ INSTALL_INCLUDE = @out@/include
|
||||
# naming the BLAS and LAPACK library (*.a or *.so) files.
|
||||
|
||||
# This is probably slow ... it might connect to the Standard Reference BLAS:
|
||||
- BLAS = -lblas -lgfortran
|
||||
- LAPACK = -llapack
|
||||
+ BLAS = @blasFlags@
|
||||
+ LAPACK = @lapackFlags@
|
||||
|
||||
# MKL
|
||||
# BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
|
||||
--
|
||||
2.1.3
|
||||
|
||||
@ -1,4 +1,8 @@
|
||||
{ stdenv, fetchurl, blas, liblapack, gfortran } :
|
||||
{ stdenv, fetchurl, gfortran, openblas }:
|
||||
|
||||
let
|
||||
int_t = if openblas.blas64 then "int64_t" else "int32_t";
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = "4.2.1";
|
||||
name = "suitesparse-${version}";
|
||||
@ -6,17 +10,35 @@ stdenv.mkDerivation rec {
|
||||
url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ;
|
||||
sha256 = "1ga69637x7kdkiy3w3lq9dvva7220bdangv2lch2wx1hpi83h0p8";
|
||||
};
|
||||
buildInputs = [blas liblapack gfortran] ;
|
||||
patches = [./disable-metis.patch];
|
||||
|
||||
nativeBuildInputs = [ gfortran ];
|
||||
buildInputs = [ openblas ];
|
||||
|
||||
preConfigure = ''
|
||||
export PREFIX=$out
|
||||
mkdir -p $out/lib
|
||||
mkdir -p $out/include
|
||||
|
||||
sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
|
||||
-e 's/METIS .*$/METIS =/' \
|
||||
-e 's/METIS_PATH .*$/METIS_PATH =/' \
|
||||
-e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
|
||||
-e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
|
||||
'';
|
||||
|
||||
makeFlags = ''PREFIX=\"$(out)\" INSTALL_LIB=$(out)/lib INSTALL_INCLUDE=$(out)/include'';
|
||||
makeFlags = [
|
||||
"PREFIX=\"$(out)\""
|
||||
"INSTALL_LIB=$(out)/lib"
|
||||
"INSTALL_INCLUDE=$(out)/include"
|
||||
"BLAS=-lopenblas"
|
||||
"LAPACK="
|
||||
];
|
||||
|
||||
NIX_CFLAGS = "-fPIC";
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;
|
||||
description = "A suite of sparse matrix algorithms";
|
||||
license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ];
|
||||
maintainers = with maintainers; [ ttuegel ];
|
||||
};
|
||||
}
|
||||
|
||||
@ -1,452 +0,0 @@
|
||||
#===============================================================================
|
||||
# SuiteSparse_config.mk: common configuration file for the SuiteSparse
|
||||
#===============================================================================
|
||||
|
||||
# This file contains all configuration settings for all packages authored or
|
||||
# co-authored by Tim Davis:
|
||||
#
|
||||
# Package Version Description
|
||||
# ------- ------- -----------
|
||||
# AMD 1.2 or later approximate minimum degree ordering
|
||||
# COLAMD 2.4 or later column approximate minimum degree ordering
|
||||
# CCOLAMD 1.0 or later constrained column approximate minimum degree ordering
|
||||
# CAMD any constrained approximate minimum degree ordering
|
||||
# UMFPACK 4.5 or later sparse LU factorization, with the BLAS
|
||||
# CHOLMOD any sparse Cholesky factorization, update/downdate
|
||||
# KLU 0.8 or later sparse LU factorization, BLAS-free
|
||||
# BTF 0.8 or later permutation to block triangular form
|
||||
# LDL 1.2 or later concise sparse LDL'
|
||||
# CXSparse any extended version of CSparse (int/long, real/complex)
|
||||
# SuiteSparseQR any sparse QR factorization
|
||||
# RBio 2.0 or later read/write sparse matrices in Rutherford-Boeing format
|
||||
#
|
||||
# By design, this file is NOT included in the CSparse makefile.
|
||||
# That package is fully stand-alone. CSparse is primarily for teaching;
|
||||
# production code should use CXSparse.
|
||||
#
|
||||
# The SuiteSparse_config directory and the above packages should all appear in
|
||||
# a single directory, in order for the Makefile's within each package to find
|
||||
# this file.
|
||||
#
|
||||
# To enable an option of the form "# OPTION = ...", edit this file and
|
||||
# delete the "#" in the first column of the option you wish to use.
|
||||
#
|
||||
# The use of METIS 4.0.1 is optional. To exclude METIS, you must compile with
|
||||
# CHOLMOD_CONFIG set to -DNPARTITION. See below for details. However, if you
|
||||
# do not have a metis-4.0 directory inside the SuiteSparse directory, the
|
||||
# */Makefile's that optionally rely on METIS will automatically detect this
|
||||
# and compile without METIS.
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Generic configuration
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Using standard definitions from the make environment, typically:
|
||||
#
|
||||
# CC cc C compiler
|
||||
# CXX g++ C++ compiler
|
||||
# CFLAGS [ ] flags for C and C++ compiler
|
||||
# CPPFLAGS [ ] flags for C and C++ compiler
|
||||
# TARGET_ARCH [ ] target architecture
|
||||
# FFLAGS [ ] flags for Fortran compiler
|
||||
# RM rm -f delete a file
|
||||
# AR ar create a static *.a library archive
|
||||
# ARFLAGS rv flags for ar
|
||||
# MAKE make make itself (sometimes called gmake)
|
||||
#
|
||||
# You can redefine them here, but by default they are used from the
|
||||
# default make environment.
|
||||
|
||||
# To use OpenMP add -openmp to the CFLAGS
|
||||
# If OpenMP is used, it is recommended to define CHOLMOD_OMP_NUM_THREADS
|
||||
# as the number of cores per socket on the machine being used to maximize
|
||||
# memory performance
|
||||
CFLAGS =
|
||||
# CFLAGS = -g
|
||||
# for the icc compiler and OpenMP:
|
||||
# CFLAGS = -openmp
|
||||
|
||||
# C and C++ compiler flags. The first three are standard for *.c and *.cpp
|
||||
# Add -DNTIMER if you do use any timing routines (otherwise -lrt is required).
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -DNTIMER
|
||||
CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC
|
||||
# for the MKL BLAS:
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -I$(MKLROOT)/include -D_GNU_SOURCE
|
||||
# with no optimization:
|
||||
# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -fexceptions -fPIC
|
||||
|
||||
# ranlib, and ar, for generating libraries. If you don't need ranlib,
|
||||
# just change it to RANLAB = echo
|
||||
RANLIB = ranlib
|
||||
ARCHIVE = $(AR) $(ARFLAGS)
|
||||
|
||||
# copy and delete a file
|
||||
CP = cp -f
|
||||
MV = mv -f
|
||||
|
||||
# Fortran compiler (not required for 'make' or 'make library')
|
||||
F77 = gfortran
|
||||
F77FLAGS = $(FFLAGS) -O
|
||||
F77LIB =
|
||||
|
||||
# C and Fortran libraries. Remove -lrt if you don't have it.
|
||||
LIB = -lm -lrt
|
||||
# Using the following requires CF = ... -DNTIMER on POSIX C systems.
|
||||
# LIB = -lm
|
||||
|
||||
# For "make install"
|
||||
INSTALL_LIB = @out@/lib
|
||||
INSTALL_INCLUDE = @out@/include
|
||||
|
||||
# Which version of MAKE you are using (default is "make")
|
||||
# MAKE = make
|
||||
# MAKE = gmake
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# BLAS and LAPACK configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# UMFPACK and CHOLMOD both require the BLAS. CHOLMOD also requires LAPACK.
|
||||
# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
|
||||
# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
|
||||
# LAPACK is at http://www.netlib.org/lapack/ . You can use the standard
|
||||
# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
|
||||
# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
|
||||
# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
|
||||
# on a 2.5Ghz dual-core AMD Opteron.
|
||||
|
||||
# These settings will probably not work, since there is no fixed convention for
|
||||
# naming the BLAS and LAPACK library (*.a or *.so) files.
|
||||
|
||||
# This is probably slow ... it might connect to the Standard Reference BLAS:
|
||||
BLAS = -lf77blas -latlas -lcblas -lgfortran
|
||||
LAPACK = -llapack -latlas -lcblas
|
||||
|
||||
# MKL
|
||||
# BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
|
||||
# LAPACK =
|
||||
|
||||
# ACML
|
||||
# BLAS = -lacml -lgfortran
|
||||
# LAPACK =
|
||||
|
||||
# OpenBLAS
|
||||
# BLAS = -lopenblas
|
||||
# LAPACK =
|
||||
|
||||
# NOTE: this next option for the "Goto BLAS" has nothing to do with a "goto"
|
||||
# statement. Rather, the Goto BLAS is written by Dr. Kazushige Goto.
|
||||
# Using the Goto BLAS:
|
||||
# BLAS = -lgoto -lgfortran -lgfortranbegin
|
||||
# BLAS = -lgoto2 -lgfortran -lgfortranbegin -lpthread
|
||||
|
||||
# Using non-optimized versions:
|
||||
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
|
||||
# LAPACK = -llapack_plain
|
||||
|
||||
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
|
||||
# LAPACK = -llapack
|
||||
|
||||
# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
|
||||
# the BLAS. Also, the standard xerbla requires the Fortran I/O library, and
|
||||
# stops the application program if an error occurs. A C version of xerbla
|
||||
# distributed with this software (SuiteSparse_config/xerbla/libcerbla.a)
|
||||
# includes a Fortran-callable xerbla routine that prints nothing and does not
|
||||
# stop the application program. This is optional.
|
||||
|
||||
# XERBLA = ../../SuiteSparse_config/xerbla/libcerbla.a
|
||||
|
||||
# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
|
||||
# use this option:
|
||||
XERBLA =
|
||||
|
||||
# If you wish to use the Fortran SuiteSparse_config/xerbla/xerbla.f instead,
|
||||
# use this:
|
||||
|
||||
# XERBLA = ../../SuiteSparse_config/xerbla/libxerbla.a
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# GPU configuration for CHOLMOD and SPQR
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# no cuda
|
||||
CUDA_ROOT =
|
||||
GPU_BLAS_PATH =
|
||||
GPU_CONFIG =
|
||||
CUDA_PATH =
|
||||
CUDART_LIB =
|
||||
CUBLAS_LIB =
|
||||
CUDA_INC_PATH =
|
||||
NV20 =
|
||||
NV30 =
|
||||
NV35 =
|
||||
NVCC = echo
|
||||
NVCCFLAGS =
|
||||
|
||||
# with cuda for CHOLMOD
|
||||
# CUDA_ROOT = /usr/local/cuda
|
||||
# GPU_BLAS_PATH = $(CUDA_ROOT)
|
||||
# with 4 cores (default):
|
||||
# GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS
|
||||
# with 10 cores:
|
||||
# GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS -DCHOLMOD_OMP_NUM_THREADS=10
|
||||
# CUDA_PATH = $(CUDA_ROOT)
|
||||
# CUDART_LIB = $(CUDA_ROOT)/lib64/libcudart.so
|
||||
# CUBLAS_LIB = $(CUDA_ROOT)/lib64/libcublas.so
|
||||
# CUDA_INC_PATH = $(CUDA_ROOT)/include/
|
||||
# NV20 = -arch=sm_20 -Xcompiler -fPIC
|
||||
# NV30 = -arch=sm_30 -Xcompiler -fPIC
|
||||
# NV35 = -arch=sm_35 -Xcompiler -fPIC
|
||||
# NVCC = $(CUDA_ROOT)/bin/nvcc
|
||||
# NVCCFLAGS = $(NV20) -O3 -gencode=arch=compute_20,code=sm_20 -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_35,code=sm_35
|
||||
|
||||
# was NVCC = $(CUDA_ROOT)/bin/nvcc $(NV35) $(NV30) $(NV20)
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# METIS, optionally used by CHOLMOD
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
|
||||
# compile CHOLMOD with the -DNPARTITION flag.
|
||||
|
||||
# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
|
||||
# You may wish to use an absolute path. METIS is optional. Compile
|
||||
# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
|
||||
# METIS_PATH = ../../metis-4.0
|
||||
# METIS = ../../metis-4.0/libmetis.a
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# UMFPACK configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Configuration flags for UMFPACK. See UMFPACK/Source/umf_config.h for details.
|
||||
#
|
||||
# -DNBLAS do not use the BLAS. UMFPACK will be very slow.
|
||||
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
|
||||
# LAPACK and the BLAS (defaults to 'int')
|
||||
# -DNSUNPERF do not use the Sun Perf. Library (default is use it on Solaris)
|
||||
# -DNRECIPROCAL do not multiply by the reciprocal
|
||||
# -DNO_DIVIDE_BY_ZERO do not divide by zero
|
||||
# -DNCHOLMOD do not use CHOLMOD as a ordering method. If -DNCHOLMOD is
|
||||
# included in UMFPACK_CONFIG, then UMFPACK does not rely on
|
||||
# CHOLMOD, CAMD, CCOLAMD, COLAMD, and METIS.
|
||||
|
||||
UMFPACK_CONFIG =
|
||||
|
||||
# uncomment this line to compile UMFPACK without CHOLMOD:
|
||||
# UMFPACK_CONFIG = -DNCHOLMOD
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# CHOLMOD configuration
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# CHOLMOD Library Modules, which appear in libcholmod.a:
|
||||
# Core requires: none
|
||||
# Check requires: Core
|
||||
# Cholesky requires: Core, AMD, COLAMD. optional: Partition, Supernodal
|
||||
# MatrixOps requires: Core
|
||||
# Modify requires: Core
|
||||
# Partition requires: Core, CCOLAMD, METIS. optional: Cholesky
|
||||
# Supernodal requires: Core, BLAS, LAPACK
|
||||
#
|
||||
# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
|
||||
# Tcov requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
|
||||
# optional: Partition
|
||||
# Valgrind same as Tcov
|
||||
# Demo requires: Core, Check, Cholesky, MatrixOps, Supernodal
|
||||
# optional: Partition
|
||||
#
|
||||
# Configuration flags:
|
||||
# -DNCHECK do not include the Check module. License GNU LGPL
|
||||
# -DNCHOLESKY do not include the Cholesky module. License GNU LGPL
|
||||
# -DNPARTITION do not include the Partition module. License GNU LGPL
|
||||
# also do not include METIS.
|
||||
# -DNCAMD do not use CAMD, etc from Partition module. GNU LGPL
|
||||
# -DNGPL do not include any GNU GPL Modules in the CHOLMOD library:
|
||||
# -DNMATRIXOPS do not include the MatrixOps module. License GNU GPL
|
||||
# -DNMODIFY do not include the Modify module. License GNU GPL
|
||||
# -DNSUPERNODAL do not include the Supernodal module. License GNU GPL
|
||||
#
|
||||
# -DNPRINT do not print anything.
|
||||
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
|
||||
# LAPACK and the BLAS (defaults to 'int')
|
||||
# -DNSUNPERF for Solaris only. If defined, do not use the Sun
|
||||
# Performance Library
|
||||
|
||||
CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
|
||||
|
||||
# uncomment this line to compile CHOLMOD without METIS:
|
||||
# CHOLMOD_CONFIG = -DNPARTITION
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# SuiteSparseQR configuration:
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# The SuiteSparseQR library can be compiled with the following options:
|
||||
#
|
||||
# -DNPARTITION do not include the CHOLMOD partition module
|
||||
# -DNEXPERT do not include the functions in SuiteSparseQR_expert.cpp
|
||||
# -DHAVE_TBB enable the use of Intel's Threading Building Blocks (TBB)
|
||||
|
||||
# default, without timing, without TBB:
|
||||
SPQR_CONFIG = $(GPU_CONFIG)
|
||||
# with TBB:
|
||||
# SPQR_CONFIG = -DHAVE_TBB
|
||||
|
||||
# This is needed for IBM AIX: (but not for and C codes, just C++)
|
||||
# SPQR_CONFIG = -DBLAS_NO_UNDERSCORE
|
||||
|
||||
# with TBB, you must select this:
|
||||
# TBB = -ltbb
|
||||
# without TBB:
|
||||
TBB =
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# code formatting
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Use "grep" only, if you do not have "indent"
|
||||
# PRETTY = grep -v "^\#"
|
||||
# PRETTY = grep -v "^\#" | indent -bl -nce -ss -bli0 -i4 -sob -l120
|
||||
PRETTY = grep -v "^\#" | indent -bl -nce -bli0 -i4 -sob -l120
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Linux
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# Using default compilers:
|
||||
# CC = gcc
|
||||
# CF = $(CFLAGS) -O3 -fexceptions
|
||||
|
||||
# alternatives:
|
||||
# CF = $(CFLAGS) -g -fexceptions \
|
||||
# -Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
|
||||
# -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi \
|
||||
# -funit-at-a-time
|
||||
# CF = $(CFLAGS) -O3 -fexceptions \
|
||||
# -Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
|
||||
# -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
|
||||
# CF = $(CFLAGS) -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
|
||||
# CF = $(CFLAGS) -O3
|
||||
# CF = $(CFLAGS) -O3 -g -fexceptions
|
||||
# CF = $(CFLAGS) -g -fexceptions \
|
||||
# -Wall -W -Wshadow \
|
||||
# -Wredundant-decls -Wdisabled-optimization -ansi
|
||||
|
||||
# consider:
|
||||
# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
|
||||
# -frename-registers -ffast-math -funroll-loops
|
||||
|
||||
# Using the Goto BLAS:
|
||||
# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
|
||||
|
||||
# Using Intel's icc and ifort compilers:
|
||||
# (does not work for mexFunctions unless you add a mexopts.sh file)
|
||||
# F77 = ifort
|
||||
# CC = icc
|
||||
# CF = $(CFLAGS) -O3 -xN -vec_report=0
|
||||
# CF = $(CFLAGS) -g
|
||||
|
||||
# 64bit:
|
||||
# F77FLAGS = -O -m64
|
||||
# CF = $(CFLAGS) -O3 -fexceptions -m64
|
||||
# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
|
||||
# LAPACK = -llapack64
|
||||
|
||||
# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto_opteron64 -lgfortran
|
||||
|
||||
# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto -lgfortran
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Mac
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# As recommended by macports, http://suitesparse.darwinports.com/
|
||||
# I've tested them myself on Mac OSX 10.6.1 and 10.6.8 (Snow Leopard),
|
||||
# on my MacBook Air, and they work fine.
|
||||
|
||||
# F77 = gfortran
|
||||
# CF = $(CFLAGS) -O3 -fno-common -fexceptions -DNTIMER
|
||||
# BLAS = -framework Accelerate
|
||||
# LAPACK = -framework Accelerate
|
||||
# LIB = -lm
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Solaris
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# 32-bit
|
||||
# CF = $(CFLAGS) -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
|
||||
|
||||
# 64-bit
|
||||
# CF = $(CFLAGS) -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
|
||||
|
||||
# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
|
||||
|
||||
# The Sun Performance Library includes both LAPACK and the BLAS:
|
||||
# BLAS = -xlic_lib=sunperf
|
||||
# LAPACK =
|
||||
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# Compaq Alpha
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# 64-bit mode only
|
||||
# CF = $(CFLAGS) -O2 -std1
|
||||
# BLAS = -ldxml
|
||||
# LAPACK =
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# IBM RS 6000
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lessl
|
||||
# LAPACK =
|
||||
|
||||
# 32-bit mode:
|
||||
# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -qproto
|
||||
# F77FLAGS = -O4 -qipa -qmaxmem=16384
|
||||
|
||||
# 64-bit mode:
|
||||
# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -q64 -qproto
|
||||
# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# SGI IRIX
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lscsl
|
||||
# LAPACK =
|
||||
|
||||
# 32-bit mode
|
||||
# CF = $(CFLAGS) -O
|
||||
|
||||
# 64-bit mode (32 bit int's and 64-bit long's):
|
||||
# CF = $(CFLAGS) -64
|
||||
# F77FLAGS = -64
|
||||
|
||||
# SGI doesn't have ranlib
|
||||
# RANLIB = echo
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# AMD Opteron (64 bit)
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
# BLAS = -lgoto_opteron64 -lg2c
|
||||
# LAPACK = -llapack_opteron64
|
||||
|
||||
# SUSE Linux 10.1, AMD Opteron
|
||||
# F77 = gfortran
|
||||
# BLAS = -lgoto_opteron64 -lgfortran
|
||||
# LAPACK = -llapack_opteron64
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# remove object files and profile output
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno
|
||||
@ -1,34 +1,53 @@
|
||||
{ stdenv, fetchurl, substituteAll
|
||||
, atlasWithLapack, gfortran }:
|
||||
{ stdenv, fetchurl, gfortran, openblas }:
|
||||
|
||||
let
|
||||
name = "suitesparse-4.4.1";
|
||||
version = "4.4.4";
|
||||
name = "suitesparse-${version}";
|
||||
|
||||
int_t = if openblas.blas64 then "int64_t" else "int32_t";
|
||||
in
|
||||
stdenv.mkDerivation {
|
||||
inherit name;
|
||||
|
||||
src = fetchurl {
|
||||
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.1.tar.gz";
|
||||
sha256 = "0y8i6dizrr556xggpjyc7wijjv4jbizhssmjj4jv8n1s7zxy2z0n";
|
||||
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${version}.tar.gz";
|
||||
sha256 = "1zdn1y0ij6amj7smmcslkqgbqv9yy5cwmbyzqc9v6drzdzllgbpj";
|
||||
};
|
||||
|
||||
patches = [
|
||||
./0001-disable-metis.patch
|
||||
./0002-set-install-dir.patch
|
||||
(substituteAll {
|
||||
src = ./0003-blas-lapack-flags.patch;
|
||||
blasFlags = "-lf77blas -latlas -lcblas -lgfortran";
|
||||
lapackFlags= "-llapack -latlas -lcblas";
|
||||
})
|
||||
];
|
||||
|
||||
preConfigure = ''
|
||||
substituteAllInPlace SuiteSparse_config/SuiteSparse_config.mk
|
||||
mkdir -p $out/lib
|
||||
mkdir -p $out/include
|
||||
|
||||
sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
|
||||
-e 's/METIS .*$/METIS =/' \
|
||||
-e 's/METIS_PATH .*$/METIS_PATH =/' \
|
||||
-e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
|
||||
-e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
|
||||
'';
|
||||
|
||||
makeFlags = [
|
||||
"PREFIX=\"$(out)\""
|
||||
"INSTALL_LIB=$(out)/lib"
|
||||
"INSTALL_INCLUDE=$(out)/include"
|
||||
"BLAS=-lopenblas"
|
||||
"LAPACK="
|
||||
];
|
||||
|
||||
NIX_CFLAGS = "-fPIC";
|
||||
|
||||
postInstall = ''
|
||||
# Build and install shared library
|
||||
(
|
||||
cd "$(mktemp -d)"
|
||||
for i in "$out"/lib/lib*.a; do
|
||||
ar -x $i
|
||||
done
|
||||
gcc *.o --shared -o "$out/lib/libsuitesparse.so"
|
||||
)
|
||||
for i in umfpack cholmod amd camd colamd spqr; do
|
||||
ln -s libsuitesparse.so "$out"/lib/lib$i.so;
|
||||
done
|
||||
|
||||
# Install documentation
|
||||
outdoc=$out/share/doc/${name}
|
||||
mkdir -p $outdoc
|
||||
@ -47,7 +66,7 @@ stdenv.mkDerivation {
|
||||
'';
|
||||
|
||||
nativeBuildInputs = [ gfortran ];
|
||||
buildInputs = [ atlasWithLapack ];
|
||||
buildInputs = [ openblas ];
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;
|
||||
|
||||
@ -1,18 +0,0 @@
|
||||
diff -Nrc SuiteSparse/UMFPACK/Demo/Makefile SuiteSparse-new/UMFPACK/Demo/Makefile
|
||||
*** SuiteSparse/UMFPACK/Demo/Makefile 2009-11-11 21:09:45.000000000 +0100
|
||||
--- SuiteSparse-new/UMFPACK/Demo/Makefile 2010-08-02 12:53:16.000000000 +0200
|
||||
***************
|
||||
*** 40,46 ****
|
||||
../../CAMD/Lib/libcamd.a:
|
||||
( cd ../../CAMD ; $(MAKE) library )
|
||||
|
||||
- $(METIS):
|
||||
- ( cd $(METIS_PATH) && $(MAKE) )
|
||||
|
||||
UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
|
||||
--- 40,44 ----
|
||||
../../CAMD/Lib/libcamd.a:
|
||||
( cd ../../CAMD ; $(MAKE) library )
|
||||
|
||||
|
||||
UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
|
||||
@ -11,9 +11,7 @@ stdenv.mkDerivation rec {
|
||||
sha256 = "1ryjlcnpfm7fpkq6444ybi576hbnh2l0w7kjhbqady5lxwjyg3pf";
|
||||
};
|
||||
|
||||
installPhase = ''
|
||||
make install prefix=$out
|
||||
'';
|
||||
makeFlags = [ "prefix=$(out)" ];
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "A clean C library for processing UTF-8 Unicode data";
|
||||
|
||||
@ -3,14 +3,14 @@
|
||||
python,
|
||||
# Name of package (e.g. numpy or scipy)
|
||||
pkgName,
|
||||
# Atlas math library
|
||||
atlas
|
||||
# OpenBLAS math library
|
||||
openblas
|
||||
}:
|
||||
|
||||
{
|
||||
# Re-export atlas here so that it can be sure that the same one will be used
|
||||
# Re-export openblas here so that it can be sure that the same one will be used
|
||||
# in the propagatedBuildInputs.
|
||||
inherit atlas;
|
||||
inherit openblas;
|
||||
|
||||
# First "install" the package, then import what was installed, and call the
|
||||
# .test() function, which will run the test suite.
|
||||
@ -48,9 +48,9 @@
|
||||
preBuild = ''
|
||||
echo "Creating site.cfg file..."
|
||||
cat << EOF > site.cfg
|
||||
[atlas]
|
||||
include_dirs = ${atlas}/include
|
||||
library_dirs = ${atlas}/lib
|
||||
[openblas]
|
||||
include_dirs = ${openblas}/include
|
||||
library_dirs = ${openblas}/lib
|
||||
EOF
|
||||
'';
|
||||
}
|
||||
|
||||
@ -997,7 +997,7 @@ let
|
||||
});
|
||||
|
||||
Mposterior = old.Mposterior.overrideDerivation (attrs: {
|
||||
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
||||
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
||||
});
|
||||
|
||||
qtbase = old.qtbase.overrideDerivation (attrs: {
|
||||
@ -1037,11 +1037,11 @@ let
|
||||
});
|
||||
|
||||
slfm = old.slfm.overrideDerivation (attrs: {
|
||||
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
||||
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
||||
});
|
||||
|
||||
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
||||
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
||||
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
||||
});
|
||||
|
||||
gputools = old.gputools.overrideDerivation (attrs: {
|
||||
@ -1087,6 +1087,7 @@ let
|
||||
|
||||
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
||||
patches = [ ./patches/BayesLogit.patch ];
|
||||
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
|
||||
});
|
||||
|
||||
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
||||
|
||||
@ -6,7 +6,7 @@ diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
|
||||
OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
|
||||
PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
|
||||
-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS)
|
||||
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -llapack -lf77blas -lcblas -latlas -lgfortran
|
||||
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -lopenblas
|
||||
# PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
|
||||
PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW
|
||||
|
||||
|
||||
@ -4022,18 +4022,11 @@ let
|
||||
jikes = callPackage ../development/compilers/jikes { };
|
||||
|
||||
julia02 = callPackage ../development/compilers/julia/0.2.nix {
|
||||
liblapack = liblapack.override {shared = true;};
|
||||
llvm = llvm_33;
|
||||
suitesparse = suitesparse_4_2;
|
||||
};
|
||||
|
||||
julia03 = let
|
||||
liblapack = liblapack_3_5_0.override {shared = true;};
|
||||
in callPackage ../development/compilers/julia/0.3.nix {
|
||||
inherit liblapack;
|
||||
suitesparse = suitesparse_4_2.override {
|
||||
inherit liblapack;
|
||||
};
|
||||
julia03 = callPackage ../development/compilers/julia/0.3.nix {
|
||||
llvm = llvm_33;
|
||||
};
|
||||
julia = julia03;
|
||||
@ -4859,6 +4852,7 @@ let
|
||||
glpk = null;
|
||||
suitesparse = null;
|
||||
jdk = null;
|
||||
openblas = openblasCompat;
|
||||
};
|
||||
octaveFull = (lowPrio (callPackage ../development/interpreters/octave {
|
||||
fltk = fltk13.override { cfg.xftSupport = true; };
|
||||
@ -8596,6 +8590,7 @@ let
|
||||
R = callPackage ../applications/science/math/R {
|
||||
inherit (xlibs) libX11 libXt;
|
||||
texLive = texLiveAggregationFun { paths = [ texLive texLiveExtra ]; };
|
||||
openblas = openblasCompat;
|
||||
withRecommendedPackages = false;
|
||||
};
|
||||
|
||||
@ -13935,9 +13930,11 @@ let
|
||||
|
||||
liblbfgs = callPackage ../development/libraries/science/math/liblbfgs { };
|
||||
|
||||
openblas = callPackage ../development/libraries/science/math/openblas {
|
||||
liblapack = liblapack_3_5_0;
|
||||
};
|
||||
openblas = callPackage ../development/libraries/science/math/openblas { };
|
||||
|
||||
# A version of OpenBLAS using 32-bit integers on all platforms for compatibility with
|
||||
# standard BLAS and LAPACK.
|
||||
openblasCompat = openblas.override { blas64 = false; };
|
||||
|
||||
mathematica = callPackage ../applications/science/math/mathematica { };
|
||||
mathematica9 = callPackage ../applications/science/math/mathematica/9.nix { };
|
||||
@ -13945,9 +13942,10 @@ let
|
||||
sage = callPackage ../applications/science/math/sage { };
|
||||
|
||||
suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { };
|
||||
suitesparse_4_4_1 = callPackage ../development/libraries/science/math/suitesparse {};
|
||||
suitesparse_4_4 = callPackage ../development/libraries/science/math/suitesparse {};
|
||||
suitesparse = suitesparse_4_4;
|
||||
|
||||
ipopt = callPackage ../development/libraries/science/math/ipopt { };
|
||||
ipopt = callPackage ../development/libraries/science/math/ipopt { openblas = openblasCompat; };
|
||||
|
||||
### SCIENCE/MOLECULAR-DYNAMICS
|
||||
|
||||
|
||||
@ -1068,7 +1068,12 @@ let
|
||||
sha256 = "f856ea2e9e2947abc1a6557625cc6b0e45228984f397a90c420b2f468dc4cb97";
|
||||
};
|
||||
doCheck = false;
|
||||
buildInputs = with pkgs; [ liblapack blas ];
|
||||
buildInputs = with pkgs; [ openblasCompat ];
|
||||
preConfigure = ''
|
||||
export CVXOPT_BLAS_LIB_DIR=${pkgs.openblasCompat}/lib
|
||||
export CVXOPT_BLAS_LIB=openblas
|
||||
export CVXOPT_LAPACK_LIB=openblas
|
||||
'';
|
||||
meta = {
|
||||
homepage = "http://cvxopt.org/";
|
||||
description = "Python Software for Convex Optimization";
|
||||
@ -7850,7 +7855,7 @@ let
|
||||
numpy = let
|
||||
support = import ../development/python-modules/numpy-scipy-support.nix {
|
||||
inherit python;
|
||||
atlas = pkgs.atlasWithLapack;
|
||||
openblas = pkgs.openblasCompat;
|
||||
pkgName = "numpy";
|
||||
};
|
||||
in buildPythonPackage ( rec {
|
||||
@ -7873,7 +7878,7 @@ let
|
||||
setupPyBuildFlags = ["--fcompiler='gnu95'"];
|
||||
|
||||
buildInputs = [ pkgs.gfortran self.nose ];
|
||||
propagatedBuildInputs = [ support.atlas ];
|
||||
propagatedBuildInputs = [ support.openblas ];
|
||||
|
||||
meta = {
|
||||
description = "Scientific tools for Python";
|
||||
@ -11322,7 +11327,7 @@ let
|
||||
scipy = let
|
||||
support = import ../development/python-modules/numpy-scipy-support.nix {
|
||||
inherit python;
|
||||
atlas = pkgs.atlasWithLapack;
|
||||
openblas = pkgs.openblasCompat;
|
||||
pkgName = "numpy";
|
||||
};
|
||||
in buildPythonPackage rec {
|
||||
@ -11360,15 +11365,14 @@ let
|
||||
};
|
||||
|
||||
buildInputs = with self; [ nose pillow pkgs.gfortran pkgs.glibcLocales ];
|
||||
propagatedBuildInputs = with self; [ numpy scipy pkgs.atlas ];
|
||||
propagatedBuildInputs = with self; [ numpy scipy pkgs.openblas ];
|
||||
|
||||
buildPhase = ''
|
||||
export ATLAS=${pkgs.atlas}
|
||||
${self.python.executable} setup.py build_ext -i --fcompiler='gnu95'
|
||||
'';
|
||||
|
||||
checkPhase = ''
|
||||
LC_ALL="en_US.UTF-8" HOME=$TMPDIR ATLAS="" nosetests
|
||||
LC_ALL="en_US.UTF-8" HOME=$TMPDIR OMP_NUM_THREADS=1 nosetests
|
||||
'';
|
||||
|
||||
meta = {
|
||||
|
||||
Loading…
Reference in New Issue
Block a user