diff --git a/pkgs/development/compilers/julia/default.nix b/pkgs/development/compilers/julia/default.nix index a594e0e68158..d0231adb73d1 100644 --- a/pkgs/development/compilers/julia/default.nix +++ b/pkgs/development/compilers/julia/default.nix @@ -1,35 +1,46 @@ -{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, blas, liblapack +{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre , readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl - , ncurses, libunistring, lighttpd, patchelf + , ncurses, libunistring, lighttpd, patchelf, openblas, liblapack } : let - liblapackShared = liblapack.override{shared=true;}; realGcc = stdenv.gcc.gcc; in stdenv.mkDerivation rec { pname = "julia"; - date = "20120501"; + date = "20120801"; name = "${pname}-git-${date}"; - grisu_ver = "1.1"; + grisu_ver = "1.1.1"; dsfmt_ver = "2.1"; - arpack_ver = "3.1.0"; + openblas_ver = "v0.2.2"; + lapack_ver = "3.4.1"; + arpack_ver = "3.1.1"; clp_ver = "1.14.5"; lighttpd_ver = "1.4.29"; grisu_src = fetchurl { url = "http://double-conversion.googlecode.com/files/double-conversion-${grisu_ver}.tar.gz"; - sha256 = "addee31d11350e4dde2b19c749eda648cb0ab38a68b0dd0d0a45dc49c7346fe7"; + sha256 = "e1cabb73fd69e74f145aea91100cde483aef8b79dc730fcda0a34466730d4d1d"; }; dsfmt_src = fetchurl { url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmt_ver}.tar.gz"; name = "dsfmt-${dsfmt_ver}.tar.gz"; sha256 = "e9d3e04bc984ec3b14033342f5ebdcd5202d8d8e40128dd737f566945612378f"; }; + openblas_src = fetchurl { + url = "https://github.com/xianyi/OpenBLAS/tarball/${openblas_ver}"; + name = "openblas-${openblas_ver}.tar.gz"; + sha256 = "19ffec70f9678f5c159feadc036ca47720681b782910fbaa95aa3867e7e86d8e"; + }; arpack_src = fetchurl { - url = "http://forge.scilab.org/index.php/p/arpack-ng/downloads/376/get/"; + url = "http://forge.scilab.org/index.php/p/arpack-ng/downloads/417/get/"; name = "arpack-ng_${arpack_ver}.tar.gz"; - sha256 = "65b7856126f06ecbf9ec450d50df92ca9260d4b0d21baf02497554ac230d6feb"; + sha256 = "be250947a7d6eac7dff8c058102fce9922c524aa06be2a090b6e0bb2d1e228cd"; + }; + lapack_src = fetchurl { + url = "http://www.netlib.org/lapack/lapack-${lapack_ver}.tgz"; + name = "lapack-${lapack_ver}.tgz"; + sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f"; }; clp_src = fetchurl { url = "http://www.coin-or.org/download/source/Clp/Clp-${clp_ver}.tgz"; @@ -43,16 +54,17 @@ stdenv.mkDerivation rec { src = fetchgit { url = "git://github.com/JuliaLang/julia.git"; - rev = "990ffabb00f0e51d326911888facdbc473fb634d"; - sha256 = "dfcf41b2d7b62dd490bfd6f6fb962713c920de3f00afaee47423bd26eba7e3b2"; + rev = "3b413ec24957e400c984002f7cdf6232f5391a7e"; + sha256 = "c019b724df9203899a1da5815f85d79291778191bbffc1361d2213ff7d2bbc1d"; }; - buildInputs = [ gfortran perl m4 gmp pcre llvm blas liblapackShared readline + buildInputs = [ gfortran perl m4 gmp pcre llvm readline fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf + openblas liblapack ]; configurePhase = '' - for i in GMP LLVM PCRE BLAS LAPACK READLINE FFTW LIBUNWIND SUITESPARSE GLPK; + for i in GMP LLVM PCRE LAPACK OPENBLAS BLAS READLINE FFTW LIBUNWIND SUITESPARSE GLPK LIGHTTPD; do sed -e "s@USE_SYSTEM_$i=0@USE_SYSTEM_$i=1@" -i Make.inc; done @@ -62,52 +74,44 @@ stdenv.mkDerivation rec { cp "$1" "$2/$(basename "$1" | sed -e 's/^[a-z0-9]*-//')" } - for i in "${grisu_src}" "${dsfmt_src}" "${arpack_src}" "${clp_src}" "${lighttpd_src}" ; do + for i in "${grisu_src}" "${dsfmt_src}" "${arpack_src}" "${clp_src}" ; do copy_kill_hash "$i" deps done copy_kill_hash "${dsfmt_src}" deps/random - sed -e '/cd SuiteSparse-SYSTEM/,+1s@find /lib /usr/lib /usr/local/lib@find ${suitesparse}/lib@' -i deps/Makefile - ${if realGcc ==null then "" else ''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -llapack -lm -lfftw3f -lfftw3 -lglpk -lunistring "''} sed -e 's@ cpp @ gcc -E @g' -i base/Makefile - sed -e '1s@#! */bin/bash@#!${stdenv.shell}@' -i deps/*.sh - export LDFLAGS="-L${suitesparse}/lib" + 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 - sed -e '/libumfpack.a/s@find @find ${suitesparse}/lib @' -i deps/Makefile - - export makeFlags="$makeFlags PREFIX=\"$out\" USR=\"$out\"" - - sed -e 's@openblas@blas@' -i base/*.jl - - sed -e '/install -v julia-release-webserver/d' -i Makefile + export makeFlags="$makeFlags PREFIX=$out" export dontPatchELF=1 ''; + preBuild = '' + make -C test/unicode all + make -C extras glpk_h.jl GLPK_PREFIX="$GLPK_PREFIX" + ''; + postInstall = '' - ln -s "$out/share/julia/julia" "$out/bin" + ld -E --whole-archive --shared ${suitesparse}/lib/lib*[a-z].a -o "$out"/lib/libsuitesparse-shared.so + for i in umfpack cholmod amd camd colamd ; do + ln -s "libsuitesparse-shared.so" "$out/lib/lib$i.so" + done + ln -s "${lighttpd}/sbin/lighttpd" "$out/sbin/" + ln -s "${lighttpd}/lib/"* "$out/lib/" - mkdir -p "$out/share/julia/ui/" - cp -r ui/website "$out/share/julia/ui/" - cp deps/lighttpd.conf "$out/share/julia/ui/" - - mkdir -p "$out/share/julia/ui/webserver/" - cp -r ui/webserver/{*.jl,*.h} "$out/share/julia/ui/webserver/" - - echo -e '#!/bin/sh' >> "$out/bin/julia-webserver" - echo -e "cd \"$out/share/julia\"" >> "$out/bin/julia-webserver" - echo -e '${lighttpd}/sbin/lighttpd -D -f ./ui/lighttpd.conf &' >> "$out/bin/julia-webserver" - echo -e "'$out/bin/julia-release-webserver' -p 2001" >> "$out/bin/julia-webserver" - chmod a+x "$out/bin/julia-webserver" + cp -r test examples "$out/lib/julia" + ls -R > "$out/ls-R" ''; meta = { diff --git a/pkgs/development/libraries/fftw/default.nix b/pkgs/development/libraries/fftw/default.nix index 845ec7720106..6b4fbe7df6ce 100644 --- a/pkgs/development/libraries/fftw/default.nix +++ b/pkgs/development/libraries/fftw/default.nix @@ -1,15 +1,19 @@ -{fetchurl, stdenv, builderDefs, stringsWithDeps, singlePrecision ? false}: -let localDefs = builderDefs.passthru.function { +{fetchurl, stdenv, builderDefs, stringsWithDeps, singlePrecision ? false, pthreads ? false}: +let + version = "3.3.2"; + localDefs = builderDefs.passthru.function { src = fetchurl { - url = ftp://ftp.fftw.org/pub/fftw/fftw-3.2.2.tar.gz; - sha256 = "13vnglardq413q2518zi4a8pam3znydrz28m9w09kss9xrjsx9va"; + url = "ftp://ftp.fftw.org/pub/fftw/fftw-${version}.tar.gz"; + sha256 = "b1236a780ca6e66fc5f8eda6ef0665d680e8253d9f01d7bf211b714a50032d01"; }; buildInputs = []; - configureFlags = ["--enable-shared" "--enable-openmp"] + configureFlags = ["--enable-shared"] # some distros seem to be shipping both versions within the same package? # why does --enable-float still result in ..3f.so instead of ..3.so? ++ (if singlePrecision then [ "--enable-single" ] else [ ]) + ++ (stdenv.lib.optional (!pthreads) "--enable-openmp") + ++ (stdenv.lib.optional pthreads "--enable-threads") # I think all i686 has sse ++ (if (stdenv.isi686 || stdenv.isx86_64) && singlePrecision then [ "--enable-sse" ] else [ ]) # I think all x86_64 has sse2 @@ -18,8 +22,8 @@ let localDefs = builderDefs.passthru.function { }; in with localDefs; stdenv.mkDerivation { - name = "fftw-3.2.2" + ( if singlePrecision then "-single" else "-double" ); - builder = writeScript "fftw-3.2.1-builder" + name = "fftw-3.3.2" + ( if singlePrecision then "-single" else "-double" ); + builder = writeScript "fftw-3.3.2-builder" (textClosure localDefs [doConfigure doMakeInstall doForceShare]); meta = { description = "Fastest Fourier Transform in the West library"; diff --git a/pkgs/development/libraries/pcre/8.30.nix b/pkgs/development/libraries/pcre/8.30.nix new file mode 100644 index 000000000000..2f636492eb61 --- /dev/null +++ b/pkgs/development/libraries/pcre/8.30.nix @@ -0,0 +1,38 @@ +{ stdenv, fetchurl, unicodeSupport ? true, cplusplusSupport ? true }: + +stdenv.mkDerivation rec { + name = "pcre-8.30"; + + src = fetchurl { + url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/${name}.tar.bz2"; + sha256 = "c1113fd7db934e97ad8b3917d432e5b642e9eb9afd127eb797804937c965f4ac"; + }; + + # The compiler on Darwin crashes with an internal error while building the + # C++ interface. Disabling optimizations on that platform remedies the + # problem. In case we ever update the Darwin GCC version, the exception for + # that platform ought to be removed. + configureFlags = '' + ${if unicodeSupport then "--enable-unicode-properties" else ""} + ${if !cplusplusSupport then "--disable-cpp" else ""} + '' + stdenv.lib.optionalString stdenv.isDarwin "CXXFLAGS=-O0"; + + doCheck = !stdenv.isCygwin; # XXX: test failure on Cygwin + + meta = { + homepage = "http://www.pcre.org/"; + description = "A library for Perl Compatible Regular Expressions"; + license = "BSD-3"; + + longDescription = '' + The PCRE library is a set of functions that implement regular + expression pattern matching using the same syntax and semantics as + Perl 5. PCRE has its own native API, as well as a set of wrapper + functions that correspond to the POSIX regular expression API. The + PCRE library is free, even for building proprietary software. + ''; + + platforms = stdenv.lib.platforms.all; + maintainers = [ stdenv.lib.maintainers.simons ]; + }; +} diff --git a/pkgs/development/libraries/science/math/liblapack/default.nix b/pkgs/development/libraries/science/math/liblapack/default.nix index e2b43b6b0531..9f25011b76f8 100644 --- a/pkgs/development/libraries/science/math/liblapack/default.nix +++ b/pkgs/development/libraries/science/math/liblapack/default.nix @@ -4,10 +4,10 @@ let usedLibExtension = if shared then ".so" else ".a"; in stdenv.mkDerivation { - name = "liblapack-3.4.0"; + name = "liblapack-3.4.1"; src = fetchurl { - url = "http://www.netlib.org/lapack/lapack-3.4.0.tgz"; - sha256 = "1sf30v1ps5icg67dvw5sbx5yhypx13am470gqg2f7l04f3wrw4x7"; + url = "http://www.netlib.org/lapack/lapack-3.4.1.tgz"; + sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f"; }; propagatedBuildInputs = [ atlasMaybeShared ]; diff --git a/pkgs/development/libraries/science/math/openblas/default.nix b/pkgs/development/libraries/science/math/openblas/default.nix new file mode 100644 index 000000000000..4d30671c4880 --- /dev/null +++ b/pkgs/development/libraries/science/math/openblas/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchurl, gfortran, perl }: + +stdenv.mkDerivation rec { + version = "0.2.2"; + lapack_version = "3.4.1"; + lapack_src = fetchurl { + url = "http://www.netlib.org/lapack/lapack-${lapack_version}.tgz"; + sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f"; + }; + + name = "openblas-${version}"; + src = fetchurl { + url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}"; + sha256 = "13kdx3knff5ajnmgn419g0dnh83plin07p7akwamr3v7z5qfrzqr"; + name = "openblas-${version}.tar.gz"; + }; + + preBuild = "cp ${lapack_src} lapack-${lapack_version}.tgz"; + + buildInputs = [gfortran perl]; + + cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system); + + target = if cpu == "i686" then "P6" else + if cpu == "x86_64" then "CORE2" else + # allow autodetect + ""; + + makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\""; + + meta = { + description = "Basic Linear Algebra Subprograms"; + license = stdenv.lib.licenses.bsd3; + homepage = "https://github.com/xianyi/OpenBLAS"; + }; +} diff --git a/pkgs/development/libraries/suitesparse/default.nix b/pkgs/development/libraries/suitesparse/default.nix index b3fe6db059ac..e3a7fbb5a086 100644 --- a/pkgs/development/libraries/suitesparse/default.nix +++ b/pkgs/development/libraries/suitesparse/default.nix @@ -1,9 +1,10 @@ { stdenv, fetchurl, blas, liblapack, gfortran } : -stdenv.mkDerivation { - name = "suitesparse"; +stdenv.mkDerivation rec { + version = "4.0.0"; + name = "suitesparse-${version}"; src = fetchurl { - url = http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-3.5.0.tar.gz ; - sha256 = "0npn7c1j5qag5m2r0cmh3bwc42c1jk8k2yg2cfyxlcrp0h7wn4rc"; + url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ; + sha256 = "1nvbdw10wa6654k8sa2vhr607q6fflcywyji5xd767cqpwag4v5j"; }; buildInputs = [blas liblapack gfortran] ; patches = [./disable-metis.patch]; @@ -14,6 +15,8 @@ stdenv.mkDerivation { mkdir -p $out/include ''; + makeFlags = ''PREFIX=\"$(out)\" INSTALL_LIB=$(out)/lib INSTALL_INCLUDE=$(out)/include''; + NIX_CFLAGS = "-fPIC"; } diff --git a/pkgs/development/libraries/suitesparse/disable-metis.patch b/pkgs/development/libraries/suitesparse/disable-metis.patch index 68fd22bc6433..5b735eb7d3c9 100644 --- a/pkgs/development/libraries/suitesparse/disable-metis.patch +++ b/pkgs/development/libraries/suitesparse/disable-metis.patch @@ -1,140 +1,18 @@ -diff -Nrc SuiteSparse/UFconfig/Makefile SuiteSparse-new/UFconfig/Makefile -*** SuiteSparse/UFconfig/Makefile 2009-11-11 20:59:08.000000000 +0100 ---- SuiteSparse-new/UFconfig/Makefile 2010-08-02 13:14:04.000000000 +0200 -*************** -*** 25,31 **** - - # install UFconfig - install: -! $(CP) Lib/libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a - ( cd $(INSTALL_LIB) ; ln -s libufconfig.$(VERSION).a libufconfig.a ) - $(CP) UFconfig.h $(INSTALL_INCLUDE) - ---- 25,31 ---- - - # install UFconfig - install: -! $(CP) libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a - ( cd $(INSTALL_LIB) ; ln -s libufconfig.$(VERSION).a libufconfig.a ) - $(CP) UFconfig.h $(INSTALL_INCLUDE) - -diff -Nrc SuiteSparse/UFconfig/UFconfig.mk SuiteSparse-new/UFconfig/UFconfig.mk -*** SuiteSparse/UFconfig/UFconfig.mk 2010-06-02 17:40:42.000000000 +0200 ---- SuiteSparse-new/UFconfig/UFconfig.mk 2010-08-02 14:55:27.000000000 +0200 -*************** -*** 34,40 **** - # performance. You should select the optimization parameters that are best - # for your system. On Linux, use "CFLAGS = -O3 -fexceptions" for example. - CC = cc -! CFLAGS = -O3 -fexceptions - - # C++ compiler (also uses CFLAGS) - CPLUSPLUS = g++ ---- 34,40 ---- - # performance. You should select the optimization parameters that are best - # for your system. On Linux, use "CFLAGS = -O3 -fexceptions" for example. - CC = cc -! CFLAGS = -O3 -fexceptions -fPIC - - # C++ compiler (also uses CFLAGS) - CPLUSPLUS = g++ -*************** -*** 71,78 **** - # MAKE = gmake - - # For "make install" -! INSTALL_LIB = /usr/local/lib -! INSTALL_INCLUDE = /usr/local/include - - #------------------------------------------------------------------------------ - # BLAS and LAPACK configuration: ---- 71,78 ---- - # MAKE = gmake - - # For "make install" -! INSTALL_LIB = $(out)/lib -! INSTALL_INCLUDE = $(out)/include - - #------------------------------------------------------------------------------ - # BLAS and LAPACK configuration: -*************** -*** 127,134 **** - # 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 - - # If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following - # options: ---- 127,134 ---- - # 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 = - - # If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following - # options: -*************** -*** 189,195 **** - # -DNSUNPERF for Solaris only. If defined, do not use the Sun - # Performance Library - -! CHOLMOD_CONFIG = - - #------------------------------------------------------------------------------ - # SuiteSparseQR configuration: ---- 189,195 ---- - # -DNSUNPERF for Solaris only. If defined, do not use the Sun - # Performance Library - -! CHOLMOD_CONFIG = -DNPARTITION - - #------------------------------------------------------------------------------ - # SuiteSparseQR configuration: -*************** -*** 203,209 **** - # -DHAVE_TBB enable the use of Intel's Threading Building Blocks (TBB) - - # default, without timing, without TBB: -! SPQR_CONFIG = - # with timing and TBB: - # SPQR_CONFIG = -DTIMING -DHAVE_TBB - # with timing ---- 203,209 ---- - # -DHAVE_TBB enable the use of Intel's Threading Building Blocks (TBB) - - # default, without timing, without TBB: -! SPQR_CONFIG = -DNPARTITION - # with timing and TBB: - # SPQR_CONFIG = -DTIMING -DHAVE_TBB - # with timing 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 *************** -*** 40,51 **** +*** 40,46 **** ../../CAMD/Lib/libcamd.a: ( cd ../../CAMD ; $(MAKE) library ) -- ../../metis-4.0/libmetis.a: -- ( cd ../../metis-4.0/Lib ; $(MAKE) ) +- $(METIS): +- ( cd $(METIS_PATH) && $(MAKE) ) UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \ - ../../CHOLMOD/Lib/libcholmod.a ../../COLAMD/Lib/libcolamd.a \ -! ../../CAMD/Lib/libcamd.a ../../metis-4.0/libmetis.a \ - ../../CCOLAMD/Lib/libccolamd.a - - libs: $(UMFPACK) ---- 40,49 ---- +--- 40,44 ---- ../../CAMD/Lib/libcamd.a: ( cd ../../CAMD ; $(MAKE) library ) UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \ - ../../CHOLMOD/Lib/libcholmod.a ../../COLAMD/Lib/libcolamd.a \ -! ../../CAMD/Lib/libcamd.a \ - ../../CCOLAMD/Lib/libccolamd.a - - libs: $(UMFPACK) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index b78c3a237ff3..438db4c127db 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -2365,7 +2365,13 @@ let jikes = callPackage ../development/compilers/jikes { }; - julia = callPackage ../development/compilers/julia { }; + julia = callPackage ../development/compilers/julia { + llvm = llvm_3_1; + pcre = pcre_8_30; + liblapack = liblapack.override {shared = true;}; + fftw = fftw.override {pthreads = true;}; + fftwSinglePrec = fftwSinglePrec.override {pthreads = true;}; + }; lazarus = builderDefsPackage (import ../development/compilers/fpc/lazarus.nix) { inherit makeWrapper gtk glib pango atk gdk_pixbuf; @@ -4552,6 +4558,11 @@ let cplusplusSupport = !stdenv ? isDietLibC; }; + pcre_8_30 = callPackage ../development/libraries/pcre/8.30.nix { + unicodeSupport = getConfig ["pcre" "unicode"] true; + cplusplusSupport = !stdenv ? isDietLibC; + }; + pdf2xml = callPackage ../development/libraries/pdf2xml {} ; phonon = callPackage ../development/libraries/phonon { }; @@ -8367,6 +8378,7 @@ let liblapack = callPackage ../development/libraries/science/math/liblapack { }; + openblas = callPackage ../development/libraries/science/math/openblas { }; ### SCIENCE/LOGIC