Merge pull request #82274 from jtojnar/suitesparese-5.6

suitesparse: 5.4.0 → 5.7.1 + clean up
2024-11-29 17:10:48 +00:00 · 2020-03-22 06:58:25 +01:00 · 2020-03-22 06:58:25 +01:00 · d951c534da
parent 81d84153c7 b552b84ae2
commit d951c534da
5 changed files with 119 additions and 102 deletions
--- a/pkgs/development/libraries/science/math/mongoose/default.nix
+++ b/pkgs/development/libraries/science/math/mongoose/default.nix
@ -0,0 +1,30 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+}:
+
+stdenv.mkDerivation rec {
+  pname = "mongoose";
+  version = "2.0.4";
+
+  outputs = [ "bin" "out" "dev" ];
+
+  src = fetchFromGitHub {
+    owner = "ScottKolo";
+    repo = "Mongoose";
+    rev = "v${version}";
+    sha256 = "0ymwd4n8p8s0ndh1vcbmjcsm0x2cc2b7v3baww5y6as12873bcrh";
+  };
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Graph Coarsening and Partitioning Library";
+    homepage = "https://github.com/ScottKolo/Mongoose";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [];
+    platforms = with platforms; unix;
+  };
+}
--- a/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
+++ b/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
@ -0,0 +1,32 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+, gnum4
+}:
+
+stdenv.mkDerivation rec {
+  pname = "suitesparse-graphblas";
+  version = "3.2.1";
+
+  outputs = [ "out" "dev" ];
+
+  src = fetchFromGitHub {
+    owner = "DrTimothyAldenDavis";
+    repo = "GraphBLAS";
+    rev = "v${version}";
+    sha256 = "AAwwzrpKFHy40Ldm6hTO6L0FWPYwi3kJj3zrshFwYas=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    gnum4
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Graph algorithms in the language of linear algebra";
+    homepage = "http://faculty.cse.tamu.edu/davis/GraphBLAS.html";
+    license = licenses.asl20;
+    maintainers = with maintainers; [];
+    platforms = with platforms; unix;
+  };
+}
--- a/pkgs/development/libraries/science/math/suitesparse/default.nix
+++ b/pkgs/development/libraries/science/math/suitesparse/default.nix
@ -1,96 +1,65 @@
-{ stdenv, fetchurl, gfortran, openblas, cmake, fixDarwinDylibNames
+{ stdenv
+, fetchFromGitHub
+, gfortran
+, openblas
+, metis
+, fixDarwinDylibNames
 , gnum4
-, enableCuda  ? false, cudatoolkit
+, enableCuda ? false
+, cudatoolkit
 }:

-let
-  version = "5.4.0";
-  name = "suitesparse-${version}";
-
-  SHLIB_EXT = stdenv.hostPlatform.extensions.sharedLibrary;
-in
 stdenv.mkDerivation rec {
-  inherit name;
+  pname = "suitesparse";
+  version = "5.7.1";

-  src = fetchurl {
-    url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${version}.tar.gz";
-    sha256 = "1lfvjj787yqyhk25w7brlrkrl7dnnn5dq4ijxws3wrbcd4vd2k9p";
+  outputs = [ "out" "dev" "doc" ];
+
+  src = fetchFromGitHub {
+    owner = "DrTimothyAldenDavis";
+    repo = "SuiteSparse";
+    rev = "v${version}";
+    sha256 = "SA9SQKRDKUI1GilNMuCXljcvovLUwRKBUi/tiQ4dl5w=";
  };

-  dontUseCmakeConfigure = true;
+  nativeBuildInputs = [
+    gnum4
+  ] ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
+
+  buildInputs = [
+    openblas
+    metis
+    gfortran.cc.lib
+  ] ++ stdenv.lib.optional enableCuda cudatoolkit;

  preConfigure = ''
-    mkdir -p $out/lib
-    mkdir -p $out/include
-    mkdir -p $out/share/doc/${name}
-
-    sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
-        -e 's/METIS .*$/METIS =/' \
-        -e 's/METIS_PATH .*$/METIS_PATH =/' \
-        -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION/'
-  ''
-  + stdenv.lib.optionalString stdenv.isDarwin ''
-    sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
-        -e 's/^[[:space:]]*\(LIB = -lm\) -lrt/\1/'
-  ''
-  + stdenv.lib.optionalString enableCuda ''
-    sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
-        -e 's|^[[:space:]]*\(CUDA_ROOT     =\)|CUDA_ROOT = ${cudatoolkit}|' \
-        -e 's|^[[:space:]]*\(GPU_BLAS_PATH =\)|GPU_BLAS_PATH = $(CUDA_ROOT)|' \
-        -e 's|^[[:space:]]*\(GPU_CONFIG    =\)|GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS -DCHOLMOD_OMP_NUM_THREADS=$(NIX_BUILD_CORES) |' \
-        -e 's|^[[:space:]]*\(CUDA_PATH     =\)|CUDA_PATH = $(CUDA_ROOT)|' \
-        -e 's|^[[:space:]]*\(CUDART_LIB    =\)|CUDART_LIB = $(CUDA_ROOT)/lib64/libcudart.so|' \
-        -e 's|^[[:space:]]*\(CUBLAS_LIB    =\)|CUBLAS_LIB = $(CUDA_ROOT)/lib64/libcublas.so|' \
-        -e 's|^[[:space:]]*\(CUDA_INC_PATH =\)|CUDA_INC_PATH = $(CUDA_ROOT)/include/|' \
-        -e 's|^[[:space:]]*\(NV20          =\)|NV20 = -arch=sm_20 -Xcompiler -fPIC|' \
-        -e 's|^[[:space:]]*\(NV30          =\)|NV30 = -arch=sm_30 -Xcompiler -fPIC|' \
-        -e 's|^[[:space:]]*\(NV35          =\)|NV35 = -arch=sm_35 -Xcompiler -fPIC|' \
-        -e 's|^[[:space:]]*\(NVCC          =\) echo|NVCC = $(CUDA_ROOT)/bin/nvcc|' \
-        -e 's|^[[:space:]]*\(NVCCFLAGS     =\)|NVCCFLAGS = $(NV20) -O3 -gencode=arch=compute_20,code=sm_20 -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_35,code=sm_35 -gencode=arch=compute_60,code=sm_60|'
+    # Mongoose and GraphBLAS are packaged separately
+    sed -i "Makefile" -e '/GraphBLAS\|Mongoose/d'
  '';

-  NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin " -DNTIMER";
+  makeFlags = [
+    "INSTALL=${placeholder "out"}"
+    "INSTALL_INCLUDE=${placeholder "dev"}/include"
+    "JOBS=$(NIX_BUILD_CORES)"
+    "BLAS=-lopenblas"
+    "MY_METIS_LIB=-lmetis"
+    "LAPACK="
+  ] ++ stdenv.lib.optionals openblas.blas64 [
+    "CFLAGS=-DBLAS64"
+  ] ++ stdenv.lib.optionals enableCuda [
+    "CUDA_PATH=${cudatoolkit}"
+    "CUDART_LIB=${cudatoolkit.lib}/lib/libcudart.so"
+    "CUBLAS_LIB=${cudatoolkit}/lib/libcublas.so"
+  ];

-  buildPhase = ''
-    runHook preBuild
+  buildFlags = [
+    # Build individual shared libraries, not demos
+    "library"
+  ];

-    # Build individual shared libraries
-    make library        \
-        JOBS=$NIX_BUILD_CORES \
-        BLAS=-lopenblas \
-        LAPACK=""       \
-        ${stdenv.lib.optionalString openblas.blas64 "CFLAGS=-DBLAS64"}
-
-    # Build libsuitesparse.so which bundles all the individual libraries.
-    # Bundling is done by building the static libraries, extracting objects from
-    # them and combining the objects into one shared library.
-    mkdir -p static
-    make static JOBS=$NIX_BUILD_CORES AR_TARGET=$(pwd)/static/'$(LIBRARY).a'
-    (
-        cd static
-        for i in lib*.a; do
-          ar -x $i
-        done
-    )
-    ${if enableCuda then "${cudatoolkit}/bin/nvcc" else "${stdenv.cc.outPath}/bin/cc"} \
-        static/*.o                                                                     \
-        ${if stdenv.isDarwin then "-dynamiclib" else "--shared"}                       \
-        -o "lib/libsuitesparse${SHLIB_EXT}"                                            \
-        -lopenblas                                                                     \
-        ${stdenv.lib.optionalString enableCuda "-lcublas"}
-
-    runHook postBuild
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out
-    cp -r lib $out/
-    cp -r include $out/
-    cp -r share $out/
-    ''
-    + stdenv.lib.optionalString stdenv.isDarwin ''
+  # Likely fixed after 5.7.1
+  # https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/f6daae26ee391e475e2295e77c839aa7c1a8b784
+  postInstall = stdenv.lib.optionalString stdenv.isDarwin ''
    # The fixDarwinDylibNames in nixpkgs can't seem to fix all the libraries.
    # We manually fix them up here.
    fixDarwinDylibNames() {
@ -109,28 +78,10 @@ stdenv.mkDerivation rec {
    }

    fixDarwinDylibNames $(find "$out" -name "*.dylib")
-    ''
-    + stdenv.lib.optionalString (!stdenv.isDarwin) ''
-    # Fix rpaths
-    cd $out
-    find -name \*.so\* -type f -exec \
-      patchelf --set-rpath "$out/lib:${stdenv.lib.makeLibraryPath buildInputs}" {} \;
-    ''
-    +
-    ''
-    runHook postInstall
  '';

-  nativeBuildInputs = [
-    cmake
-    gnum4
-  ] ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
-
-  buildInputs = [ openblas gfortran.cc.lib ]
-    ++ stdenv.lib.optional enableCuda cudatoolkit;
-
  meta = with stdenv.lib; {
-    homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;
+    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 ];
--- a/pkgs/development/python-modules/cvxopt/default.nix
+++ b/pkgs/development/python-modules/cvxopt/default.nix
@ -31,8 +31,8 @@ buildPythonPackage rec {
    export CVXOPT_BLAS_LIB_DIR=${openblasCompat}/lib
    export CVXOPT_BLAS_LIB=openblas
    export CVXOPT_LAPACK_LIB=openblas
-    export CVXOPT_SUITESPARSE_LIB_DIR=${suitesparse}/lib
-    export CVXOPT_SUITESPARSE_INC_DIR=${suitesparse}/include
+    export CVXOPT_SUITESPARSE_LIB_DIR=${lib.getLib suitesparse}/lib
+    export CVXOPT_SUITESPARSE_INC_DIR=${lib.getDev suitesparse}/include
  '' + lib.optionalString withGsl ''
    export CVXOPT_BUILD_GSL=1
    export CVXOPT_GSL_LIB_DIR=${gsl}/lib
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -24404,6 +24404,8 @@ in
  suitesparse_5_3 = callPackage ../development/libraries/science/math/suitesparse {};
  suitesparse = suitesparse_5_3;

+  suitesparse-graphblas = callPackage ../development/libraries/science/math/suitesparse-graphblas {};
+
  superlu = callPackage ../development/libraries/science/math/superlu {};

  symmetrica = callPackage ../applications/science/math/symmetrica {};
@ -25253,6 +25255,8 @@ in

  mongoc = callPackage ../development/libraries/mongoc { };

+  mongoose = callPackage ../development/libraries/science/math/mongoose {};
+
  morph = callPackage ../tools/package-management/morph { };

  mupen64plus = callPackage ../misc/emulators/mupen64plus { };