Merge remote-tracking branch 'upstream/master' into staging

pkgs/development/libraries/science/benchmark/papi/default.nix

@@ -0,0 +1,30 @@
+{ stdenv
+, fetchurl
+}:
+
+stdenv.mkDerivation rec {
+  version = "5.6.0";
+  name = "papi-${version}";
+
+  src = fetchurl {
+    url = "https://bitbucket.org/icl/papi/get/papi-5-6-0-t.tar.gz";
+    sha256 = "13mngf9kl0y2wfxqvkad0smdaag7k8fvw82b4312gx62nwhc1i6r";
+  };
+
+  buildInputs = [ stdenv ];
+
+  preConfigure = ''
+    cd src
+  '';
+
+  doCheck = true;
+  checkTarget = "test";
+
+  meta = with stdenv.lib; {
+    homepage = https://icl.utk.edu/papi/;
+    description = "PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors";
+    license = licenses.bsdOriginal;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/libraries/science/math/atlas/default.nix

@@ -110,6 +110,7 @@ stdenv.mkDerivation {
     homepage = http://math-atlas.sourceforge.net/;
     description = "Automatically Tuned Linear Algebra Software (ATLAS)";
     license = stdenv.lib.licenses.bsd3;
+    broken = stdenv.isDarwin;  # test when updating to >=3.10.3
     platforms = stdenv.lib.platforms.unix;
 
     longDescription = ''

pkgs/development/libraries/science/math/parmetis/default.nix

@@ -0,0 +1,33 @@
+{ stdenv
+, fetchurl
+, cmake
+, mpi
+}:
+
+stdenv.mkDerivation rec {
+  name = "parmetis-${version}";
+  version = "4.0.3";
+
+  src = fetchurl {
+    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-${version}.tar.gz";
+    sha256 = "0pvfpvb36djvqlcc3lq7si0c5xpb2cqndjg8wvzg35ygnwqs5ngj";
+  };
+
+  buildInputs = [ cmake mpi ];
+
+  # metis and GKlib are packaged with distribution
+  # AUR https://aur.archlinux.org/packages/parmetis/ has reported that
+  # it easier to build with the included packages as opposed to using the metis
+  # package. Compilation time is short.
+  configurePhase = ''
+    make config metis_path=$PWD/metis gklib_path=$PWD/metis/GKlib prefix=$out
+  '';
+
+  meta = with stdenv.lib; {
+    description = "ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices";
+    homepage = http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview;
+    platforms = platforms.all;
+    license = licenses.unfree;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/libraries/science/math/scalapack/default.nix

@@ -0,0 +1,29 @@
+{ stdenv
+, fetchurl
+, gfortran
+, cmake
+, blas
+, liblapack
+, mpi
+}:
+
+stdenv.mkDerivation rec {
+  name = "scalapack-${version}";
+  version = "2.0.2";
+
+  src = fetchurl {
+    url = "http://www.netlib.org/scalapack/scalapack-${version}.tgz";
+    sha256 = "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c";
+  };
+
+  buildInputs = [ cmake mpi liblapack blas gfortran ];
+
+  meta = with stdenv.lib; {
+    homepage = http://www.netlib.org/scalapack/;
+    description = "Library of high-performance linear algebra routines for parallel distributed memory machines";
+    license = licenses.bsdOriginal;
+    platforms = platforms.all;
+    maintainers = [ maintainers.costrouc ];
+  };
+
+}

pkgs/development/libraries/science/math/scs/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, blas, liblapack, gfortran }:
+{ stdenv, fetchFromGitHub, blas, liblapack, gfortran, fixDarwinDylibNames }:
 
 stdenv.mkDerivation rec {
   name = "scs-${version}";
@@ -11,24 +11,30 @@ stdenv.mkDerivation rec {
     sha256 = "17lbcmcsniqlyzgbzmjipfd0rrk25a8hzh7l5wl2wp1iwsd8c3a9";
   };
 
-  buildInputs = [ blas liblapack gfortran.cc.lib ];
-
   # Actually link and add libgfortran to the rpath
-  patchPhase = ''
-    sed -i 's/#-lgfortran/-lgfortran/' scs.mk
+  postPatch = ''
+    substituteInPlace scs.mk \
+      --replace "#-lgfortran" "-lgfortran" \
+      --replace "gcc" "cc"
   '';
 
+  nativeBuildInputs = stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
+
+  buildInputs = [ blas liblapack gfortran.cc.lib ];
+
   doCheck = true;
 
-  # Test demo requires passing any int as $1; 42 chosen arbitrarily
-  checkPhase = ''
-    ./out/demo_socp_indirect 42
+  # Test demo requires passing data and seed; numbers chosen arbitrarily.
+  postCheck = ''
+    ./out/demo_socp_indirect 42 0.42 0.42 42
   '';
 
   installPhase = ''
+    runHook preInstall
     mkdir -p $out/lib
     cp -r include $out/
-    cp out/*.a out/*.so $out/lib/
+    cp out/*.a out/*.so out/*.dylib $out/lib/
+    runHook postInstall
   '';
 
   meta = with stdenv.lib; {