Merge branch 'master' into staging-next

Hydra: ?compare=1473892

15 files changed, 371 insertions, 94 deletions

diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix
index 7ede379fb499..ee19077065e0 100644
--- a/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/pkgs/applications/science/astronomy/gildas/default.nix
@@ -7,13 +7,13 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "jul18a";
-  version = "20180701_a";
+  srcVersion = "aug18a";
+  version = "20180801_a";
   name = "gildas-${version}";
 
   src = fetchurl {
-    url = "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz";
-    sha256 = "0kl3zf6b1kv8hgsfrarsnm2gnrdax3vi8f856249y4nxsa7lbv2i";
+    url = "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz";
+    sha256 = "0mg3wijrj8x1p912vkgrhxbypjx7aj9b1492yxvq2y3fxban6bj1";
   };
 
   enableParallelBuilding = true;
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ];
 
-  patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ./mod.patch ./aarch64.patch ];
+  patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ./aarch64.patch ];
 
   configurePhase=''
     substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out
diff --git a/pkgs/applications/science/astronomy/gildas/mod.patch b/pkgs/applications/science/astronomy/gildas/mod.patch
deleted file mode 100644
index c917b4674f13..000000000000
--- a/pkgs/applications/science/astronomy/gildas/mod.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff -ruN gildas-src-jul18a/admin/Makefile.build gildas-src-jul18a.mod/admin/Makefile.build
---- gildas-src-jul18a/admin/Makefile.build	2018-06-14 14:36:54.000000000 +0200
-+++ gildas-src-jul18a.mod/admin/Makefile.build	2018-07-06 13:31:46.000000000 +0200
-@@ -291,6 +291,13 @@
- 	win-$(LIB_IDENTITY)-und.def -o $@ $(FLDLIBS) $(LIB_DEPENDS) $(ADD_LIBS) $(SYS_LIBS))
- endif
- 
-+# Dummy rules for modules just so that make consider the module a
-+# valid dependency when first parsing the makefiles. This rule should
-+# never be applied as the modules are a by-product of the compilation
-+# of the object
-+$(builddir)/%.mod:
-+	echo "dummy" > /dev/null
-+
- # Fortran executables
- $(bindir)/% : $(builddir)/%.o | $(bindir)
- 	$(FC) $(ALL_FLDFLAGS) $< $(OBJECTS) -o $@ \
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index a08a54c94ecd..0ddbdab4c1b1 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.18.10";
+  version = "2.18.11";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "1px5ar6iizm4czpc66hyyafandw6g9x9s1abj8klc78alvihciw4";
+    sha256 = "03wkyz3bjx3n8bwambhz9lr09271r1wxycmx4p7m2naqs4afxb89";
   };
 
   buildInputs = [ jre makeWrapper ];
diff --git a/pkgs/applications/science/logic/aiger/default.nix b/pkgs/applications/science/logic/aiger/default.nix
index 1a60c5e148cc..03524fc6b222 100644
--- a/pkgs/applications/science/logic/aiger/default.nix
+++ b/pkgs/applications/science/logic/aiger/default.nix
@@ -13,18 +13,15 @@ stdenv.mkDerivation rec {
 
   configurePhase = ''
     # Set up picosat, so we can build 'aigbmc'
-    echo $(pwd)
-    ls ..
     mkdir ../picosat
     ln -s ${picosat}/include/picosat/picosat.h ../picosat/picosat.h
     ln -s ${picosat}/lib/picosat.o             ../picosat/picosat.o
     ln -s ${picosat}/share/picosat.version     ../picosat/VERSION
-    ls ..
     ./configure.sh
   '';
 
   installPhase = ''
-    mkdir -p $out/bin
+    mkdir -p $out/bin $dev/include $lib/lib
 
     # Do the installation manually, as the Makefile has odd
     # cyrillic characters, and this is easier than adding
@@ -41,8 +38,13 @@ stdenv.mkDerivation rec {
     for x in ''${BINS[*]}; do
       install -m 755 -s $x $out/bin/$x
     done
+
+    cp -v aiger.o $lib/lib
+    cp -v aiger.h $dev/include
   '';
 
+  outputs = [ "out" "dev" "lib" ];
+
   meta = {
     description = "And-Inverter Graph (AIG) utilities";
     homepage    = http://fmv.jku.at/aiger/;
diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix
index aa815e48db41..8e0ad22bba18 100644
--- a/pkgs/applications/science/logic/boolector/default.nix
+++ b/pkgs/applications/science/logic/boolector/default.nix
@@ -1,41 +1,50 @@
-{ stdenv, fetchurl, writeShellScriptBin }:
+{ stdenv, fetchFromGitHub
+, cmake, lingeling, btor2tools
+}:
 
 stdenv.mkDerivation rec {
   name    = "boolector-${version}";
-  version = "2.4.1";
-  src = fetchurl {
-    url    = "http://fmv.jku.at/boolector/boolector-${version}-with-lingeling-bbc.tar.bz2";
-    sha256 = "0mdf7hwix237pvknvrpazcx6s3ininj5k7vhysqjqgxa7lxgq045";
+  version = "3.0.0";
+
+  src = fetchFromGitHub {
+    owner  = "boolector";
+    repo   = "boolector";
+    rev    = "refs/tags/${version}";
+    sha256 = "15i3ni5klss423m57wcy1gx0m5wfrjmglapwg85pm7fb3jj1y7sz";
   };
 
-  prePatch =
-    let
-      lingelingPatch = writeShellScriptBin "lingeling-patch" ''
-        sed -i -e "1i#include <stdint.h>" lingeling/lglib.h
-
-        ${crossFix}/bin/crossFix lingeling
-      '';
-      crossFix = writeShellScriptBin "crossFix" ''
-        # substituteInPlace not available here
-        sed -i $1/makefile.in \
-          -e 's@ar rc@$(AR) rc@' \
-          -e 's@ranlib@$(RANLIB)@'
-      '';
-    in ''
-    sed -i -e 's@mv lingeling\* lingeling@\0 \&\& ${lingelingPatch}/bin/lingeling-patch@' makefile
-    sed -i -e 's@mv boolector\* boolector@\0 \&\& ${crossFix}/bin/crossFix boolector@' makefile
-  '';
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ lingeling btor2tools ];
+
+  cmakeFlags =
+    [ "-DSHARED=ON"
+      "-DUSE_LINGELING=YES"
+      "-DBTOR2_INCLUDE_DIR=${btor2tools.dev}/include"
+      "-DBTOR2_LIBRARIES=${btor2tools.lib}/lib/libbtor2parser.so"
+      "-DLINGELING_INCLUDE_DIR=${lingeling.dev}/include"
+      "-DLINGELING_LIBRARIES=${lingeling.lib}/lib/liblgl.a"
+    ];
 
   installPhase = ''
-    mkdir $out
-    mv boolector/bin $out
+    mkdir -p $out/bin $lib/lib $dev/include
+
+    cp -vr bin/* $out/bin
+    cp -vr lib/* $lib/lib
+
+    rm -rf $out/bin/{examples,test}
+
+    cd ../src
+    find . -iname '*.h' -exec cp --parents '{}' $dev/include \;
+    rm -rf $dev/include/tests
   '';
 
-  meta = {
-    license = stdenv.lib.licenses.unfreeRedistributable;
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
     description = "An extremely fast SMT solver for bit-vectors and arrays";
-    homepage    = "http://fmv.jku.at/boolector";
-    platforms   = stdenv.lib.platforms.linux;
-    maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
+    homepage    = https://boolector.github.io;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
   };
 }
diff --git a/pkgs/applications/science/logic/btor2tools/default.nix b/pkgs/applications/science/logic/btor2tools/default.nix
new file mode 100644
index 000000000000..ed3d9e638121
--- /dev/null
+++ b/pkgs/applications/science/logic/btor2tools/default.nix
@@ -0,0 +1,33 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "btor2tools-${version}";
+  version = "pre55_8c150b39";
+
+  src = fetchFromGitHub {
+    owner  = "boolector";
+    repo   = "btor2tools";
+    rev    = "8c150b39cdbcdef4247344acf465d75ef642365d";
+    sha256 = "1r5pid4x567nms02ajjrz3v0zj18k0fi5pansrmc2907rnx2acxx";
+  };
+
+  configurePhase = "./configure.sh -shared";
+
+  installPhase = ''
+    mkdir -p $out $dev/include/btor2parser/ $lib/lib
+
+    cp -vr bin $out
+    cp -v  src/btor2parser/btor2parser.h $dev/include/btor2parser
+    cp -v  build/libbtor2parser.* $lib/lib
+  '';
+
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
+    description = "Fast SAT solver";
+    homepage    = http://fmv.jku.at/lingeling/;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}
diff --git a/pkgs/applications/science/logic/lingeling/default.nix b/pkgs/applications/science/logic/lingeling/default.nix
new file mode 100644
index 000000000000..000587a22e67
--- /dev/null
+++ b/pkgs/applications/science/logic/lingeling/default.nix
@@ -0,0 +1,49 @@
+{ stdenv, fetchFromGitHub
+, aiger
+}:
+
+stdenv.mkDerivation rec {
+  name = "lingeling-${version}";
+  # This is the version used in satcomp2018, which was
+  # relicensed, and also known as version 'bcj'
+  version = "pre1_03b4860d";
+
+  src = fetchFromGitHub {
+    owner  = "arminbiere";
+    repo   = "lingeling";
+    rev    = "03b4860d14016f42213ea271014f2f13d181f504";
+    sha256 = "1lw1yfy219p7rrk88sbq4zl24b70040zapbjdrpv5a6i0jsblksx";
+  };
+
+  configurePhase = ''
+    ./configure.sh
+
+    # Rather than patch ./configure, just sneak in use of aiger here, since it
+    # doesn't handle real build products very well (it works on a build-time
+    # dir, not installed copy)... This is so we can build 'blimc'
+    substituteInPlace ./makefile \
+      --replace 'targets: liblgl.a' 'targets: liblgl.a blimc'      \
+      --replace '$(AIGER)/aiger.o'  '${aiger.lib}/lib/aiger.o'     \
+      --replace '$(AIGER)/aiger.h'  '${aiger.dev}/include/aiger.h' \
+      --replace '-I$(AIGER)'        '-I${aiger.dev}/include'
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $lib/lib $dev/include
+
+    cp lglib.h  $dev/include
+    cp liblgl.a $lib/lib
+
+    cp lingeling plingeling treengeling ilingeling blimc $out/bin
+  '';
+
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
+    description = "Fast SAT solver";
+    homepage    = http://fmv.jku.at/lingeling/;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}
diff --git a/pkgs/applications/science/math/caffe/darwin.patch b/pkgs/applications/science/math/caffe/darwin.patch
new file mode 100644
index 000000000000..e8fa6a683f73
--- /dev/null
+++ b/pkgs/applications/science/math/caffe/darwin.patch
@@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index c823f66e..65b90c5e 100644
+--- a/Makefile
++++ b/Makefile
+@@ -32,9 +32,9 @@ SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \
+ LIBRARY_NAME := $(PROJECT)
+ LIB_BUILD_DIR := $(BUILD_DIR)/lib
+ STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a
+-DYNAMIC_VERSION_MAJOR 		:= 1
+-DYNAMIC_VERSION_MINOR 		:= 0
+-DYNAMIC_VERSION_REVISION 	:= 0
++DYNAMIC_VERSION_MAJOR		:= 1
++DYNAMIC_VERSION_MINOR		:= 0
++DYNAMIC_VERSION_REVISION	:= 0
+ DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so
+ #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR)
+ DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION)
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index c48255c8..cf4c580e 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -105,7 +105,6 @@ if(USE_OPENCV)
+ endif()
+ 
+ # ---[ BLAS
+-if(NOT APPLE)
+   set(BLAS "Atlas" CACHE STRING "Selected BLAS library")
+   set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL")
+ 
+@@ -123,17 +122,6 @@ if(NOT APPLE)
+     list(APPEND Caffe_LINKER_LIBS PUBLIC ${MKL_LIBRARIES})
+     list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_MKL)
+   endif()
+-elseif(APPLE)
+-  find_package(vecLib REQUIRED)
+-  list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${vecLib_INCLUDE_DIR})
+-  list(APPEND Caffe_LINKER_LIBS PUBLIC ${vecLib_LINKER_LIBS})
+-
+-  if(VECLIB_FOUND)
+-    if(NOT vecLib_INCLUDE_DIR MATCHES "^/System/Library/Frameworks/vecLib.framework.*")
+-      list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_ACCELERATE)
+-    endif()
+-  endif()
+-endif()
+ 
+ # ---[ Python
+ if(BUILD_python)
diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index d7357c5048d5..e56c63e01bf0 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -1,27 +1,39 @@
-{ stdenv, lib
+{ stdenv, lib, runCommand
 , fetchFromGitHub
+, fetchurl
 , cmake
 , boost
 , google-gflags
 , glog
 , hdf5-cpp
-, leveldb
-, lmdb
 , opencv3
 , protobuf
-, snappy
 , doxygen
 , openblas
-, cudaSupport ? true, cudatoolkit
+, Accelerate, CoreGraphics, CoreVideo
+, lmdbSupport ? true, lmdb
+, leveldbSupport ? true, leveldb, snappy
+, cudaSupport ? stdenv.isLinux, cudatoolkit
 , cudnnSupport ? false, cudnn ? null
 , ncclSupport ? false, nccl ? null
 , pythonSupport ? false, python ? null, numpy ? null
 }:
 
+assert leveldbSupport -> (leveldb != null && snappy != null);
 assert cudnnSupport -> cudaSupport;
 assert ncclSupport -> cudaSupport;
 assert pythonSupport -> (python != null && numpy != null);
 
+let
+  toggle = bool: if bool then "ON" else "OFF";
+
+  test_model_weights = fetchurl {
+    url = "http://dl.caffe.berkeleyvision.org/bvlc_reference_caffenet.caffemodel";
+    sha256 = "472d4a06035497b180636d8a82667129960371375bd10fcb6df5c6c7631f25e0";
+  };
+
+in
+
 stdenv.mkDerivation rec {
   name = "caffe-${version}";
   version = "1.0";
@@ -44,19 +56,27 @@ stdenv.mkDerivation rec {
            "-DCUDA_ARCH_NAME=All"
            "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
          ] else [ "-DCPU_ONLY=ON" ])
-      ++ lib.optional ncclSupport "-DUSE_NCCL=ON";
+      ++ ["-DUSE_NCCL=${toggle ncclSupport}"]
+      ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"]
+      ++ ["-DUSE_LMDB=${toggle lmdbSupport}"];
 
-  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp lmdb leveldb snappy opencv3 openblas ]
+  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp opencv3 openblas ]
                 ++ lib.optional cudaSupport cudatoolkit
                 ++ lib.optional cudnnSupport cudnn
+                ++ lib.optional lmdbSupport lmdb
                 ++ lib.optional ncclSupport nccl
-                ++ lib.optionals pythonSupport [ python numpy ];
+                ++ lib.optionals leveldbSupport [ leveldb snappy ]
+                ++ lib.optionals pythonSupport [ python numpy ]
+                ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]
+                ;
 
   propagatedBuildInputs = lib.optional pythonSupport python.pkgs.protobuf;
 
   outputs = [ "bin" "out"];
   propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
 
+  patches = [ ./darwin.patch ];
+
   preConfigure = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
     # CUDA 9.0 doesn't support sm_20
     sed -i 's,20 21(20) ,,' cmake/Cuda.cmake
@@ -71,6 +91,9 @@ stdenv.mkDerivation rec {
     # Internal static library.
     rm $out/lib/libproto.a
 
+    # Install models
+    cp -a ../models $out/share/Caffe/models
+
     moveToOutput "bin" "$bin"
   '' + lib.optionalString pythonSupport ''
     mkdir -p $out/${python.sitePackages}
@@ -78,6 +101,16 @@ stdenv.mkDerivation rec {
     rm -rf $out/python
   '';
 
+  doInstallCheck = false; # build takes more than 30 min otherwise
+  installCheckPhase = ''
+    model=bvlc_reference_caffenet
+    m_path="$out/share/Caffe/models/$model"
+    $bin/bin/caffe test \
+      -model "$m_path/deploy.prototxt" \
+      -solver "$m_path/solver.prototxt" \
+      -weights "${test_model_weights}"
+  '';
+
   meta = with stdenv.lib; {
     description = "Deep learning framework";
     longDescription = ''
@@ -88,6 +121,6 @@ stdenv.mkDerivation rec {
     homepage = http://caffe.berkeleyvision.org/;
     maintainers = with maintainers; [ jb55 ];
     license = licenses.bsd2;
-    platforms = platforms.linux;
+    platforms = platforms.linux ++ platforms.darwin;
   };
 }
diff --git a/pkgs/applications/science/math/cplex/default.nix b/pkgs/applications/science/math/cplex/default.nix
new file mode 100644
index 000000000000..fe3913648f87
--- /dev/null
+++ b/pkgs/applications/science/math/cplex/default.nix
@@ -0,0 +1,82 @@
+{ stdenv, makeWrapper, openjdk, gtk2, xorg, glibcLocales, releasePath }:
+
+# To use this package, you need to download your own cplex installer from IBM
+# and override the releasePath attribute to point to the location of the file.  
+#
+# Note: cplex creates an individual build for each license which screws
+# somewhat with the use of functions like requireFile as the hash will be
+# different for every user.
+
+stdenv.mkDerivation rec {
+  name = "cplex-${version}";
+  version = "128";
+  
+  src =
+    if builtins.isNull releasePath then
+      throw ''
+        This nix expression requires that the cplex installer is already
+        downloaded to your machine. Get it from IBM: 
+        https://developer.ibm.com/docloud/blog/2017/12/20/cplex-optimization-studio-12-8-now-available/ 
+
+        Set `cplex.releasePath = /path/to/download;` in your
+        ~/.config/nixpkgs/config.nix for `nix-*` commands, or
+        `config.cplex.releasePath = /path/to/download;` in your
+        `configuration.nix` for NixOS.
+      ''
+    else
+      releasePath;
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ openjdk gtk2 xorg.libXtst glibcLocales ];
+
+  unpackPhase = "cp $src $name";
+
+  patchPhase = ''
+    sed -i -e 's|/usr/bin/tr"|tr"         |' $name
+  '';
+
+  buildPhase = ''
+    sh $name -i silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR=$out
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    ln -s $out/opl/bin/x86-64_linux/oplrun\
+      $out/opl/bin/x86-64_linux/oplrunjava\
+      $out/opl/oplide/oplide\
+      $out/cplex/bin/x86-64_linux/cplex\
+      $out/cpoptimizer/bin/x86-64_linux/cpoptimizer\
+      $out/bin
+  '';
+
+  fixupPhase = 
+  let 
+    libraryPath = stdenv.lib.makeLibraryPath [ stdenv.cc.cc gtk2 xorg.libXtst ];
+  in ''
+    interpreter=${stdenv.glibc}/lib/ld-linux-x86-64.so.2
+
+    for pgm in $out/opl/bin/x86-64_linux/oplrun $out/opl/bin/x86-64_linux/oplrunjava $out/opl/oplide/oplide;
+    do
+      patchelf --set-interpreter "$interpreter" $pgm;
+      wrapProgram $pgm \
+        --prefix LD_LIBRARY_PATH : $out/opl/bin/x86-64_linux:${libraryPath} \
+        --set LOCALE_ARCHIVE ${glibcLocales}/lib/locale/locale-archive;
+    done
+
+    for pgm in $out/cplex/bin/x86-64_linux/cplex $out/cpoptimizer/bin/x86-64_linux/cpoptimizer $out/opl/oplide/jre/bin/*; 
+    do
+      if grep ELF $pgm > /dev/null;
+      then
+        patchelf --set-interpreter "$interpreter" $pgm;
+      fi
+    done
+  '';
+  
+  meta = with stdenv.lib; {
+    description = "Optimization solver for mathematical programming";
+    homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex";
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ bfortz ];
+  };
+}
diff --git a/pkgs/applications/science/math/gfan/default.nix b/pkgs/applications/science/math/gfan/default.nix
index 65d551f39a71..d2d1ddb65846 100644
--- a/pkgs/applications/science/math/gfan/default.nix
+++ b/pkgs/applications/science/math/gfan/default.nix
@@ -9,15 +9,20 @@ stdenv.mkDerivation rec {
     sha256 = "02pihqb1lb76a0xbfwjzs1cd6ay3ldfxsm8dvsbl6qs3vkjxax56";
   };
 
-  makeFlags = ''PREFIX=$(out) CC=cc CXX=c++ cddnoprefix=1'';
-  buildInputs = [gmp mpir cddlib];
+  patchPhase = stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace Makefile --replace "-fno-guess-branch-probability" ""
+  '';
+
+  buildFlags = [ "CC=cc" "CXX=c++" "cddnoprefix=1" ];
+  installFlags = [ ''PREFIX=$(out)'' ];
+  buildInputs = [ gmp mpir cddlib ];
 
   meta = {
     inherit version;
     description = ''A software package for computing Gröbner fans and tropical varieties'';
     license = stdenv.lib.licenses.gpl2 ;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://home.math.au.dk/jensen/software/gfan/gfan.html;
   };
 }
diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix
index 7990088ffbe9..59dbfdb509dc 100644
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "qalculate-gtk-${version}";
-  version = "2.6.1";
+  version = "2.6.2";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "19jw1w29x0r1qq5r8gmqrqr00ml2pfi2w433723vjzxpfg2pp70r";
+    sha256 = "1yzw6avhka7bbi071z9d8cipcghyjq2bg9x3arv1cf395xlnrmb9";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/math/ratpoints/default.nix b/pkgs/applications/science/math/ratpoints/default.nix
index 82a6836bd623..2dd4778234df 100644
--- a/pkgs/applications/science/math/ratpoints/default.nix
+++ b/pkgs/applications/science/math/ratpoints/default.nix
@@ -1,20 +1,36 @@
-{stdenv, fetchurl, gmp}:
+{ stdenv, fetchurl, fetchpatch, gmp }:
 stdenv.mkDerivation rec {
   name = "ratpoints-${version}";
-  version = "2.1.3";
+  version = "2.1.3.p4";
+
   src = fetchurl {
     url = "http://www.mathe2.uni-bayreuth.de/stoll/programs/ratpoints-${version}.tar.gz";
     sha256 = "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4";
   };
-  buildInputs = [gmp];
-  makeFlags = "INSTALL_DIR=$(out)";
+
+  enableParallelBuilding = true;
+
+  patches = [
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/sturm_and_rp_private.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a";
+      sha256 = "0q3wajncyfr3gahd8gwk9x7g56zw54lpywrl63lqk7drkf60mrcl";
+    })
+  ];
+
+  buildInputs = [ gmp ];
+
+  makeFlags = [ "CC=cc" ];
+  buildFlags = stdenv.lib.optional stdenv.isDarwin ["CCFLAGS2=-lgmp -lc -lm" "CCFLAGS=-UUSE_SSE"];
+  installFlags = [ "INSTALL_DIR=$(out)" ];
+
   preInstall = ''mkdir -p "$out"/{bin,share,lib,include}'';
+
   meta = {
     inherit version;
     description = ''A program to find rational points on hyperelliptic curves'';
     license = stdenv.lib.licenses.gpl2Plus;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://www.mathe2.uni-bayreuth.de/stoll/programs/;
     updateWalker = true;
   };
diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix
index 6123fd7306d9..a641993b393b 100644
--- a/pkgs/applications/science/math/symmetrica/default.nix
+++ b/pkgs/applications/science/math/symmetrica/default.nix
@@ -5,20 +5,15 @@
 stdenv.mkDerivation rec {
   name = "symmetrica-${version}";
   version = "2.0";
+
   src = fetchurl {
     url = "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/SYM2_0_tar.gz";
     sha256 = "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz";
     name = "symmetrica-2.0.tar.gz";
   };
+
   sourceRoot = ".";
-  installPhase = ''
-    mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica}
-    ar crs libsymmetrica.a *.o
-    ranlib libsymmetrica.a
-    cp libsymmetrica.a "$out/lib"
-    cp *.h "$out/include/symmetrica"
-    cp README *.doc "$out/share/doc/symmetrica"
-  '';
+
   patches = [
       # don't show banner ("SYMMETRICA VERSION X - STARTING)
       # it doesn't contain very much helpful information and a banner is not ideal for a library
@@ -34,13 +29,34 @@ stdenv.mkDerivation rec {
         url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/int32.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
         sha256 = "0p33c85ck4kd453z687ni4bdcqr1pqx2756j7aq11bf63vjz4cyz";
       })
+
+      (fetchpatch {
+        url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/return_values.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a";
+        sha256 = "0dmczkicwl50sivc07w3wm3jpfk78wm576dr25999jdj2ipsb7nk";
+      })
   ];
+
+  postPatch = ''
+    substituteInPlace makefile --replace gcc cc
+  '';
+
+  enableParallelBuilding = true;
+
+  installPhase = ''
+    mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica}
+    ar crs libsymmetrica.a *.o
+    ranlib libsymmetrica.a
+    cp libsymmetrica.a "$out/lib"
+    cp *.h "$out/include/symmetrica"
+    cp README *.doc "$out/share/doc/symmetrica"
+  '';
+
   meta = {
     inherit version;
     description = ''A collection of routines for representation theory and combinatorics'';
     license = stdenv.lib.licenses.publicDomain;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://www.symmetrica.de/;
   };
 }
diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix
index 17a1719ba1ed..b6cd8c294c1b 100644
--- a/pkgs/applications/science/misc/simgrid/default.nix
+++ b/pkgs/applications/science/misc/simgrid/default.nix
@@ -1,11 +1,11 @@
-{ stdenv, fetchFromGitHub, cmake, elfutils, perl, python3, boost, valgrind
+{ stdenv, fetchFromGitHub, cmake, perl, python3, boost, valgrind
 # Optional requirements
 # Lua 5.3 needed and not available now
 #, luaSupport ? false, lua5
 , fortranSupport ? false, gfortran
 , buildDocumentation ? false, transfig, ghostscript, doxygen
 , buildJavaBindings ? false, openjdk
-, modelCheckingSupport ? false, libunwind, libevent # Inside elfutils - , libelf, libevent, libdw
+, modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw
 , debug ? false
 , moreTests ? false
 }:
@@ -18,20 +18,20 @@ in
 
 stdenv.mkDerivation rec {
   name = "simgrid-${version}";
-  version = "3.19.1";
+  version = "3.20";
 
   src = fetchFromGitHub {
     owner = "simgrid";
     repo = "simgrid";
     rev = "v${version}";
-    sha256 = "0vpgcp40xv20hcpslx5wz2mf2phaq41f7x8yr0bm7mknqd3zwxih";
+    sha256 = "0xb20qhvsah2dz2hvn850i3w9a5ghsbcx8vka2ap6xsdkxf593gy";
   };
 
-  nativeBuildInputs = [ cmake perl elfutils python3 boost valgrind ]
+  nativeBuildInputs = [ cmake perl python3 boost valgrind ]
       ++ optionals fortranSupport [ gfortran ]
       ++ optionals buildJavaBindings [ openjdk ]
       ++ optionals buildDocumentation [ transfig ghostscript doxygen ]
-      ++ optionals modelCheckingSupport [ libunwind libevent ];
+      ++ optionals modelCheckingSupport [ libunwind libevent elfutils ];
 
   #buildInputs = optional luaSupport lua5;
 
@@ -83,13 +83,15 @@ stdenv.mkDerivation rec {
   '';
 
   doCheck = true;
-  
+
   checkPhase = ''
     runHook preCheck
-    ctest --output-on-failure -E smpi-replay-multiple
+
+    ctest -j $NIX_BUILD_CORES --output-on-failure -E smpi-replay-multiple
+
     runHook postCheck
   '';
-    
+
   enableParallelBuilding = true;
 
   meta = {