Merge remote-tracking branch 'upstream/master' into wrapper-pname-support

2019-11-24 17:25:07 +00:00
parent 9b090ccbca 195c263a81
commit d0d5136cce
5772 changed files with 168373 additions and 134383 deletions
@@ -1,15 +1,15 @@
-{ stdenv, fetchurl, cmake, itk, python }:
+{ stdenv, fetchFromGitHub, cmake, itk, python }:

 stdenv.mkDerivation rec {
  pname    = "elastix";
-  pversion = "4.9.0";
-  name  = "${pname}-${pversion}";
+  version = "5.0.0";

-  src = fetchurl {
-    url    = "https://github.com/SuperElastix/${pname}/archive/${pversion}.tar.gz";
-    sha256 = "02pbln36nq98xxfyqwlxg7b6gmigdq4fgfqr9mym1qn58aj04shg";
+  src = fetchFromGitHub {
+    owner  = "SuperElastix";
+    repo   = pname;
+    rev    = version;
+    sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
  };
-
  nativeBuildInputs = [ cmake python ];
  buildInputs = [ itk ];

@@ -31,6 +31,6 @@ stdenv.mkDerivation rec {
    license = licenses.mit;
    homepage = http://www.htslib.org/;
    platforms = platforms.unix;
-    maintainers = [ maintainers.mimadrid ];
+    maintainers = [ maintainers.mimame ];
  };
 }
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
    homepage = https://sourceforge.net/projects/niftilib;
    description = "Medical imaging format C API";
    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
    license = licenses.publicDomain;
  };
 }
@@ -41,6 +41,6 @@ stdenv.mkDerivation rec {
    description = "Legacy version of PolyBoRi maintained by sagemath developers";
    license = licenses.gpl2Plus;
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -33,6 +33,6 @@ stdenv.mkDerivation rec {
    '';
    license = licenses.gpl2Plus;
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -1,4 +1,4 @@
-{ callPackage, cudatoolkit_7, cudatoolkit_7_5, cudatoolkit_8, cudatoolkit_9_0, cudatoolkit_9_1, cudatoolkit_9_2, cudatoolkit_10_0 }:
+{ callPackage, cudatoolkit_7, cudatoolkit_7_5, cudatoolkit_8, cudatoolkit_9_0, cudatoolkit_9_1, cudatoolkit_9_2, cudatoolkit_10_0, cudatoolkit_10_1 }:

 let
  generic = args: callPackage (import ./generic.nix (removeAttrs args ["cudatoolkit"])) {
@@ -65,5 +65,12 @@ in rec {
    sha256 = "18ys0apiz9afid2s6lvy9qbyi8g66aimb2a7ikl1f3dm09mciprf";
  };

-  cudnn_cudatoolkit_10 = cudnn_cudatoolkit_10_0;
+  cudnn_cudatoolkit_10_1 = generic rec {
+    version = "7.6.3";
+    cudatoolkit = cudatoolkit_10_1;
+    srcName = "cudnn-${cudatoolkit.majorVersion}-linux-x64-v7.6.3.30.tgz";
+    sha256 = "0qc9f1xpyfibwqrpqxxq2v9h6w90j0dbx564akwy44c1dls5f99m";
+  };
+
+  cudnn_cudatoolkit_10 = cudnn_cudatoolkit_10_1;
 }
@@ -46,7 +46,7 @@ stdenv.mkDerivation {

  passthru = {
    inherit cudatoolkit;
-    majorVersion = lib.head (lib.splitString "." version);
+    majorVersion = lib.versions.major version;
  };

  meta = with stdenv.lib; {
@@ -104,10 +104,10 @@ index 84e4e88..56ca676 100644
 -	cp -rf ../include $(INSTALL_DIR)/include/Lfunction
 +	install -d $(INSTALL_DIR)/bin
 +	install -d $(INSTALL_DIR)/$(LIB_DIR)
-+	install -d $(INSTALL_DIR)/include/libLfunction
+	install -d $(INSTALL_DIR)/include/Lfunction
 +	install lcalc $(INSTALL_DIR)/bin
 +	install libLfunction.so $(INSTALL_DIR)/$(LIB_DIR)
-+	install -m 644 -t $(INSTALL_DIR)/include/libLfunction ../include/*.h
+	install -m 644 -t $(INSTALL_DIR)/include/Lfunction ../include/*.h
 
 
 SRCS = Lcommandline.cc Lcommandline_elliptic.cc Lcommandline_globals.cc Lcommandline_misc.cc Lcommandline_numbertheory.cc Lcommandline_twist.cc Lcommandline_values_zeros.cc Lgamma.cc Lglobals.cc Lmisc.cc Lriemannsiegel.cc Lriemannsiegel_blfi.cc cmdline.c
@@ -23,8 +23,8 @@ stdenv.mkDerivation {
  nativeBuildInputs = [ python2 ];

  cmakeFlags = [
-    "-DUSE_OPTIMIZED_BLAS=ON"
    "-DCMAKE_Fortran_FLAGS=-fPIC"
+    "-DLAPACKE=ON"
  ]
  ++ (optional shared "-DBUILD_SHARED_LIBS=ON");

@@ -25,6 +25,6 @@ stdenv.mkDerivation rec {
    description = "Library to do fast arithmetic with dense matrices over F_2";
    license = licenses.gpl2Plus;
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -34,6 +34,6 @@ stdenv.mkDerivation rec {
    '';
    license = licenses.gpl2Plus;
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -24,6 +24,10 @@ in stdenv.mkDerivation {

  MKLROOT = optionalString mklSupport mkl;

+  preConfigure = ''
+    export CC=${cudatoolkit.cc}/bin/gcc CXX=${cudatoolkit.cc}/bin/g++
+  '';
+
  enableParallelBuilding=true;
  buildFlags = [ "magma" "magma_sparse" ];

@@ -3,11 +3,25 @@
  For details on using mkl as a blas provider for python packages such as numpy,
  numexpr, scipy, etc., see the Python section of the NixPkgs manual.
 */
-stdenvNoCC.mkDerivation (rec {
-  name = "mkl-${version}";
-  version = "${date}.${rel}";
-  date = "2019.3";
-  rel = "199";
+let
+  # Release notes and download URLs are here:
+  # https://registrationcenter.intel.com/en/products/
+  version = "${year}.${spot}.${rel}";
+  year = "2019";
+
+  # Darwin is pinned to 2019.3 because the DMG does not unpack; see here for details:
+  # https://github.com/matthewbauer/undmg/issues/4
+  spot = if stdenvNoCC.isDarwin then "3" else "5";
+  rel = if stdenvNoCC.isDarwin then "199" else "281";
+
+  rpm-ver = "${year}.${spot}-${rel}-${year}.${spot}-${rel}";
+
+  # Intel openmp uses its own versioning, but shares the spot release patch.
+  openmp-ver = "19.0.${spot}-${rel}-19.0.${spot}-${rel}";
+
+in stdenvNoCC.mkDerivation {
+  pname = "mkl";
+  inherit version;

  src = if stdenvNoCC.isDarwin
    then
@@ -17,29 +31,42 @@ stdenvNoCC.mkDerivation (rec {
      })
    else
      (fetchurl {
-        url = "http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/l_mkl_${version}.tgz";
-        sha256 = "13rb2v2872jmvzcqm4fqsvhry0j2r5cn4lqql4wpqbl1yia2pph6";
+        url = "https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/l_mkl_${version}.tgz";
+        sha256 = "0zkk4rrq7g44acxaxhpd2053r66w169mww6917an0lxhd52fm5cr";
      });

  nativeBuildInputs = if stdenvNoCC.isDarwin
    then
-      [ undmg
-        darwin.cctools
-      ]
+      [ undmg darwin.cctools ]
    else
      [ rpmextract ];

  buildPhase = if stdenvNoCC.isDarwin then ''
-      for f in Contents/Resources/pkg/*.tgz; do
-          tar xzvf $f
-      done
+    for f in Contents/Resources/pkg/*.tgz; do
+      tar xzvf $f
+    done
  '' else ''
-    rpmextract rpm/intel-mkl-common-c-${date}-${rel}-${date}-${rel}.noarch.rpm
-    rpmextract rpm/intel-mkl-core-rt-${date}-${rel}-${date}-${rel}.x86_64.rpm
-    rpmextract rpm/intel-openmp-19.0.3-${rel}-19.0.3-${rel}.x86_64.rpm
+    rpmextract rpm/intel-mkl-cluster-rt-${rpm-ver}.x86_64.rpm
+    rpmextract rpm/intel-mkl-common-c-${rpm-ver}.noarch.rpm
+    rpmextract rpm/intel-mkl-core-${rpm-ver}.x86_64.rpm
+    rpmextract rpm/intel-mkl-core-rt-${rpm-ver}.x86_64.rpm
+    rpmextract rpm/intel-openmp-${openmp-ver}.x86_64.rpm
  '';

-  installPhase = if stdenvNoCC.isDarwin then ''
+  installPhase = ''
+    for f in $(find . -name 'mkl*.pc') ; do
+      bn=$(basename $f)
+      substituteInPlace $f \
+        --replace "prefix=<INSTALLDIR>/mkl" "prefix=$out" \
+        --replace "lib/intel64_lin" "lib"
+    done
+
+    for f in $(find opt/intel -name 'mkl*iomp.pc') ; do
+      substituteInPlace $f \
+        --replace "../compiler/lib" "lib"
+    done
+  '' +
+    (if stdenvNoCC.isDarwin then ''
      mkdir -p $out/lib

      cp -r compilers_and_libraries_${version}/mac/mkl/include $out/
@@ -48,6 +75,9 @@ stdenvNoCC.mkDerivation (rec {
      cp -r compilers_and_libraries_${version}/mac/compiler/lib/* $out/lib/
      cp -r compilers_and_libraries_${version}/mac/mkl/lib/* $out/lib/
      cp -r compilers_and_libraries_${version}/mac/tbb/lib/* $out/lib/
+
+      mkdir -p $out/lib/pkgconfig
+      cp -r compilers_and_libraries_${version}/mac/mkl/bin/pkgconfig/* $out/lib/pkgconfig
  '' else ''
      mkdir -p $out/lib

@@ -56,18 +86,21 @@ stdenvNoCC.mkDerivation (rec {
      cp -r opt/intel/compilers_and_libraries_${version}/linux/compiler/lib/intel64_lin/* $out/lib/
      cp -r opt/intel/compilers_and_libraries_${version}/linux/mkl/lib/intel64_lin/* $out/lib/
      cp license.txt $out/lib/
-  '';
+
+      mkdir -p $out/lib/pkgconfig
+      cp -r opt/intel/compilers_and_libraries_${version}/linux/mkl/bin/pkgconfig/* $out/lib/pkgconfig
+  '');

  # fixDarwinDylibName fails for libmkl_cdft_core.dylib because the
  # larger updated load commands do not fit. Use install_name_tool
  # explicitly and ignore the error.
  postFixup = stdenvNoCC.lib.optionalString stdenvNoCC.isDarwin ''
-      for f in $out/lib/*.dylib; do
-          install_name_tool -id $out/lib/$(basename $f) $f || true
-      done
-      install_name_tool -change @rpath/libiomp5.dylib $out/lib/libiomp5.dylib $out/lib/libmkl_intel_thread.dylib
-      install_name_tool -change @rpath/libtbb.dylib $out/lib/libtbb.dylib $out/lib/libmkl_tbb_thread.dylib
-      install_name_tool -change @rpath/libtbbmalloc.dylib $out/lib/libtbbmalloc.dylib $out/lib/libtbbmalloc_proxy.dylib
+    for f in $out/lib/*.dylib; do
+      install_name_tool -id $out/lib/$(basename $f) $f || true
+    done
+    install_name_tool -change @rpath/libiomp5.dylib $out/lib/libiomp5.dylib $out/lib/libmkl_intel_thread.dylib
+    install_name_tool -change @rpath/libtbb.dylib $out/lib/libtbb.dylib $out/lib/libmkl_tbb_thread.dylib
+    install_name_tool -change @rpath/libtbbmalloc.dylib $out/lib/libtbbmalloc.dylib $out/lib/libtbbmalloc_proxy.dylib
  '';

  # Per license agreement, do not modify the binary
@@ -85,12 +118,6 @@ stdenvNoCC.mkDerivation (rec {
    homepage = https://software.intel.com/en-us/mkl;
    license = licenses.issl;
    platforms = [ "x86_64-linux" "x86_64-darwin" ];
-    maintainers = [ maintainers.bhipple ];
+    maintainers = with maintainers; [ bhipple ];
  };
- } // stdenvNoCC.lib.optionalAttrs stdenvNoCC.isLinux {
-  # Since on Linux binaries are unmodified, we can make them
-  # fixed-output derivations.
-	outputHashAlgo = "sha256";
-	outputHashMode = "recursive";
-	outputHash = "101krzh2mjbfx8kvxim2zphdvgg7iijhbf9xdz3ad3ncgybxbdvw";
- })
+}
@@ -0,0 +1,5 @@
+--- a/makefiles/Makefile.python.mk
+++ b/makefiles/Makefile.python.mk
+@@ -1070 +1070 @@ $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/data: $(PYDATA_LIBS) | $(PYPI_ARCHIVE_T
+-$(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/util: $(PYUTIL_LIBS) | $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools
+$(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools/util: $(PYSORTED_INTERVAL_LIST_LIBS) | $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools
@@ -5,15 +5,20 @@

 stdenv.mkDerivation rec {
  pname = "or-tools";
-  version = "v7.0";
+  version = "7.3";

  src = fetchFromGitHub {
    owner = "google";
    repo = "or-tools";
-    rev = version;
-    sha256 = "09rs2j3w4ljw9qhhnsjlvfii297njjszwvkbgj1i6kns3wnlr7cp";
+    rev = "v${version}";
+    sha256 = "0q06vxmds6nm3dpjw4y5jzr8j98qgfb9i8pbm9pfhmqigv791hwc";
  };

+  patches = [
+    ./build.patch # https://github.com/google/or-tools/pull/1619
+    ./protobuf.patch # Otherwise it tries to install protobuf from pypi.
+  ];
+
  # The original build system uses cmake which does things like pull
  # in dependencies through git and Makefile creation time. We
  # obviously don't want to do this so instead we provide the
@@ -0,0 +1,10 @@
+--- a/makefiles/Makefile.third_party.unix.mk
+++ b/makefiles/Makefile.third_party.unix.mk
+@@ -24,1 +24,1 @@ GLOG_TAG = 0.4.0
+-PROTOBUF_TAG = 3.9.0
+PROTOBUF_TAG = 3.7.0
+--- a/makefiles/Makefile.third_party.win.mk
+++ b/makefiles/Makefile.third_party.win.mk
+@@ -40 +40 @@ GLOG_TAG = 0.4.0
+-PROTOBUF_TAG = 3.9.0
+PROTOBUF_TAG = 3.7.0
@@ -22,6 +22,6 @@ stdenv.mkDerivation rec {
    description = "Calculates rank-width and rank-decompositions";
    license = with licenses; [ gpl2Plus ];
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -76,6 +76,6 @@ stdenv.mkDerivation rec {
      mit # Dik T. Winter's software
    ];
    maintainers = with maintainers; [ timokau ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };
 }
@@ -1,20 +1,19 @@
-{ stdenv, fetchurl, cmake, openssh
+{ stdenv, fetchFromGitHub, cmake, openssh
 , gfortran, mpi, openblasCompat
 } :


 stdenv.mkDerivation rec {
  pname = "scalapack";
-  version = "2.0.2";
+  version = "2.1";

-  src = fetchurl {
-    url = "http://www.netlib.org/scalapack/scalapack-${version}.tgz";
-    sha256 = "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c";
+  src = fetchFromGitHub {
+    owner = "Reference-ScaLAPACK";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "042q9kc383h7y0had9a37702z4s0szavss063ljvfdsbjy07gzb1";
  };

-  # patch to rename outdated MPI functions
-  patches = [ ./openmpi4.patch ];
-
  nativeBuildInputs = [ cmake openssh ];
  buildInputs = [ mpi gfortran openblasCompat ];

@@ -1,143 +0,0 @@
-diff --git a/BLACS/SRC/blacs_get_.c b/BLACS/SRC/blacs_get_.c
-index e979767..d4b04cf 100644
--- a/BLACS/SRC/blacs_get_.c
-+++ b/BLACS/SRC/blacs_get_.c
-@@ -23,7 +23,7 @@ F_VOID_FUNC blacs_get_(int *ConTxt, int *what, int *val)
-    case SGET_MSGIDS:
-       if (BI_COMM_WORLD == NULL) Cblacs_pinfo(val, &val[1]);
-       iptr = &val[1];
-      ierr=MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, (BVOID **) &iptr,val);
-+      ierr=MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_TAG_UB, (BVOID **) &iptr,val);
-       val[0] = 0;
-       val[1] = *iptr;
-       break;
-diff --git a/BLACS/SRC/cgamn2d_.c b/BLACS/SRC/cgamn2d_.c
-index 2db6ccb..6958f32 100644
--- a/BLACS/SRC/cgamn2d_.c
-+++ b/BLACS/SRC/cgamn2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC cgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/cgamx2d_.c b/BLACS/SRC/cgamx2d_.c
-index 707c0b6..f802d01 100644
--- a/BLACS/SRC/cgamx2d_.c
-+++ b/BLACS/SRC/cgamx2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC cgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/dgamn2d_.c b/BLACS/SRC/dgamn2d_.c
-index dff23b4..a2627ac 100644
--- a/BLACS/SRC/dgamn2d_.c
-+++ b/BLACS/SRC/dgamn2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC dgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/dgamx2d_.c b/BLACS/SRC/dgamx2d_.c
-index a51f731..2a644d0 100644
--- a/BLACS/SRC/dgamx2d_.c
-+++ b/BLACS/SRC/dgamx2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC dgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/igamn2d_.c b/BLACS/SRC/igamn2d_.c
-index 16bc003..f6a7859 100644
--- a/BLACS/SRC/igamn2d_.c
-+++ b/BLACS/SRC/igamn2d_.c
-@@ -218,7 +218,7 @@ F_VOID_FUNC igamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/igamx2d_.c b/BLACS/SRC/igamx2d_.c
-index 8165cbe..a7cfcc6 100644
--- a/BLACS/SRC/igamx2d_.c
-+++ b/BLACS/SRC/igamx2d_.c
-@@ -218,7 +218,7 @@ F_VOID_FUNC igamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/sgamn2d_.c b/BLACS/SRC/sgamn2d_.c
-index d6c95e5..569c797 100644
--- a/BLACS/SRC/sgamn2d_.c
-+++ b/BLACS/SRC/sgamn2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC sgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/sgamx2d_.c b/BLACS/SRC/sgamx2d_.c
-index 4b0af6f..8897ece 100644
--- a/BLACS/SRC/sgamx2d_.c
-+++ b/BLACS/SRC/sgamx2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC sgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/zgamn2d_.c b/BLACS/SRC/zgamn2d_.c
-index 9de2b23..37897df 100644
--- a/BLACS/SRC/zgamn2d_.c
-+++ b/BLACS/SRC/zgamn2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC zgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
-diff --git a/BLACS/SRC/zgamx2d_.c b/BLACS/SRC/zgamx2d_.c
-index 414c381..0e9d474 100644
--- a/BLACS/SRC/zgamx2d_.c
-+++ b/BLACS/SRC/zgamx2d_.c
-@@ -221,7 +221,7 @@ F_VOID_FUNC zgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
-       {
- #endif
-       i = 2;
-      ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
-+      ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
-       ierr=MPI_Type_commit(&MyType);
-       bp->N = bp2->N = 1;
-       bp->dtype = bp2->dtype = MyType;
@@ -1,6 +1,6 @@
 { stdenv
 , fetchurl
-, patchelf
+, addOpenGLRunpath
 , cudaSupport ? false, symlinkJoin, cudatoolkit, cudnn, nvidia_x11
 }:

@@ -35,6 +35,9 @@ let
    else ''
      patchelf --set-rpath "${rpath}:$out/lib" $out/lib/libtensorflow.so
      patchelf --set-rpath "${rpath}" $out/lib/libtensorflow_framework.so
+      ${optionalString cudaSupport ''
+        addOpenGLRunpath $out/lib/libtensorflow.so $out/lib/libtensorflow_framework.so
+      ''}
    '';

 in stdenv.mkDerivation rec {
@@ -43,6 +46,8 @@ in stdenv.mkDerivation rec {

  src = fetchurl url;

+  nativeBuildInputs = optional cudaSupport addOpenGLRunpath;
+
  # Patch library to use our libc, libstdc++ and others
  buildCommand = ''
    mkdir -pv $out
@@ -1,5 +1,5 @@
 { stdenv
-, fetchFromGitHub
+, fetchFromGitLab
 , python
 , wafHook

@@ -22,75 +22,89 @@
 , dia, tetex ? null, ghostscript ? null, texlive ? null

 # generates python bindings
-, generateBindings ? false, ncurses ? null
+, pythonSupport ? false, ncurses ? null

 # All modules can be enabled by choosing 'all_modules'.
 # we include here the DCE mandatory ones
 , modules ? [ "core" "network" "internet" "point-to-point" "fd-net-device" "netanim"]
-, gcc6
 , lib
 }:

 let
  pythonEnv = python.withPackages(ps:
    stdenv.lib.optional withManual ps.sphinx
-    ++ stdenv.lib.optionals generateBindings (with ps;[ pybindgen pygccxml ])
+    ++ stdenv.lib.optionals pythonSupport (with ps;[ pybindgen pygccxml ])
  );
 in
 stdenv.mkDerivation rec {
+  pname = "ns-3";
+  version = "30";

-  name = "ns-3.${version}";
-  version = "28";
-
-  # the all in one https://www.nsnam.org/release/ns-allinone-3.27.tar.bz2;
-  # fetches everything (netanim, etc), this package focuses on ns3-core
-  src = fetchFromGitHub {
-    owner  = "nsnam";
-    repo   = "ns-3-dev-git";
-    rev    = name;
-    sha256 = "17kzfjpgw2mvyx1c9bxccnvw67jpk09fxmcnlkqx9xisk10qnhng";
+  src = fetchFromGitLab {
+    owner = "nsnam";
+    repo   = "ns-3-dev";
+    rev    = "ns-3.${version}";
+    sha256 = "0smdi3gglmafpc7a20hj2lbmwks3d5fpsicpn39lmm3svazw0bvp";
  };

  nativeBuildInputs = [ wafHook ];
-  # ncurses is a hidden dependency of waf when checking python
-  buildInputs = lib.optionals generateBindings [ castxml ncurses ]
-    ++ stdenv.lib.optional enableDoxygen [ doxygen graphviz imagemagick ]
-    ++ stdenv.lib.optional withManual [ dia tetex ghostscript texlive.combined.scheme-medium ];

-  propagatedBuildInputs = [ gcc6 pythonEnv ];
+  outputs = [ "out" ] ++ lib.optional pythonSupport "py";
+
+  # ncurses is a hidden dependency of waf when checking python
+  buildInputs = lib.optionals pythonSupport [ castxml ncurses ]
+    ++ lib.optional enableDoxygen [ doxygen graphviz imagemagick ]
+    ++ lib.optional withManual [ dia tetex ghostscript texlive.combined.scheme-medium ];
+
+  propagatedBuildInputs = [ pythonEnv ];

  postPatch = ''
    patchShebangs doc/ns3_html_theme/get_version.sh
  '';

  wafConfigureFlags = with stdenv.lib; [
-      "--enable-modules=${stdenv.lib.concatStringsSep "," modules}"
+      "--enable-modules=${concatStringsSep "," modules}"
      "--with-python=${pythonEnv.interpreter}"
  ]
  ++ optional (build_profile != null) "--build-profile=${build_profile}"
-  ++ optional generateBindings [  ]
  ++ optional withExamples " --enable-examples "
  ++ optional doCheck " --enable-tests "
  ;

+  doCheck = true;
+
  buildTargets = "build"
    + lib.optionalString enableDoxygen " doxygen"
    + lib.optionalString withManual "sphinx";

-  doCheck = true;
+  # to prevent fatal error: 'backward_warning.h' file not found
+  CXXFLAGS = "-D_GLIBCXX_PERMIT_BACKWARD_HASH";

-  # we need to specify the proper interpreter else ns3 can check against a
-  # different version even though we
-  checkPhase =  ''
-    ${pythonEnv.interpreter} ./test.py
+  postBuild = with stdenv.lib; let flags = concatStringsSep ";" (
+      optional enableDoxygen "./waf doxygen"
+      ++ optional withManual "./waf sphinx"
+    );
+    in "${flags}"
+  ;
+
+  postInstall = ''
+    moveToOutput "${pythonEnv.libPrefix}" "$py"
  '';

-  hardeningDisable = [ "fortify" ];
+  # we need to specify the proper interpreter else ns3 can check against a
+  # different version
+  checkPhase =  ''
+    ${pythonEnv.interpreter} ./test.py --nowaf
+  '';

-  meta = {
-    homepage = http://www.nsnam.org;
-    license = stdenv.lib.licenses.gpl3;
+  # strictoverflow prevents clang from discovering pyembed when bindings
+  hardeningDisable = [ "fortify" "strictoverflow"];
+
+  meta = with stdenv.lib; {
+    homepage = "http://www.nsnam.org";
+    license = licenses.gpl3;
    description = "A discrete time event network simulator";
-    platforms = with stdenv.lib.platforms; unix;
+    platforms = with platforms; unix;
+    maintainers = with maintainers; [ teto ];
  };
 }