Merge remote-tracking branch 'origin/master' into gcc-9

11 files changed, 40 insertions, 174 deletions

diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix
index 9105b1c52ac..4cfc07c1cba 100644
--- a/pkgs/development/libraries/science/biology/elastix/default.nix
+++ b/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -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 ];
 
@@ -19,6 +19,5 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.linux;
     license = licenses.asl20;
-    broken = true;
   };
 }
diff --git a/pkgs/development/libraries/science/biology/nifticlib/default.nix b/pkgs/development/libraries/science/biology/nifticlib/default.nix
index 51eed36312d..8c7da7968f5 100644
--- a/pkgs/development/libraries/science/biology/nifticlib/default.nix
+++ b/pkgs/development/libraries/science/biology/nifticlib/default.nix
@@ -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;
   };
 }
diff --git a/pkgs/development/libraries/science/math/QuadProgpp/default.nix b/pkgs/development/libraries/science/math/QuadProgpp/default.nix
index d4333146406..69ccbfc26b4 100644
--- a/pkgs/development/libraries/science/math/QuadProgpp/default.nix
+++ b/pkgs/development/libraries/science/math/QuadProgpp/default.nix
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
       A C++ library for Quadratic Programming which implements the
       Goldfarb-Idnani active-set dual method.
     '';
-    maintainers = with maintainers; [ fuuzetsu ];
+    maintainers = with maintainers; [ ];
     platforms = with platforms; linux;
   };
 }
diff --git a/pkgs/development/libraries/science/math/brial/default.nix b/pkgs/development/libraries/science/math/brial/default.nix
index f08f6425655..56a78b00cd6 100644
--- a/pkgs/development/libraries/science/math/brial/default.nix
+++ b/pkgs/development/libraries/science/math/brial/default.nix
@@ -8,14 +8,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.2.5";
+  version = "1.2.6";
   pname = "brial";
 
   src = fetchFromGitHub {
     owner = "BRiAl";
     repo = "BRiAl";
     rev = version;
-    sha256 = "1nv56fp3brpzanxj7vwvxqdafqfsfhdgq5imr3m94psw5gdfqwja";
+    sha256 = "1mc1zjr3mxcx6bg0js5k9jx65japg7644b0aj1al75m4nwh2ygab";
   };
 
   # FIXME package boost-test and enable checks
diff --git a/pkgs/development/libraries/science/math/caffe2/default.nix b/pkgs/development/libraries/science/math/caffe2/default.nix
index 26ec1237601..a5c373ecde9 100644
--- a/pkgs/development/libraries/science/math/caffe2/default.nix
+++ b/pkgs/development/libraries/science/math/caffe2/default.nix
@@ -57,7 +57,7 @@ let
     dst = "pybind11";
   };
 
-  ccVersion = (builtins.parseDrvName stdenv.cc.name).version;
+  ccVersion = lib.getVersion stdenv.cc;
 in
 
 stdenv.mkDerivation rec {
diff --git a/pkgs/development/libraries/science/math/cudnn/default.nix b/pkgs/development/libraries/science/math/cudnn/default.nix
index a33e3ec2009..8cd74939959 100644
--- a/pkgs/development/libraries/science/math/cudnn/default.nix
+++ b/pkgs/development/libraries/science/math/cudnn/default.nix
@@ -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;
 }
diff --git a/pkgs/development/libraries/science/math/liblapack/default.nix b/pkgs/development/libraries/science/math/liblapack/default.nix
index 076376dc3c1..a7d01e22d96 100644
--- a/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -1,6 +1,6 @@
 {
   stdenv,
-  fetchurl,
+  fetchFromGitHub,
   gfortran,
   cmake,
   python2,
@@ -8,19 +8,22 @@
 }:
 let
   inherit (stdenv.lib) optional;
-  version = "3.8.0";
+  version = "3.9.0";
 in
 
 stdenv.mkDerivation {
   pname = "liblapack";
   inherit version;
-  src = fetchurl {
-    url = "http://www.netlib.org/lapack/lapack-${version}.tar.gz";
-    sha256 = "1xmwi2mqmipvg950gb0rhgprcps8gy8sjm8ic9rgy2qjlv22rcny";
+
+  src = fetchFromGitHub {
+    owner = "Reference-LAPACK";
+    repo = "lapack";
+    rev = "v${version}";
+    sha256 = "0sxnc97z67i7phdmcnq8f8lmxgw10wdwvr8ami0w3pb179cgrbpb";
   };
 
-  buildInputs = [ gfortran cmake ];
-  nativeBuildInputs = [ python2 ];
+  buildInputs = [ gfortran ];
+  nativeBuildInputs = [ python2 cmake ];
 
   cmakeFlags = [
     "-DCMAKE_Fortran_FLAGS=-fPIC"
diff --git a/pkgs/development/libraries/science/math/mkl/default.nix b/pkgs/development/libraries/science/math/mkl/default.nix
index c1a5ea2969e..382d2c303e3 100644
--- a/pkgs/development/libraries/science/math/mkl/default.nix
+++ b/pkgs/development/libraries/science/math/mkl/default.nix
@@ -46,6 +46,7 @@ in stdenvNoCC.mkDerivation {
       tar xzvf $f
     done
   '' else ''
+    rpmextract rpm/intel-mkl-cluster-rt-${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
diff --git a/pkgs/development/libraries/science/math/or-tools/default.nix b/pkgs/development/libraries/science/math/or-tools/default.nix
index 224f4239a22..15aea5803bf 100644
--- a/pkgs/development/libraries/science/math/or-tools/default.nix
+++ b/pkgs/development/libraries/science/math/or-tools/default.nix
@@ -69,7 +69,7 @@ stdenv.mkDerivation rec {
     description = ''
       Google's software suite for combinatorial optimization.
     '';
-    maintainers = with maintainers; [ fuuzetsu ];
+    maintainers = with maintainers; [ ];
     platforms = with platforms; linux;
   };
 }
diff --git a/pkgs/development/libraries/science/math/scalapack/default.nix b/pkgs/development/libraries/science/math/scalapack/default.nix
index 14277c8c631..bff0d9a85fa 100644
--- a/pkgs/development/libraries/science/math/scalapack/default.nix
+++ b/pkgs/development/libraries/science/math/scalapack/default.nix
@@ -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 ];
 
diff --git a/pkgs/development/libraries/science/math/scalapack/openmpi4.patch b/pkgs/development/libraries/science/math/scalapack/openmpi4.patch
deleted file mode 100644
index 5d0afb58c02..00000000000
--- a/pkgs/development/libraries/science/math/scalapack/openmpi4.patch
+++ /dev/null
@@ -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;