diff options
Diffstat (limited to 'infra/libkookie/nixpkgs/pkgs/development/libraries/science')
35 files changed, 197 insertions, 101 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix index 7ee63e9bb413..9da6595e7a43 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "htslib"; - version = "1.10.2"; + version = "1.11"; src = fetchurl { url = "https://github.com/samtools/htslib/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "0f8rglbvf4aaw41i2sxlpq7pvhly93sjqiz0l4q3hwki5zg47dg3"; + sha256 = "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"; }; # perl is only used during the check phase. diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix new file mode 100644 index 000000000000..7e73354363ea --- /dev/null +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix @@ -0,0 +1,49 @@ +{ lib +, mkDerivation +, fetchFromGitHub +, cmake +, csxcad +, tinyxml +, vtkWithQt5 +, qtbase +}: + +mkDerivation { + pname = "qcsxcad"; + version = "unstable-2020-01-04"; + + src = fetchFromGitHub { + owner = "thliebig"; + repo = "QCSXCAD"; + rev = "0dabbaf2bc1190adec300871cf309791af842c8e"; + sha256 = "11kbh0mxbdfh7s5azqin3i2alic5ihmdfj0jwgnrhlpjk4cbf9rn"; + }; + + outputs = [ "out" "dev" ]; + + nativeBuildInputs = [ + cmake + ]; + + cmakeFlags = [ + "-DCSXCAD_ROOT_DIR=${csxcad}" + "-DENABLE_RPATH=OFF" + ]; + + buildInputs = [ + csxcad + tinyxml + vtkWithQt5 + qtbase + ]; + + enableParallelBuilding = true; + + meta = with lib; { + description = "Qt library for CSXCAD"; + homepage = "https://github.com/thliebig/QCSXCAD"; + license = licenses.gpl3; + maintainers = with maintainers; [ matthuszagh ]; + platforms = platforms.linux; + }; +} diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix index 42ba4f25204e..3943c4dbbcaa 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix @@ -17,13 +17,13 @@ let blasIntSize = if blas64 then "64" else "32"; in stdenv.mkDerivation rec { pname = "blis"; - version = "0.7.0"; + version = "0.8.0"; src = fetchFromGitHub { owner = "flame"; repo = "blis"; rev = version; - sha256 = "13g9kg7x8j9icg4frdq3wpl2cmp0jnh93mw48daa7ym399w17423"; + sha256 = "0fp0nskydan3i7sj7qkabwc9sjh7mw73pjpgzh50qchkkcv0s3n1"; }; inherit blas64; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix index 90d7357cc07e..175de67ad7ee 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix @@ -8,14 +8,14 @@ }: stdenv.mkDerivation rec { - version = "1.2.8"; + version = "1.2.10"; pname = "brial"; src = fetchFromGitHub { owner = "BRiAl"; repo = "BRiAl"; rev = version; - sha256 = "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"; + sha256 = "1qg6ssp87rb8p37kahxmm88fbxqg6r540cky5v7wq7l19n2b1bss"; }; # FIXME package boost-test and enable checks @@ -40,7 +40,7 @@ stdenv.mkDerivation rec { homepage = "https://github.com/BRiAl/BRiAl"; description = "Legacy version of PolyBoRi maintained by sagemath developers"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix index e56952abcb28..7fe80c323f68 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { easy to use. ''; license = licenses.gpl2Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix index 9495366eaaa8..d99149c0e965 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix @@ -79,7 +79,7 @@ in rec { sha256 = "084c13vzjdkb5s1996yilybg6dgav1lscjr1xdcgvlmfrbr6f0k0"; }; - cudnn_cudatoolkit_10 = cudnn_cudatoolkit_10_1; + cudnn_cudatoolkit_10 = cudnn_cudatoolkit_10_2; cudnn_cudatoolkit_11_0 = generic rec { version = "8.0.2"; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix index 327fea3955d2..32fb70978cf9 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { homepage = "https://github.com/sagemath/FlintQS"; description = "Highly optimized multi-polynomial quadratic sieve for integer factorization"; license = with licenses; [ gpl2 ]; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.all; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix index 3f00547efcec..6f80e1fd23e0 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix @@ -91,7 +91,7 @@ stdenv.mkDerivation rec { homepage = "http://oto.math.uwaterloo.ca/~mrubinst/L_function_public/L.html"; description = "A program for calculating with L-functions"; license = with licenses; [ gpl2 ]; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.all; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix index 2c6bc4c8711e..36d4ad54c3df 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { A library to compute several properties of braids, including centralizer and conjugacy check. ''; license = licenses.gpl3; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.all; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix index d9b50a0fb2d1..788f534cc779 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { homepage = "https://github.com/miguelmarco/libhomfly/"; description = "Library to compute the homfly polynomial of knots and links"; license = licenses.unlicense; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.all; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix index 3ae462705868..7c78f61af694 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix @@ -12,9 +12,9 @@ }: let - version = "1.6.0"; + version = "1.7.0"; device = if cudaSupport then "cuda" else "cpu"; - srcs = import ./binary-hashes.nix; + srcs = import ./binary-hashes.nix version; unavailable = throw "libtorch is not available for this platform"; in stdenv.mkDerivation { inherit version; @@ -45,6 +45,14 @@ in stdenv.mkDerivation { # We do not care about Java support... rm -f $out/lib/lib*jni* 2> /dev/null || true + + # Fix up library paths for split outputs + substituteInPlace $dev/share/cmake/Torch/TorchConfig.cmake \ + --replace \''${TORCH_INSTALL_PREFIX}/lib "$out/lib" \ + + substituteInPlace \ + $dev/share/cmake/Caffe2/Caffe2Targets-release.cmake \ + --replace \''${_IMPORT_PREFIX}/lib "$out/lib" \ ''; postFixup = let @@ -100,7 +108,7 @@ in stdenv.mkDerivation { outputs = [ "out" "dev" ]; - passthru.tests = callPackage ./test { }; + passthru.tests.cmake = callPackage ./test { }; meta = with stdenv.lib; { description = "C++ API of the PyTorch machine learning framework"; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix index 92a2e05e0ba3..6048fe8676b7 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix @@ -1,14 +1,14 @@ -{ +version: { x86_64-darwin-cpu = { - url = "https://download.pytorch.org/libtorch/cpu/libtorch-macos-1.6.0.zip"; - sha256 = "0d4n7la31qzl4s9pwvm07la7q6lhcwiww0yjpfz3kw6nvx84p22r"; + url = "https://download.pytorch.org/libtorch/cpu/libtorch-macos-${version}.zip"; + sha256 = "1912lklil0i7i10j1fm4qzcq96cc8c281l9fn5gfbwa2wwry0r59"; }; x86_64-linux-cpu = { - url = "https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.6.0%2Bcpu.zip"; - sha256 = "1975b4zvyihzh89vnwspw0vf9qr05sxj8939vcrlmv3gzvdspcxz"; + url = "https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-${version}%2Bcpu.zip"; + sha256 = "0jdd7bjcy20xz2gfv8f61zdrbzxz5425bnqaaqgrwpzvd45ay8px"; }; x86_64-linux-cuda = { - url = "https://download.pytorch.org/libtorch/cu102/libtorch-cxx11-abi-shared-with-deps-1.6.0.zip"; - sha256 = "127qnfyi1faqbm40sbnsyqxjhrqj82bzwqyz7c1hs2bm0zgrrpya"; + url = "https://download.pytorch.org/libtorch/cu102/libtorch-cxx11-abi-shared-with-deps-${version}.zip"; + sha256 = "1ag6lvf3a400ivqq4g9cxpmxzlfrga0y5ssjy0rfpw6i1xljibn6"; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt index b302449ef772..4e96704a4c17 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt @@ -1,3 +1,4 @@ +cmake_minimum_required(VERSION 3.0) find_package(Torch REQUIRED) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") add_executable(test test.cpp) diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix index d661ec28db98..e69807871f46 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix @@ -6,16 +6,12 @@ stdenv.mkDerivation { src = ./.; - postPatch = '' - cat CMakeLists.txt - ''; - - makeFlags = [ "VERBOSE=1" ]; - nativeBuildInputs = [ cmake ]; buildInputs = [ libtorch-bin ]; + doCheck = true; + installPhase = '' touch $out ''; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp index 5537724ce5f6..ca238fba521d 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp @@ -1,7 +1,20 @@ -#include <torch/torch.h> +#undef NDEBUG +#include <cassert> + #include <iostream> +#include <torch/torch.h> + int main() { torch::Tensor tensor = torch::eye(3); - std::cout << tensor << std::endl; + + float checkData[] = { + 1, 0, 0, + 0, 1, 0, + 0, 0, 1 + }; + + torch::Tensor check = torch::from_blob(checkData, {3, 3}); + + assert(tensor.allclose(check)); } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix index d8b4cbbffb48..f50c15abbdf1 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { homepage = "https://malb.bitbucket.io/m4ri/"; description = "Library to do fast arithmetic with dense matrices over F_2"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix index e1f86b346d7f..532285991a3c 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { It uses the M4RI library, implementing the same operations over the finite field F2. ''; license = licenses.gpl2Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix index 2079ace021b6..b4ac119ce6cf 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix @@ -2,14 +2,14 @@ with stdenv.lib; -let version = "2.5.3"; +let version = "2.5.4"; in stdenv.mkDerivation { pname = "magma"; inherit version; src = fetchurl { url = "https://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-${version}.tar.gz"; - sha256 = "1xjy3irdx0w1zyhvn4x47zni5fwsh6z97xd4yqldz8zrm5lx40n6"; + sha256 = "0rrvd21hczxlm8awc9z54fj7iqpjmsb518fy32s6ghz0g90znd3p"; name = "magma-${version}.tar.gz"; }; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix index 2be3baed4497..1887d53e3066 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix @@ -1,4 +1,5 @@ -{ stdenvNoCC +{ callPackage +, stdenvNoCC , fetchurl , rpmextract , undmg @@ -19,12 +20,11 @@ let # Darwin is pinned to 2019.3 because the DMG does not unpack; see here for details: # https://github.com/matthewbauer/undmg/issues/4 year = if stdenvNoCC.isDarwin then "2019" else "2020"; - spot = if stdenvNoCC.isDarwin then "3" else "3"; - rel = if stdenvNoCC.isDarwin then "199" else "279"; + spot = if stdenvNoCC.isDarwin then "3" else "4"; + rel = if stdenvNoCC.isDarwin then "199" else "304"; - # Replace `openmpSpot` by `spot` after 2020.3. Release 2020.03 - # adresses performance regressions and does not update OpenMP. - openmpSpot = if stdenvNoCC.isDarwin then spot else "2"; + # Replace `openmpSpot` by `spot` after 2020. + openmpSpot = if stdenvNoCC.isDarwin then spot else "3"; rpm-ver = "${year}.${spot}-${rel}-${year}.${spot}-${rel}"; @@ -46,8 +46,8 @@ in stdenvNoCC.mkDerivation { }) else (fetchurl { - url = "https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16903/l_mkl_${version}.tgz"; - sha256 = "013shn3c823bjfssq4jyl3na5lbzj99s09ds608ljqllri7473ib"; + url = "https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/l_mkl_${version}.tgz"; + hash = "sha256-IxTUZTaXTb0I8qTk+emhVdx+eeJ5jHTn3fqtAKWRfqU="; }); nativeBuildInputs = [ validatePkgConfig ] ++ (if stdenvNoCC.isDarwin @@ -90,7 +90,8 @@ in stdenvNoCC.mkDerivation { substituteInPlace $f \ --replace "prefix=<INSTALLDIR>/mkl" "prefix=$out" \ --replace $\{MKLROOT} "$out" \ - --replace "lib/intel64_lin" "lib" + --replace "lib/intel64_lin" "lib" \ + --replace "lib/intel64" "lib" done for f in $(find opt/intel -name 'mkl*iomp.pc') ; do @@ -156,6 +157,8 @@ in stdenvNoCC.mkDerivation { dontStrip = true; dontPatchELF = true; + passthru.tests.pkg-config = callPackage ./test { }; + meta = with stdenvNoCC.lib; { description = "Intel Math Kernel Library"; longDescription = '' diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix new file mode 100644 index 000000000000..688c0ec7c399 --- /dev/null +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix @@ -0,0 +1,33 @@ +{ stdenv, pkg-config, mkl }: + +stdenv.mkDerivation { + pname = "mkl-test"; + version = mkl.version; + + src = ./.; + + nativeBuildInputs = [ pkg-config ]; + + buildInputs = [ mkl ]; + + doCheck = true; + + buildPhase = '' + # Check regular Nix build. + gcc $(pkg-config --cflags --libs mkl-dynamic-ilp64-seq) test.c -o test + + # Clear flags to ensure that we are purely relying on options + # provided by pkg-config. + NIX_CFLAGS_COMPILE="" \ + NIX_LDFLAGS="" \ + gcc $(pkg-config --cflags --libs mkl-dynamic-ilp64-seq) test.c -o test + ''; + + installPhase = '' + touch $out + ''; + + checkPhase = '' + ./test + ''; +} diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c new file mode 100644 index 000000000000..9413ac0c68e9 --- /dev/null +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c @@ -0,0 +1,12 @@ +#include <assert.h> + +#include <mkl_cblas.h> + +int main() { + float u[] = {1., 2., 3.}; + float v[] = {4., 5., 6.}; + + float dp = cblas_sdot(3, u, 1, v, 1); + + assert(dp == 32.); +} diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch deleted file mode 100644 index 1da1f3fb3190..000000000000 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch +++ /dev/null @@ -1,26 +0,0 @@ -From 6cb9aa7c69c20a677ca9fb1bc5fa1580e3236fbd Mon Sep 17 00:00:00 2001 -From: Tom Hall <tahall256@protonmail.ch> -Date: Sat, 14 Mar 2020 11:55:45 +0000 -Subject: [PATCH] Disable optimised aarch64 dgemm_beta pending fix - -Identified as source of https://github.com/xianyi/OpenBLAS/issues/2496, -but not yet fixed. ---- - kernel/arm64/KERNEL.ARMV8 | 1 - - 1 file changed, 1 deletion(-) - -diff --git a/kernel/arm64/KERNEL.ARMV8 b/kernel/arm64/KERNEL.ARMV8 -index fe32d313..33d12f94 100644 ---- a/kernel/arm64/KERNEL.ARMV8 -+++ b/kernel/arm64/KERNEL.ARMV8 -@@ -102,7 +102,6 @@ CDOTKERNEL = zdot.S - ZDOTKERNEL = zdot.S - DSDOTKERNEL = dot.S - --DGEMM_BETA = dgemm_beta.S - SGEMM_BETA = sgemm_beta.S - - SGEMMKERNEL = sgemm_kernel_$(SGEMM_UNROLL_M)x$(SGEMM_UNROLL_N).S --- -2.24.1 - diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix index b03e2b3a8ca8..d670a40f321d 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix @@ -106,7 +106,7 @@ let in stdenv.mkDerivation rec { pname = "openblas"; - version = "0.3.10"; + version = "0.3.12"; outputs = [ "out" "dev" ]; @@ -114,7 +114,7 @@ stdenv.mkDerivation rec { owner = "xianyi"; repo = "OpenBLAS"; rev = "v${version}"; - sha256 = "174id98ga82bhz2v7sy9yj6pqy0h0088p3mkdikip69p9rh3d17b"; + sha256 = "0mk1kjkr96bvvcq2zigzjrs0cnhwsf6gfi0855mp9yifn8lvp20y"; }; inherit blas64; @@ -144,12 +144,6 @@ stdenv.mkDerivation rec { buildPackages.stdenv.cc ]; - # Disable an optimisation which seems to cause issues, pending an - # upstream fix: https://github.com/xianyi/OpenBLAS/issues/2496 - patches = stdenv.lib.optionals stdenv.hostPlatform.isAarch64 [ - ./0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch - ]; - makeFlags = mkMakeFlagsFromConfig (config // { FC = "${stdenv.cc.targetPrefix}gfortran"; CC = "${stdenv.cc.targetPrefix}${if stdenv.cc.isClang then "clang" else "cc"}"; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix index 560f39e4e99a..17197823d6ef 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix @@ -2,17 +2,17 @@ stdenv.mkDerivation rec { pname = "openlibm"; - version = "0.7.1"; + version = "0.7.3"; src = fetchurl { url = "https://github.com/JuliaLang/openlibm/archive/v${version}.tar.gz"; - sha256 = "0yg8sfibr38hpb4s5ri7i0ivp96c7khdwhlxngjiymvl3jvm5cnl"; + sha256 = "0m3khv7qidhfly634bf5w0ci5qnvndmihc4a836a0cy047pw9g6k"; }; makeFlags = [ "prefix=$(out)" ]; meta = { description = "High quality system independent, portable, open source libm implementation"; - homepage = "https://www.openlibm.org/"; + homepage = "https://openlibm.org/"; license = stdenv.lib.licenses.mit; maintainers = [ stdenv.lib.maintainers.ttuegel ]; platforms = stdenv.lib.platforms.all; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix index 97023d07c7f3..8f24356c7336 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - description = "ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices"; + description = "An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices"; homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"; platforms = platforms.all; license = licenses.unfree; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix index 82a0d063570d..608064353ca7 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "petsc"; - version = "3.13.4"; + version = "3.14.1"; src = fetchurl { url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; - sha256 = "1n2paqw5c0ja392s1qhp7q2ypwav8s5drxxz2w5m2cn31vbspy1c"; + sha256 = "1y3fhg0l69qp9qn6vjyqdhqhhbvsa7jp8g7zcm0pwzm7gkcldqnx"; }; nativeBuildInputs = [ blas gfortran gfortran.cc.lib lapack python ]; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix index 7767e23934cf..b1d6a072e130 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { homepage = "https://github.com/graph-algorithms/edge-addition-planarity-suite"; description = "A library for implementing graph algorithms"; license = licenses.bsd3; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix index ded7b7dc90ac..53f4313a2069 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Calculates rank-width and rank-decompositions"; license = with licenses; [ gpl2Plus ]; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix index 6eeaddba0418..44f8150386e7 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix @@ -75,7 +75,7 @@ stdenv.mkDerivation rec { gpl2 # Michael Reid's and Eric Dietz software mit # Dik T. Winter's software ]; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix index 953f5a70b8aa..c55a1b8002e1 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix @@ -15,6 +15,10 @@ stdenv.mkDerivation rec { ./spooles.patch ]; + postPatch = stdenv.lib.optionalString stdenv.hostPlatform.isDarwin '' + substituteInPlace makefile --replace '-Wl,-soname' '-Wl,-install_name' + ''; + buildPhase = '' make lib ''; diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch index c0c93c9365c9..71fb4a7f44e1 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch @@ -166,7 +166,7 @@ index f014c7d..7c8042a 100755 #cd MPI ; make lib -#cd MT ; make lib + cd MT ; make lib -+ gcc -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lpthread -lm ++ $(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lpthread -lm + ln -s libspooles.so.2.2 libspooles.so global : diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix index d50e065efc61..2e76050aa989 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix @@ -4,14 +4,15 @@ , blas, lapack , metis , fixDarwinDylibNames -, gnum4 +, gmp +, mpfr , enableCuda ? false , cudatoolkit }: stdenv.mkDerivation rec { pname = "suitesparse"; - version = "5.7.2"; + version = "5.8.1"; outputs = [ "out" "dev" "doc" ]; @@ -19,17 +20,19 @@ stdenv.mkDerivation rec { owner = "DrTimothyAldenDavis"; repo = "SuiteSparse"; rev = "v${version}"; - sha256 = "1imndff7yygjrbbrcscsmirdi8w0lkwj5dbhydxmf7lklwn4j3q6"; + sha256 = "0qjlyfxs8s48rs63c2fzspisgq1kk4bwkgnhmh125hgkdhrq2w1c"; }; nativeBuildInputs = [ - gnum4 ] ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames; - buildInputs = [ + # Use compatible indexing for lapack and blas used + buildInputs = assert (blas.isILP64 == lapack.isILP64); [ blas lapack metis gfortran.cc.lib + gmp + mpfr ] ++ stdenv.lib.optional enableCuda cudatoolkit; preConfigure = '' @@ -41,8 +44,6 @@ stdenv.mkDerivation rec { "INSTALL=${placeholder "out"}" "INSTALL_INCLUDE=${placeholder "dev"}/include" "JOBS=$(NIX_BUILD_CORES)" - "BLAS=-lblas" - "LAPACK=-llapack" "MY_METIS_LIB=-lmetis" ] ++ stdenv.lib.optionals blas.isILP64 [ "CFLAGS=-DBLAS64" @@ -50,7 +51,13 @@ stdenv.mkDerivation rec { "CUDA_PATH=${cudatoolkit}" "CUDART_LIB=${cudatoolkit.lib}/lib/libcudart.so" "CUBLAS_LIB=${cudatoolkit}/lib/libcublas.so" - ]; + ] ++ stdenv.lib.optionals stdenv.isDarwin [ + # Unless these are set, the build will attempt to use `Accelerate` on darwin, see: + # https://github.com/DrTimothyAldenDavis/SuiteSparse/blob/v5.8.1/SuiteSparse_config/SuiteSparse_config.mk#L368 + "BLAS=-lblas" + "LAPACK=-llapack" + ] + ; buildFlags = [ # Build individual shared libraries, not demos diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix index ae7a7c778de0..a83e2c835461 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix @@ -68,7 +68,7 @@ stdenv.mkDerivation rec { fullName = "Custom, BSD-like. See COPYING file."; free = true; }; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.linux; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix index a94a52936e8f..0d1a331798cf 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix @@ -68,7 +68,7 @@ stdenv.mkDerivation rec { homepage = "http://web.maths.unsw.edu.au/~davidharvey/code/zn_poly/"; description = "Polynomial arithmetic over Z/nZ"; license = with licenses; [ gpl3 ]; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix index 73be2a8ca6c2..b611a2baf8e2 100644 --- a/infra/libkookie/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix @@ -26,7 +26,7 @@ # 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"] +, modules ? [ "core" "network" "internet" "point-to-point" "point-to-point-layout" "fd-net-device" "netanim" ] , lib }: @@ -38,13 +38,13 @@ let in stdenv.mkDerivation rec { pname = "ns-3"; - version = "30"; + version = "32"; src = fetchFromGitLab { owner = "nsnam"; repo = "ns-3-dev"; rev = "ns-3.${version}"; - sha256 = "0smdi3gglmafpc7a20hj2lbmwks3d5fpsicpn39lmm3svazw0bvp"; + sha256 = "158yjhsrmslj1q4zcq5p16hv9i82qnxx714l7idicncn0wzrfx7k"; }; nativeBuildInputs = [ wafHook ]; @@ -60,6 +60,8 @@ stdenv.mkDerivation rec { postPatch = '' patchShebangs doc/ns3_html_theme/get_version.sh + # FIX/Remove when https://github.com/NixOS/nixpkgs/pull/69310 gets merged + sed -i 's/program.ns3_module_dependencies.copy()/program.ns3_module_dependencies[:]/g' wscript ''; wafConfigureFlags = with stdenv.lib; [ |