diff options
Diffstat (limited to 'nixpkgs/pkgs/development/libraries/science/math')
15 files changed, 88 insertions, 72 deletions
diff --git a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix index 36576de05631..89f3aa94247b 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix @@ -30,9 +30,9 @@ stdenv.mkDerivation { ]; preCheck = if stdenv.isDarwin then '' - export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:`pwd`/lib + export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH''${DYLD_LIBRARY_PATH:+:}`pwd`/lib '' else '' - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}`pwd`/lib '' + '' # Prevent tests from using all cores export OMP_NUM_THREADS=2 diff --git a/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix index 56a78b00cd64..4ffe147b27f2 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix @@ -8,14 +8,14 @@ }: stdenv.mkDerivation rec { - version = "1.2.6"; + version = "1.2.7"; pname = "brial"; src = fetchFromGitHub { owner = "BRiAl"; repo = "BRiAl"; rev = version; - sha256 = "1mc1zjr3mxcx6bg0js5k9jx65japg7644b0aj1al75m4nwh2ygab"; + sha256 = "1s0wmbb42sq6a5kxgzsz5srphclmfa4cvxdx2h9kzp0da2zcp3cm"; }; # FIXME package boost-test and enable checks diff --git a/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix index 8cd74939959d..765d634a91f9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/cudnn/default.nix +++ b/nixpkgs/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, cudatoolkit_10_1 }: +{ callPackage, cudatoolkit_7, cudatoolkit_7_5, cudatoolkit_8, cudatoolkit_9_0, cudatoolkit_9_1, cudatoolkit_9_2, cudatoolkit_10_0, cudatoolkit_10_1, cudatoolkit_10_2 }: let generic = args: callPackage (import ./generic.nix (removeAttrs args ["cudatoolkit"])) { @@ -72,5 +72,12 @@ in rec { sha256 = "0qc9f1xpyfibwqrpqxxq2v9h6w90j0dbx564akwy44c1dls5f99m"; }; + cudnn_cudatoolkit_10_2 = generic rec { + version = "7.6.5"; + cudatoolkit = cudatoolkit_10_2; + srcName = "cudnn-${cudatoolkit.majorVersion}-linux-x64-v7.6.5.32.tgz"; + sha256 = "084c13vzjdkb5s1996yilybg6dgav1lscjr1xdcgvlmfrbr6f0k0"; + }; + cudnn_cudatoolkit_10 = cudnn_cudatoolkit_10_1; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix index 77973a954494..2ba69a34a4a7 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "ecos"; - version = "2.0.6"; + version = "2.0.7"; src = fetchFromGitHub { owner = "embotech"; repo = "ecos"; - rev = "v${version}"; - sha256 = "11v958j66wq30gxpjpkgl7n3rvla845lygz8fl39pgf1vk9sdyc7"; + rev = version; + sha256 = "1hsndim5kjvcwk5svqa4igawzahj982180xj1d7yd0dbjlgxc7w7"; }; buildPhase = '' @@ -29,9 +29,10 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A lightweight conic solver for second-order cone programming"; - homepage = https://www.embotech.com/ECOS; + homepage = "https://www.embotech.com/ECOS"; + downloadPage = "https://github.com/embotech/ecos/releases"; license = licenses.gpl3; platforms = platforms.all; - maintainers = [ maintainers.bhipple ]; + maintainers = with maintainers; [ bhipple ]; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix index 50e0c576e696..e6c5cac77d29 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix @@ -4,14 +4,14 @@ }: stdenv.mkDerivation rec { - version = "20200115"; + version = "20200125"; pname = "m4ri"; src = fetchFromBitbucket { owner = "malb"; repo = "m4ri"; rev = "release-${version}"; - sha256 = "1c17casrw6dvwj067kfcgyjjajfisz56s30wjv7fwaw55mqrny19"; + sha256 = "1dxgbv6zdyki3h61qlv7003wzhy6x14zmcaz9x19md1i7ng07w1k"; }; doCheck = true; diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch b/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch new file mode 100644 index 000000000000..1da1f3fb3190 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/0001-Disable-optimised-aarch64-dgemm_beta-pending-fix.patch @@ -0,0 +1,26 @@ +From 6cb9aa7c69c20a677ca9fb1bc5fa1580e3236fbd Mon Sep 17 00:00:00 2001 +From: Tom Hall <tahall256@protonmail.ch> +Date: Sat, 14 Mar 2020 11:55:45 +0000 +Subject: [PATCH] Disable optimised aarch64 dgemm_beta pending fix + +Identified as source of https://github.com/xianyi/OpenBLAS/issues/2496, +but not yet fixed. +--- + kernel/arm64/KERNEL.ARMV8 | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/kernel/arm64/KERNEL.ARMV8 b/kernel/arm64/KERNEL.ARMV8 +index fe32d313..33d12f94 100644 +--- a/kernel/arm64/KERNEL.ARMV8 ++++ b/kernel/arm64/KERNEL.ARMV8 +@@ -102,7 +102,6 @@ CDOTKERNEL = zdot.S + ZDOTKERNEL = zdot.S + DSDOTKERNEL = dot.S + +-DGEMM_BETA = dgemm_beta.S + SGEMM_BETA = sgemm_beta.S + + SGEMMKERNEL = sgemm_kernel_$(SGEMM_UNROLL_M)x$(SGEMM_UNROLL_N).S +-- +2.24.1 + diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix index a26cf38a9d09..38ad31cc6257 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix @@ -88,12 +88,12 @@ let in stdenv.mkDerivation rec { pname = "openblas"; - version = "0.3.7"; + version = "0.3.8"; src = fetchFromGitHub { owner = "xianyi"; repo = "OpenBLAS"; rev = "v${version}"; - sha256 = "0vs1dlzyla02wajpkfzz8x3lfpgmwiaaizq2nmdjbkzkb7jnxhhz"; + sha256 = "0s017qqi4n6jzrxl9cyx625wj26smnyn5g8s699s7h8v1srlrw6p"; }; inherit blas64; @@ -123,6 +123,12 @@ 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/nixpkgs/pkgs/development/libraries/science/math/or-tools/build.patch b/nixpkgs/pkgs/development/libraries/science/math/or-tools/build.patch deleted file mode 100644 index a67e137ff4af..000000000000 --- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/build.patch +++ /dev/null @@ -1,5 +0,0 @@ ---- 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) | $(PYPI_ARCHIVE_TEMP_DIR)/ortools/ortools diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix index 15aea5803bf1..688d14256819 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix @@ -1,24 +1,22 @@ { stdenv, fetchFromGitHub, cmake, abseil-cpp, gflags, which -, lsb-release, glog, protobuf, cbc, zlib -, ensureNewerSourcesForZipFilesHook, python, swig -, pythonProtobuf }: +, lsb-release, glog, protobuf3_11, cbc, zlib +, ensureNewerSourcesForZipFilesHook, python, swig }: -stdenv.mkDerivation rec { +let + protobuf = protobuf3_11; + pythonProtobuf = python.pkgs.protobuf.override { inherit protobuf; }; + +in stdenv.mkDerivation rec { pname = "or-tools"; - version = "7.3"; + version = "7.5"; src = fetchFromGitHub { owner = "google"; repo = "or-tools"; rev = "v${version}"; - sha256 = "0q06vxmds6nm3dpjw4y5jzr8j98qgfb9i8pbm9pfhmqigv791hwc"; + sha256 = "1p9jwdwzcsaa58ap912hdf2w27vna3xl9g4lh6kjskddwi8l3wac"; }; - 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 @@ -69,7 +67,7 @@ stdenv.mkDerivation rec { description = '' Google's software suite for combinatorial optimization. ''; - maintainers = with maintainers; [ ]; + maintainers = with maintainers; [ andersk ]; platforms = with platforms; linux; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/protobuf.patch b/nixpkgs/pkgs/development/libraries/science/math/or-tools/protobuf.patch deleted file mode 100644 index b0cce40434c6..000000000000 --- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/protobuf.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- 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 diff --git a/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix index 6dc7e746fd35..b6f367ff4fe9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { pname = "osi"; - version = "0.108.4"; + version = "0.108.6"; src = fetchurl { url = "https://www.coin-or.org/download/source/Osi/Osi-${version}.tgz"; - sha256 = "13bwhdh01g37vp3kjwl9nvij5s5ikh5f7zgrqgwrqfyk35q2x9s5"; + sha256 = "1n2jlpq4aikbp0ncs16f7q1pj7yk6kny1bh4fmjaqnwrjw63zvsp"; }; buildInputs = diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix index c2eda9dac48b..492ad63f27b6 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix @@ -1,17 +1,12 @@ -{ stdenv -, fetchurl -, blas -, gfortran -, liblapack -, python }: +{ stdenv , fetchurl , blas , gfortran , liblapack , python }: stdenv.mkDerivation rec { pname = "petsc"; - version = "3.8.4"; + version = "3.12.4"; src = fetchurl { url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; - sha256 = "1iy49gagxncx09d88kxnwkj876p35683mpfk33x37165si6xqy4z"; + sha256 = "1hw4f12v2xwrs37gjh83dbixhg0yxandqx7s7k5vlfx91l9l3aan"; }; nativeBuildInputs = [ blas gfortran.cc.lib liblapack python ]; @@ -26,7 +21,7 @@ stdenv.mkDerivation rec { configureFlagsArray=( $configureFlagsArray "--CC=$CC" - "--with-cxx=0" + "--with-cxx=g++" "--with-fc=0" "--with-mpi=0" "--with-blas-lib=[${blas}/lib/libblas.a,${gfortran.cc.lib}/lib/libgfortran.a]" @@ -34,17 +29,14 @@ stdenv.mkDerivation rec { ) ''; - postInstall = '' - rm $out/bin/petscmpiexec - rm $out/bin/popup - rm $out/bin/uncrustify.cfg - rm -rf $out/bin/win32fe - ''; - - meta = { - description = "Library of linear algebra algorithms for solving partial differential equations"; - homepage = https://www.mcs.anl.gov/petsc/index.html; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.bsd2; + meta = with stdenv.lib; { + description = '' + Library of linear algebra algorithms for solving partial differential + equations + ''; + homepage = "https://www.mcs.anl.gov/petsc/index.html"; + license = licenses.bsd2; + maintainers = with maintainers; [ wucke13 ]; + platforms = platforms.all; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix index bff0d9a85fa2..a226dd2fc63d 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation rec { pname = "scalapack"; - version = "2.1"; + version = "2.1.0"; src = fetchFromGitHub { owner = "Reference-ScaLAPACK"; repo = pname; rev = "v${version}"; - sha256 = "042q9kc383h7y0had9a37702z4s0szavss063ljvfdsbjy07gzb1"; + sha256 = "1c10d18gj3kvpmyv5q246x35hjxaqn4ygy1cygaydhyxnm4klzdj"; }; nativeBuildInputs = [ cmake openssh ]; @@ -40,7 +40,7 @@ stdenv.mkDerivation rec { # Run single threaded export OMP_NUM_THREADS=1 - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}`pwd`/lib ''; meta = with stdenv.lib; { diff --git a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix index 51a72585c0cf..db808b093fee 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "scs"; - version = "2.0.2"; + version = "2.1.1"; src = fetchFromGitHub { owner = "cvxgrp"; repo = "scs"; - rev = "v${version}"; - sha256 = "17lbcmcsniqlyzgbzmjipfd0rrk25a8hzh7l5wl2wp1iwsd8c3a9"; + rev = version; + sha256 = "14g5m3lcvrbwpq1bq0liq00jh0gm1947lg3z4jfsp43f6p5alb20"; }; # Actually link and add libgfortran to the rpath @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { longDescription = '' Numerical optimization package for solving large-scale convex cone problems ''; - homepage = https://github.com/cvxgrp/scs; + homepage = "https://github.com/cvxgrp/scs"; license = licenses.mit; platforms = platforms.all; maintainers = [ maintainers.bhipple ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix index a6c803be260a..f72574cff583 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix @@ -56,6 +56,7 @@ stdenv.mkDerivation rec { # Build individual shared libraries make library \ + JOBS=$NIX_BUILD_CORES \ BLAS=-lopenblas \ LAPACK="" \ ${stdenv.lib.optionalString openblas.blas64 "CFLAGS=-DBLAS64"} @@ -64,7 +65,7 @@ stdenv.mkDerivation rec { # Bundling is done by building the static libraries, extracting objects from # them and combining the objects into one shared library. mkdir -p static - make static AR_TARGET=$(pwd)/static/'$(LIBRARY).a' + make static JOBS=$NIX_BUILD_CORES AR_TARGET=$(pwd)/static/'$(LIBRARY).a' ( cd static for i in lib*.a; do |