diff options
Diffstat (limited to 'nixpkgs/pkgs/development/libraries/science')
136 files changed, 7500 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/darwin-rpath-universal.patch b/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/darwin-rpath-universal.patch new file mode 100644 index 000000000000..0ea3b55ef708 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/darwin-rpath-universal.patch @@ -0,0 +1,21 @@ +diff -ruN cfitsio/configure cfitsio-rpath-universal/configure +--- cfitsio/configure 2018-05-09 21:16:00.000000000 +0200 ++++ cfitsio-rpath-universal/configure 2021-10-27 12:02:25.000000000 +0200 +@@ -4829,16 +4829,7 @@ + SHLIB_SUFFIX=".dylib" + CFITSIO_SHLIB="lib\${PACKAGE}.\${CFITSIO_SONAME}.\${CFITSIO_MAJOR}.\${CFITSIO_MINOR}\${SHLIB_SUFFIX}" + CFITSIO_SHLIB_SONAME="lib\${PACKAGE}.\${CFITSIO_SONAME}\${SHLIB_SUFFIX}" +- case $host in +- *darwin[56789]*) +- SHLIB_LD="$CC -dynamiclib -install_name lib\${PACKAGE}.\${CFITSIO_SONAME}\${SHLIB_SUFFIX} -compatibility_version \${CFITSIO_SONAME} -current_version \${CFITSIO_SONAME}.\${CFITSIO_MAJOR}.\${CFITSIO_MINOR}.\${CFITSIO_MICRO}" +- ;; +- *) +- # Build 'Universal' binaries (i386 & x86_64 architectures) and +- # use rpath token on Darwin 10.x or newer: +- SHLIB_LD="$CC -dynamiclib $C_UNIV_SWITCH -headerpad_max_install_names -install_name @rpath/lib\${PACKAGE}.\${CFITSIO_SONAME}\${SHLIB_SUFFIX} -compatibility_version \${CFITSIO_SONAME} -current_version \${CFITSIO_SONAME}.\${CFITSIO_MAJOR}.\${CFITSIO_MINOR}.\${CFITSIO_MICRO}" +- ;; +- esac ++ SHLIB_LD="$CC -dynamiclib -install_name ${out}/lib/lib\${PACKAGE}.\${CFITSIO_SONAME}\${SHLIB_SUFFIX} -compatibility_version \${CFITSIO_SONAME} -current_version \${CFITSIO_SONAME}.\${CFITSIO_MAJOR}.\${CFITSIO_MINOR}" + + lhea_shlib_cflags="-fPIC -fno-common" + ;; diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/default.nix new file mode 100644 index 000000000000..65f7d61d0269 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/cfitsio/default.nix @@ -0,0 +1,59 @@ +{ stdenv +, lib +, fetchurl +, bzip2 +, curl +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "cfitsio"; + version = "4.4.0"; + + src = fetchurl { + url = "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-${finalAttrs.version}.tar.gz"; + hash = "sha256-lZAM+VrnYIOefLlninsvrQhY1qwSI0+TS9HLa/wka6k="; + }; + + patches = [ + ./darwin-rpath-universal.patch + ]; + + buildInputs = [ + bzip2 + curl + zlib + ]; + + configureFlags = [ + "--with-bzip2=${bzip2.out}" + "--enable-reentrant" + ]; + + hardeningDisable = [ "format" ]; + + # Shared-only build + buildFlags = [ "shared" ]; + + postPatch = '' + sed -e '/^install:/s/libcfitsio.a //' -e 's@/bin/@@g' -i Makefile.in + ''; + + meta = { + homepage = "https://heasarc.gsfc.nasa.gov/fitsio/"; + description = "Library for reading and writing FITS data files"; + longDescription = '' + CFITSIO is a library of C and Fortran subroutines for reading and + writing data files in FITS (Flexible Image Transport System) data + format. CFITSIO provides simple high-level routines for reading and + writing FITS files that insulate the programmer from the internal + complexities of the FITS format. CFITSIO also provides many + advanced features for manipulating and filtering the information in + FITS files. + ''; + changelog = "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/docs/changes.txt"; + license = lib.licenses.mit; + maintainers = with lib.maintainers; [ xbreak hjones2199 ]; + platforms = lib.platforms.linux ++ lib.platforms.darwin; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix new file mode 100644 index 000000000000..f0d25defe122 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix @@ -0,0 +1,87 @@ +{ stdenv +, lib +, fetchFromGitHub +, bash +, cmake +, cfitsio +, libusb1 +, kmod +, zlib +, boost +, libev +, libnova +, curl +, libjpeg +, gsl +, fftw +, gtest +, indi-full +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "indilib"; + version = "2.0.6"; + + src = fetchFromGitHub { + owner = "indilib"; + repo = "indi"; + rev = "v${finalAttrs.version}"; + hash = "sha256-3MeF2G/rr//c7cgGzqDzmqoNKvR+7Kkbid1g8znKPkg="; + }; + + nativeBuildInputs = [ + cmake + ]; + + buildInputs = [ + curl + cfitsio + libev + libusb1 + zlib + boost + libnova + libjpeg + gsl + fftw + ]; + + cmakeFlags = [ + "-DCMAKE_INSTALL_LIBDIR=lib" + "-DUDEVRULES_INSTALL_DIR=lib/udev/rules.d" + ] ++ lib.optional finalAttrs.finalPackage.doCheck [ + "-DINDI_BUILD_UNITTESTS=ON" + "-DINDI_BUILD_INTEGTESTS=ON" + ]; + + checkInputs = [ gtest ]; + + doCheck = true; + + # Socket address collisions between tests + enableParallelChecking = false; + + postFixup = lib.optionalString stdenv.isLinux '' + for f in $out/lib/udev/rules.d/*.rules + do + substituteInPlace $f --replace "/bin/sh" "${bash}/bin/sh" \ + --replace "/sbin/modprobe" "${kmod}/sbin/modprobe" + done + ''; + + passthru.tests = { + # make sure 3rd party drivers compile with this indilib + indi-full = indi-full.override { + indilib = finalAttrs.finalPackage; + }; + }; + + meta = with lib; { + homepage = "https://www.indilib.org/"; + description = "Implementation of the INDI protocol for POSIX operating systems"; + changelog = "https://github.com/indilib/indi/releases/tag/v${finalAttrs.version}"; + license = licenses.lgpl2Plus; + maintainers = with maintainers; [ hjones2199 sheepforce ]; + platforms = platforms.unix; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-3rdparty.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-3rdparty.nix new file mode 100644 index 000000000000..9dafb64e9292 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-3rdparty.nix @@ -0,0 +1,100 @@ +{ stdenv +, lib +, bash +, cmake +, coreutils +, cfitsio +, libusb1 +, zlib +, boost +, libnova +, curl +, libjpeg +, gsl +, fftw +, indilib +, libgphoto2 +, libraw +, libftdi1 +, libdc1394 +, gpsd +, ffmpeg +, limesuite +, pkg-config +, zeromq +, version +, src +, withFirmware ? false +, firmware ? null +}: + +let + libusb-with-fxload = libusb1.override { withExamples = true;}; +in + +stdenv.mkDerivation rec { + pname = "indi-3rdparty"; + + inherit version src; + + nativeBuildInputs = [ cmake pkg-config ]; + + buildInputs = [ + indilib libnova curl cfitsio libusb1 zlib boost gsl gpsd + libjpeg libgphoto2 libraw libftdi1 libdc1394 ffmpeg fftw + limesuite zeromq + ] ++ lib.optionals withFirmware [ + firmware + ]; + + postPatch = '' + for f in $(find . -name "CMakeLists.txt"); do + substituteInPlace $f \ + --replace "/lib/udev/rules.d" "lib/udev/rules.d" \ + --replace "/etc/udev/rules.d" "lib/udev/rules.d" \ + --replace "/lib/firmware" "lib/firmware" + done + + substituteInPlace libpktriggercord/CMakeLists.txt \ + --replace "set (PK_DATADIR /usr/share/pktriggercord)" "set (PK_DATADIR $out/share/pkgtriggercord)" + + sed '1i#include <ctime>' -i indi-duino/libfirmata/src/firmata.cpp # gcc12 + ''; + + cmakeFlags = [ + "-DINDI_DATA_DIR=share/indi" + "-DCMAKE_INSTALL_LIBDIR=lib" + "-DUDEVRULES_INSTALL_DIR=lib/udev/rules.d" + "-DRULES_INSTALL_DIR=lib/udev/rules.d" + ] ++ lib.optionals (!withFirmware) [ + "-DWITH_ATIK=off" + "-DWITH_APOGEE=off" + "-DWITH_DSI=off" + "-DWITH_QHY=off" + "-DWITH_ARMADILLO=off" + "-DWITH_FISHCAMP=off" + "-DWITH_SBIG=off" + ]; + + postFixup = lib.optionalString stdenv.isLinux '' + for f in $out/lib/udev/rules.d/*.rules + do + substituteInPlace $f --replace "/sbin/fxload" "${libusb-with-fxload}/sbin/fxload" \ + --replace "/lib/firmware/" "$out/lib/firmware/" \ + --replace "/bin/sleep" "${coreutils}/bin/sleep" \ + --replace "/bin/cat" "${coreutils}/bin/cat" \ + --replace "/bin/echo" "${coreutils}/bin/echo" \ + --replace "/bin/sh" "${bash}/bin/sh" + done + ''; + + + meta = with lib; { + homepage = "https://www.indilib.org/"; + description = "Third party drivers for the INDI astronomical software suite"; + changelog = "https://github.com/indilib/indi-3rdparty/releases/tag/v${version}"; + license = licenses.lgpl2Plus; + maintainers = with maintainers; [ hjones2199 sheepforce ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-firmware.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-firmware.nix new file mode 100644 index 000000000000..1eedfd3fea0b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-firmware.nix @@ -0,0 +1,82 @@ +{ stdenv +, lib +, bash +, cmake +, cfitsio +, coreutils +, libusb1 +, zlib +, boost +, libnova +, curl +, libjpeg +, gsl +, fftw +, indilib +, libgphoto2 +, libraw +, libftdi1 +, libdc1394 +, gpsd +, ffmpeg +, version +, src +, autoPatchelfHook +}: +let + libusb-with-fxload = libusb1.override { withExamples = true;}; +in +stdenv.mkDerivation rec { + pname = "indi-firmware"; + + inherit version src; + + nativeBuildInputs = [ cmake autoPatchelfHook ]; + + buildInputs = [ + indilib libnova curl cfitsio libusb1 zlib boost gsl gpsd + libjpeg libgphoto2 libraw libftdi1 libdc1394 ffmpeg fftw + ]; + + cmakeFlags = [ + "-DINDI_DATA_DIR=\${CMAKE_INSTALL_PREFIX}/share/indi" + "-DCMAKE_INSTALL_LIBDIR=lib" + "-DUDEVRULES_INSTALL_DIR=lib/udev/rules.d" + "-DRULES_INSTALL_DIR=lib/udev/rules.d" + "-DFIRMWARE_INSTALL_DIR=lib/firmware" + "-DQHY_FIRMWARE_INSTALL_DIR=\${CMAKE_INSTALL_PREFIX}/lib/firmware/qhy" + "-DCONF_DIR=etc" + "-DBUILD_LIBS=1" + "-DWITH_PENTAX=off" + "-DWITH_AHP_XC=off" + ]; + + postPatch = '' + for f in {libfishcamp,libsbig,libqhy}/CMakeLists.txt + do + substituteInPlace $f --replace "/lib/firmware" "lib/firmware" + done + ''; + + postFixup = lib.optionalString stdenv.isLinux '' + for f in $out/lib/udev/rules.d/*.rules + do + substituteInPlace "$f" --replace "/sbin/fxload" "${libusb-with-fxload}/sbin/fxload" \ + --replace "/bin/sleep" "${coreutils}/bin/sleep" \ + --replace "/bin/cat" "${coreutils}/bin/cat" \ + --replace "/bin/echo" "${coreutils}/bin/echo" \ + --replace "/bin/sh" "${bash}/bin/sh" \ + --replace "/lib/firmware/" "$out/lib/firmware/" + sed -e 's|-D $env{DEVNAME}|-p $env{BUSNUM},$env{DEVNUM}|' -i "$f" + done + ''; + + meta = with lib; { + homepage = "https://www.indilib.org/"; + description = "Third party firmware for the INDI astronomical software suite"; + changelog = "https://github.com/indilib/indi-3rdparty/releases/tag/v${version}"; + license = licenses.lgpl2Plus; + maintainers = with maintainers; [ hjones2199 sheepforce ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix new file mode 100644 index 000000000000..4dd80c3f0275 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix @@ -0,0 +1,29 @@ +{ stdenv, lib, callPackage, fetchFromGitHub, indilib }: + +let + inherit (indilib) version; + indi-3rdparty-src = fetchFromGitHub { + owner = "indilib"; + repo = "indi-3rdparty"; + rev = "v${version}"; + hash = "sha256-KNoyYldZWsXB9ubu0EYDgckRtpQgSCmzKlx7Erx4MRQ="; + }; + indi-firmware = callPackage ./indi-firmware.nix { + inherit version; + src = indi-3rdparty-src; + }; + indi-3rdparty = callPackage ./indi-3rdparty.nix { + inherit version; + src = indi-3rdparty-src; + withFirmware = stdenv.isx86_64 || stdenv.isAarch64; + firmware = indi-firmware; + }; +in +callPackage ./indi-with-drivers.nix { + pname = "indi-full"; + inherit version; + extraDrivers = [ + indi-3rdparty + ] ++ lib.optional (stdenv.isx86_64 || stdenv.isAarch64) indi-firmware + ; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-with-drivers.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-with-drivers.nix new file mode 100644 index 000000000000..f1201df1d8a0 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-with-drivers.nix @@ -0,0 +1,18 @@ +{ buildEnv, makeBinaryWrapper, indilib ? indilib, pname ? "indi-with-drivers", version ? null, extraDrivers ? null }: + +buildEnv { + name = "${pname}-${version}"; + paths = [ + indilib + ] + ++ extraDrivers; + + nativeBuildInputs = [ makeBinaryWrapper ]; + + postBuild = '' + makeBinaryWrapper ${indilib}/bin/indiserver $out/bin/indiserver --set-default INDIPREFIX $out + ''; + + + inherit (indilib) meta; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/libnova/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/libnova/default.nix new file mode 100644 index 000000000000..f6a8d01ab845 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/libnova/default.nix @@ -0,0 +1,25 @@ +{ lib, stdenv, fetchgit, autoreconfHook }: + +stdenv.mkDerivation rec { + pname = "libnova"; + version = "0.16"; + + # pull from git repo because upstream stopped tarball releases after v0.15 + src = fetchgit { + url = "https://git.code.sf.net/p/libnova/${pname}"; + rev = "v${version}"; + sha256 = "0icwylwkixihzni0kgl0j8dx3qhqvym6zv2hkw2dy6v9zvysrb1b"; + }; + + nativeBuildInputs = [ + autoreconfHook + ]; + + meta = with lib; { + description = "Celestial Mechanics, Astrometry and Astrodynamics Library"; + homepage = "http://libnova.sf.net"; + license = licenses.gpl2; + maintainers = with maintainers; [ hjones2199 ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/0001-Fix-pkg-config-paths.patch b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/0001-Fix-pkg-config-paths.patch new file mode 100644 index 000000000000..c26a2bbc8814 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/0001-Fix-pkg-config-paths.patch @@ -0,0 +1,23 @@ +From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001 +From: Nicolas Benes <nbenes.gh@xandea.de> +Date: Mon, 22 May 2023 09:25:27 +0200 +Subject: [PATCH] Fix pkg-config paths + + +diff --git a/libxisf.pc.in b/libxisf.pc.in +index b0b8b53..944b068 100644 +--- a/libxisf.pc.in ++++ b/libxisf.pc.in +@@ -1,7 +1,7 @@ + prefix="@CMAKE_INSTALL_PREFIX@" + exec_prefix="${prefix}" +-libdir="${exec_prefix}/@CMAKE_INSTALL_LIBDIR@" +-includedir="${prefix}/@CMAKE_INSTALL_INCLUDEDIR@" ++libdir="@CMAKE_INSTALL_FULL_LIBDIR@" ++includedir="@CMAKE_INSTALL_FULL_INCLUDEDIR@" + + Name: @PROJECT_NAME@ + Description: @CMAKE_PROJECT_DESCRIPTION@ +-- +2.38.5 + diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix new file mode 100644 index 000000000000..19fb83ca78be --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix @@ -0,0 +1,53 @@ +{ lib +, stdenv +, fetchFromGitea +, cmake +, pkg-config +, lz4 +, pugixml +, zlib +, zstd +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "libxisf"; + version = "0.2.11"; + + src = fetchFromGitea { + domain = "gitea.nouspiro.space"; + owner = "nou"; + repo = "libXISF"; + rev = "v${finalAttrs.version}"; + hash = "sha256-wXIbU9/xUyECluL6k1oKS3NBpoC/qjQdW9e485qmlgo="; + }; + + patches = [ + ./0001-Fix-pkg-config-paths.patch + ]; + + nativeBuildInputs = [ + cmake + pkg-config + ]; + + cmakeFlags = [ + "-DUSE_BUNDLED_LIBS=OFF" + ] ++ lib.optional stdenv.hostPlatform.isStatic "-DBUILD_SHARED_LIBS=OFF"; + + buildInputs = [ + lz4 + pugixml + zlib + zstd + ]; + + doCheck = true; + + meta = with lib; { + description = "Library to load and write XISF format from PixInsight"; + homepage = "https://gitea.nouspiro.space/nou/libXISF"; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ panicgh ]; + platforms = platforms.linux; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/stellarsolver/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/stellarsolver/default.nix new file mode 100644 index 000000000000..8c6eb60d1d2b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/stellarsolver/default.nix @@ -0,0 +1,30 @@ +{ lib, mkDerivation, fetchFromGitHub, cmake, + qtbase, cfitsio, gsl, wcslib, withTester ? false }: + +mkDerivation rec { + pname = "stellarsolver"; + version = "2.5"; + + src = fetchFromGitHub { + owner = "rlancaste"; + repo = pname; + rev = version; + sha256 = "sha256-0bFGHlkZnAZlnxlj8tY3s9yTWgkNtSsPFfudB3uvyOA="; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ qtbase cfitsio gsl wcslib ]; + + cmakeFlags = [ + "-DBUILD_TESTER=${if withTester then "on" else "off"}" + ]; + + meta = with lib; { + homepage = "https://github.com/rlancaste/stellarsolver"; + description = "Astrometric plate solving library"; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ hjones2199 ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix new file mode 100644 index 000000000000..a2bcdfdb7c34 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv, fetchurl, flex }: + +stdenv.mkDerivation rec { + pname = "wcslib"; + version = "8.2.2"; + + src = fetchurl { + url = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/${pname}-${version}.tar.bz2"; + sha256 = "sha256-YpgiCugX9OVSJkOsTD2iYjvnCjSEsaTzcGC+4+S9eDM="; + }; + + nativeBuildInputs = [ flex ]; + + enableParallelBuilding = true; + + outputs = [ "out" "man" ]; + + meta = with lib; { + homepage = "https://www.atnf.csiro.au/people/mcalabre/WCS/"; + description = "World Coordinate System library for astronomy"; + longDescription = '' + Library for world coordinate systems for spherical geometries + and their conversion to image coordinate systems. This is the + standard library for this purpose in astronomy. + ''; + maintainers = with maintainers; [ hjones2199 ]; + license = licenses.lgpl3Plus; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix b/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix new file mode 100644 index 000000000000..7e022bafbb40 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix @@ -0,0 +1,28 @@ +{ lib, stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + version = "7.0.1"; + pname = "papi"; + + src = fetchurl { + url = "https://bitbucket.org/icl/papi/get/papi-${lib.replaceStrings ["."] ["-"] version}-t.tar.gz"; + sha256 = "sha256-VajhmPW8sEJksfhLjBVlpBH7+AZr4fwKZPAtZxRF1Bk="; + }; + + setSourceRoot = '' + sourceRoot=$(echo */src) + ''; + + doCheck = true; + checkTarget = "test"; + + meta = with lib; { + homepage = "https://icl.utk.edu/papi/"; + description = "Library providing access to various hardware performance counters"; + license = licenses.bsdOriginal; + platforms = platforms.linux; + maintainers = with maintainers; [ costrouc zhaofengli ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix new file mode 100644 index 000000000000..4f98874b2595 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix @@ -0,0 +1,33 @@ +{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu, GLUT }: + +stdenv.mkDerivation rec { + pname = "bicgl"; + version = "unstable-2018-04-06"; + + owner = "BIC-MNI"; + + src = fetchFromGitHub { + inherit owner; + repo = pname; + rev = "61a035751c9244fcca1edf94d6566fa2a709ce90"; + sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc bicpl mesa_glu ] + ++ lib.optionals stdenv.isDarwin [ GLUT ] + ++ lib.optionals stdenv.isLinux [ freeglut ]; + + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DBICPL_DIR=${bicpl}/lib" + ]; + + meta = with lib; { + homepage = "https://github.com/${owner}/${pname}"; + description = "Brain Imaging Centre graphics library"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix new file mode 100644 index 000000000000..5cf63e342242 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv, fetchFromGitHub, cmake, libminc, netpbm }: + +stdenv.mkDerivation rec { + pname = "bicpl"; + version = "unstable-2020-10-15"; + + # current master is significantly ahead of most recent release, so use Git version: + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "a58af912a71a4c62014975b89ef37a8e72de3c9d"; + sha256 = "0iw0pmr8xrifbx5l8a0xidfqbm1v8hwzqrw0lcmimxlzdihyri0g"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc netpbm ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ]; + + doCheck = false; + # internal_volume_io.h: No such file or directory + + meta = with lib; { + homepage = "https://github.com/BIC-MNI/bicpl"; + description = "Brain Imaging Centre programming library"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix new file mode 100644 index 000000000000..0d0e3c114920 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix @@ -0,0 +1,39 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake }: + +stdenv.mkDerivation rec { + pname = "bpp-core"; + version = "2.4.1"; + + src = fetchFromGitHub { owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"; + }; + + patches = [ + (fetchpatch { + url = "https://github.com/BioPP/bpp-core/commit/d450e8033b06e80dff9c2236fb7ce1f3ced5dcbb.patch"; + hash = "sha256-9t68mrK7KNs5BxljKMaA+XskCcKDNv8DNCVUYunoNdw="; + }) + ]; + + nativeBuildInputs = [ cmake ]; + + postFixup = '' + substituteInPlace $out/lib/cmake/bpp-core/bpp-core-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = with lib; { + homepage = "https://github.com/BioPP/bpp-core"; + changelog = "https://github.com/BioPP/bpp-core/blob/master/ChangeLog"; + description = "C++ bioinformatics libraries and tools"; + maintainers = with maintainers; [ bcdarwin ]; + license = licenses.cecill20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix new file mode 100644 index 000000000000..0b18dbfcf19a --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-phyl"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + homepage = "https://github.com/BioPP/bpp-phyl"; + changelog = "https://github.com/BioPP/bpp-phyl/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix new file mode 100644 index 000000000000..2cb89b4bbd38 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-popgen"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + homepage = "https://github.com/BioPP/bpp-popgen"; + changelog = "https://github.com/BioPP/bpp-popgen/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix new file mode 100644 index 000000000000..2f6fbf9e362c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core }: + +stdenv.mkDerivation rec { + pname = "bpp-seq"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core ]; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + homepage = "https://github.com/BioPP/bpp-seq"; + changelog = "https://github.com/BioPP/bpp-seq/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/ciftilib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/ciftilib/default.nix new file mode 100644 index 000000000000..85b0b1c8a0e5 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/ciftilib/default.nix @@ -0,0 +1,39 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, boost +, libxmlxx +, pkg-config +, zlib +}: + +stdenv.mkDerivation rec { + pname = "ciftilib"; + version = "1.6.0"; + + src = fetchFromGitHub { + owner = "Washington-University"; + repo = "CiftiLib"; + rev = "v${version}"; + hash = "sha256-xc2dpMse4SozYEV/w3rXCrh1LKpTThq5nHB2y5uAD0A="; + }; + + nativeBuildInputs = [ cmake pkg-config ]; + buildInputs = [ boost libxmlxx zlib ]; + + cmakeFlags = [ "-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;'big|datatype-md5'" ]; + + # error: no member named 'file_string' in 'boost::filesystem::path' + env.NIX_CFLAGS_COMPILE = "-UCIFTILIB_BOOST_NO_FSV3"; + + doCheck = true; + + meta = with lib; { + homepage = "https://github.com/Washington-University/CiftiLib"; + description = "Library for reading and writing CIFTI files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.bsd2; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/edlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/edlib/default.nix new file mode 100644 index 000000000000..b8ea4a55291a --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/edlib/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv, fetchFromGitHub, cmake }: + +stdenv.mkDerivation rec { + pname = "edlib"; + version = "unstable-2021-08-20"; + + src = fetchFromGitHub { + owner = "Martinsos"; + repo = pname; + rev = "f8afceb49ab0095c852e0b8b488ae2c88e566afd"; + hash = "sha256-P/tFbvPBtA0MYCNDabW+Ypo3ltwP4S+6lRDxwAZ1JFo="; + }; + + nativeBuildInputs = [ cmake ]; + + doCheck = true; + checkPhase = '' + runHook preCheck + bin/runTests + runHook postCheck + ''; + + meta = with lib; { + homepage = "https://martinsos.github.io/edlib"; + description = "Lightweight, fast C/C++ library for sequence alignment using edit distance"; + maintainers = with maintainers; [ bcdarwin ]; + license = licenses.mit; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix new file mode 100644 index 000000000000..0344559f8a8f --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix @@ -0,0 +1,26 @@ +{ lib, stdenv, fetchFromGitHub, cmake, itk, Cocoa }: + +stdenv.mkDerivation rec { + pname = "elastix"; + version = "5.1.0"; + + src = fetchFromGitHub { + owner = "SuperElastix"; + repo = pname; + rev = version; + hash = "sha256-wFeLU8IwiF43a9TAvecQG+QMw88PQZdJ8sI1Zz3ZeXc="; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ itk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; + + doCheck = !stdenv.isDarwin; # usual dynamic linker issues + + meta = with lib; { + homepage = "https://elastix.lumc.nl"; + description = "Image registration toolkit based on ITK"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.x86_64; # libitkpng linker issues with ITK 5.1 + license = licenses.asl20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix new file mode 100644 index 000000000000..306324129cbd --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix @@ -0,0 +1,34 @@ +{ lib, stdenv, fetchFromGitHub, cmake, expat, nifticlib, zlib }: + +stdenv.mkDerivation rec { + pname = "gifticlib"; + version = "unstable-2020-07-07"; + + src = fetchFromGitHub { + owner = "NIFTI-Imaging"; + repo = "gifti_clib"; + rev = "5eae81ba1e87ef3553df3b6ba585f12dc81a0030"; + sha256 = "0gcab06gm0irjnlrkpszzd4wr8z0fi7gx8f7966gywdp2jlxzw19"; + }; + + cmakeFlags = [ "-DUSE_SYSTEM_NIFTI=ON" "-DDOWNLOAD_TEST_DATA=OFF" ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ expat nifticlib zlib ]; + + # without the test data, this is only a few basic tests + doCheck = !stdenv.isDarwin; + checkPhase = '' + runHook preCheck + ctest -LE 'NEEDS_DATA' + runHook postCheck + ''; + + meta = with lib; { + homepage = "https://www.nitrc.org/projects/gifti"; + description = "Medical imaging geometry format C API"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.publicDomain; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix new file mode 100644 index 000000000000..8b1aa7d01e81 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix @@ -0,0 +1,52 @@ +{ lib, stdenv, fetchurl, zlib, bzip2, xz, curl, perl }: + +stdenv.mkDerivation rec { + pname = "htslib"; + version = "1.19.1"; + + src = fetchurl { + url = "https://github.com/samtools/htslib/releases/download/${version}/${pname}-${version}.tar.bz2"; + sha256 = "sha256-Ii1001dPtnsVjGmIyYDuqrqKBlb15P+3a1+lfwNZM+w="; + }; + + # perl is only used during the check phase. + nativeBuildInputs = [ perl ]; + + buildInputs = [ zlib bzip2 xz curl ]; + + configureFlags = if ! stdenv.hostPlatform.isStatic + then [ "--enable-libcurl" ] # optional but strongly recommended + else [ "--disable-libcurl" "--disable-plugins" ]; + + + # In the case of static builds, we need to replace the build and install phases + buildPhase = lib.optional stdenv.hostPlatform.isStatic '' + make AR=$AR lib-static + make LDFLAGS=-static bgzip htsfile tabix + ''; + + installPhase = lib.optional stdenv.hostPlatform.isStatic '' + install -d $out/bin + install -d $out/lib + install -d $out/include/htslib + install -D libhts.a $out/lib + install -m644 htslib/*h $out/include/htslib + install -D bgzip htsfile tabix $out/bin + ''; + + preCheck = '' + patchShebangs test/ + ''; + + enableParallelBuilding = true; + + doCheck = true; + + meta = with lib; { + description = "A C library for reading/writing high-throughput sequencing data"; + license = licenses.mit; + homepage = "http://www.htslib.org/"; + platforms = platforms.unix; + maintainers = [ maintainers.mimame ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix new file mode 100644 index 000000000000..9af6793ef997 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix @@ -0,0 +1,72 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, python3 +, boost +, eigen +, libGLU +, fltk +, itk +, vtk +, zlib +, tbb +}: + +stdenv.mkDerivation rec { + pname = "mirtk"; + version = "unstable-2022-07-22"; + + src = fetchFromGitHub { + owner = "BioMedIA"; + repo = "MIRTK"; + rev = "973ce2fe3f9508dec68892dbf97cca39067aa3d6"; + hash = "sha256-vKgkDrbyGOcbaYlxys1duC8ZNG0Y2nqh3TtSQ06Ox0Q="; + fetchSubmodules = true; + }; + + cmakeFlags = [ + "-DWITH_VTK=ON" + "-DBUILD_ALL_MODULES=ON" + "-DWITH_TBB=ON" + "-DWITH_ITK=ON" + "-DWITH_GIFTICLIB=ON" + "-DWITH_NIFTILIB=ON" + ]; + + # tries to download data during configuration + postPatch = '' + substituteInPlace Packages/DrawEM/CMakeLists.txt --replace "include(Atlases.cmake)" "" + ''; + + # tests don't seem to be maintained and gtest fails to link with BUILD_TESTING=ON; + # unclear if specific to Nixpkgs + doCheck = false; + + postInstall = '' + install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk + ''; + + env.NIX_CFLAGS_COMPILE = "-Wno-changes-meaning"; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ + boost + eigen + fltk + itk + libGLU.dev + python3 + tbb + vtk + zlib + ]; + + meta = with lib; { + homepage = "https://github.com/BioMedIA/MIRTK"; + description = "Medical image registration library and tools"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.linux; + license = licenses.asl20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix new file mode 100644 index 000000000000..fee2ea8772b4 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix @@ -0,0 +1,33 @@ +{ lib, stdenv, fetchFromGitHub, cmake, zlib }: + +stdenv.mkDerivation rec { + pname = "nifticlib"; + version = "3.0.1"; + + src = fetchFromGitHub { + owner = "NIFTI-Imaging"; + repo = "nifti_clib"; + rev = "v${version}"; + sha256 = "0hamm6nvbjdjjd5md4jahzvn5559frigxaiybnjkh59ckxwb1hy4"; + }; + + cmakeFlags = [ "-DDOWNLOAD_TEST_DATA=OFF" ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib ]; + + checkPhase = '' + runHook preCheck + ctest -LE 'NEEDS_DATA' + runHook postCheck + ''; + doCheck = true; + + meta = with lib; { + homepage = "https://nifti-imaging.github.io"; + description = "Medical imaging format C API"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.publicDomain; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix new file mode 100644 index 000000000000..7f1112311d6b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix @@ -0,0 +1,39 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, libminc +, bicpl +, arguments +, pcre-cpp }: + +stdenv.mkDerivation rec { + pname = "oobicpl"; + version = "unstable-2020-08-12"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "a9409da8a5bb4925438f32aff577b6333faec28b"; + sha256 = "0b4chjhr32wbb1sash8cq1jfnr7rzdq84hif8anlrjqd3l0gw357"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ libminc bicpl arguments pcre-cpp ]; + + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DBICPL_DIR=${bicpl}/lib" + "-DARGUMENTS_DIR=${arguments}/lib" + "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" + ]; + + meta = with lib; { + homepage = "https://github.com/BIC-MNI/oobicpl"; + description = "Brain Imaging Centre object-oriented programming library (and tools)"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix new file mode 100644 index 000000000000..e50bde243e85 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix @@ -0,0 +1,89 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib, eigen, libGL, doxygen, spglib +, mmtf-cpp, glew, python3, libarchive, libmsym, msgpack, qttools, wrapQtAppsHook +}: + +let + pythonWP = python3.withPackages (p: with p; [ openbabel-bindings numpy ]); + + # Pure data repositories + moleculesRepo = fetchFromGitHub { + owner = "OpenChemistry"; + repo = "molecules"; + rev = "1.0.0"; + sha256 = "guY6osnpv7Oqt+HE1BpIqL10POp+x8GAci2kY0bLmqg="; + }; + crystalsRepo = fetchFromGitHub { + owner = "OpenChemistry"; + repo = "crystals"; + rev = "1.0.1"; + sha256 = "sH/WuvLaYu6akOc3ssAKhnxD8KNoDxuafDSozHqJZC4="; + }; + fragmentsRepo = fetchFromGitHub { + owner = "OpenChemistry"; + repo = "fragments"; + rev = "8dc711a59d016604b3e9b6d59dec178b8e6ccd36"; + hash = "sha256-Valc5zwlaZ//eDupFouCfWCeID7/4ObU1SDLFJ/mo/g="; + }; + +in stdenv.mkDerivation rec { + pname = "avogadrolibs"; + version = "1.99.0"; + + src = fetchFromGitHub { + owner = "OpenChemistry"; + repo = pname; + rev = version; + hash = "sha256-3jUbzEd7tUeHlVFAO9KJ+LOQlkLzJQvwmHp8gOriZRI="; + }; + + postUnpack = '' + cp -r ${moleculesRepo} molecules + cp -r ${crystalsRepo} crystals + cp -r ${fragmentsRepo} fragments + ''; + + patches = [ + # Fix a Cmake error when searching the fragments directory. + # Can be removed upon next release + (fetchpatch { + url = "https://github.com/OpenChemistry/avogadrolibs/commit/6e2e84dbb088a40d69117c1836f4306792f57acd.patch"; + hash = "sha256-0tY9kHh6e5IDZQ8cWPgTpwIBhfZQlgUEZbPHOmtOVUQ="; + }) + ]; + + nativeBuildInputs = [ + cmake + wrapQtAppsHook + pythonWP + ]; + + buildInputs = [ + eigen + zlib + libGL + spglib + mmtf-cpp + glew + libarchive + libmsym + msgpack + qttools + ]; + + # Fix the broken CMake files to use the correct paths + postInstall = '' + substituteInPlace $out/lib/cmake/${pname}/AvogadroLibsConfig.cmake \ + --replace "$out/" "" + + substituteInPlace $out/lib/cmake/${pname}/AvogadroLibsTargets.cmake \ + --replace "_IMPORT_PREFIX}/$out" "_IMPORT_PREFIX}/" + ''; + + meta = with lib; { + description = "Molecule editor and visualizer"; + maintainers = with maintainers; [ sheepforce ]; + homepage = "https://github.com/OpenChemistry/avogadrolibs"; + platforms = platforms.linux; + license = licenses.gpl2Only; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/fragments.patch b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/fragments.patch new file mode 100644 index 000000000000..0f886a8a63a5 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/avogadrolibs/fragments.patch @@ -0,0 +1,13 @@ +diff --git a/avogadro/qtplugins/templatetool/CMakeLists.txt b/avogadro/qtplugins/templatetool/CMakeLists.txt +index 3f68e6dd..822de4e5 100644 +--- a/avogadro/qtplugins/templatetool/CMakeLists.txt ++++ b/avogadro/qtplugins/templatetool/CMakeLists.txt +@@ -24,7 +24,7 @@ avogadro_plugin(TemplateTool + ) + + # Install the fragments +-set(_fragments "${AvogadroLibs_SOURCE_DIR}/../fragments") ++set(_fragments "${AvogadroLibs_SOURCE_DIR}/fragments") + + # Look in parallel directory for the molecule fragment repository + if(NOT EXISTS "${_fragments}") diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/cppe/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/cppe/default.nix new file mode 100644 index 000000000000..9781ce780660 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/cppe/default.nix @@ -0,0 +1,26 @@ +{ stdenv, lib, fetchFromGitHub, cmake, llvmPackages }: + +stdenv.mkDerivation rec { + pname = "cppe"; + version = "0.3.1"; + + src = fetchFromGitHub { + owner = "maxscheurer"; + repo = pname; + rev = "v${version}"; + sha256 = "sha256-guM7+ZWDJLcAUJtPkKLvC4LYSA2eBvER7cgwPZ7FxHw="; + }; + + nativeBuildInputs = [ cmake ] + ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ]; + + cmakeFlags = [ "-DCMAKE_INSTALL_LIBDIR=lib" ]; + + meta = with lib; { + description = "C++ and Python library for Polarizable Embedding"; + homepage = "https://github.com/maxscheurer/cppe"; + license = licenses.lgpl3Only; + platforms = platforms.unix; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix new file mode 100644 index 000000000000..d791a7d4e3d6 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix @@ -0,0 +1,54 @@ +{ stdenv +, lib +, fetchFromGitHub +, cmake +, gfortran +, blas +, lapack +, mctc-lib +, mstore +, multicharge +}: + +assert !blas.isILP64 && !lapack.isILP64; + +stdenv.mkDerivation rec { + pname = "dftd4"; + version = "3.6.0"; + + src = fetchFromGitHub { + owner = "dftd4"; + repo = pname; + rev = "v${version}"; + hash = "sha256-VIV9953hx0MZupOARdH+P1h7JtZeJmTlqtO8si+lwdU="; + }; + + nativeBuildInputs = [ cmake gfortran ]; + + buildInputs = [ blas lapack mctc-lib mstore multicharge ]; + + outputs = [ "out" "dev" ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + doCheck = true; + preCheck = '' + export OMP_NUM_THREADS=2 + ''; + + meta = with lib; { + description = "Generally Applicable Atomic-Charge Dependent London Dispersion Correction"; + license = with licenses; [ lgpl3Plus gpl3Plus ]; + homepage = "https://github.com/grimme-lab/dftd4"; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/harminv/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/harminv/default.nix new file mode 100644 index 000000000000..54c0d03979ab --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/harminv/default.nix @@ -0,0 +1,42 @@ +{ lib +, stdenv +, fetchFromGitHub +, autoreconfHook +, gfortran +, blas +, lapack +}: + +assert !blas.isILP64; +assert !lapack.isILP64; + +stdenv.mkDerivation rec { + pname = "harminv"; + version = "1.4.2"; + + src = fetchFromGitHub { + owner = "NanoComp"; + repo = pname; + rev = "v${version}"; + hash = "sha256-EXEt7l69etcBdDdEDlD1ODOdhTBZCVjgY1jhRUDd/W0="; + }; + + # File is missing in the git checkout but required by autotools + postPatch = '' + touch ChangeLog + ''; + + nativeBuildInputs = [ autoreconfHook gfortran ]; + + buildInputs = [ blas lapack ]; + + configureFlags = [ "--enable-shared" ]; + + meta = with lib; { + description = "Harmonic inversion algorithm of Mandelshtam: decompose signal into sum of decaying sinusoids"; + homepage = "https://github.com/NanoComp/harminv"; + license = with licenses; [ gpl2Only ]; + maintainers = with maintainers; [ sheepforce markuskowa ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/libGDSII/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/libGDSII/default.nix new file mode 100644 index 000000000000..c3257bad3e26 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/libGDSII/default.nix @@ -0,0 +1,32 @@ +{ lib +, stdenv +, fetchFromGitHub +, autoreconfHook +}: + +stdenv.mkDerivation rec { + pname = "libGDSII"; + version = "0.21"; + + src = fetchFromGitHub { + owner = "HomerReid"; + repo = pname; + rev = "v${version}"; + hash = "sha256-EXEt7l69etcBdDdEDlD1ODOdhTBZCVjgY1jhRUDd/W0="; + }; + + # File is missing in the repo but automake requires it + postPatch = '' + touch ChangeLog + ''; + + nativeBuildInputs = [ autoreconfHook ]; + + meta = with lib; { + description = "Library and command-line utility for reading GDSII geometry files"; + homepage = "https://github.com/HomerReid/libGDSII"; + license = [ licenses.gpl2Only ]; + maintainers = with maintainers; [ sheepforce markuskowa ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix new file mode 100644 index 000000000000..fdcf7d00e3ba --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/libmsym/default.nix @@ -0,0 +1,23 @@ +{ stdenv, lib, fetchFromGitHub, cmake } : + +stdenv.mkDerivation rec { + pname = "libmsym"; + version = "0.2.3"; + + src = fetchFromGitHub { + owner = "mcodev31"; + repo = pname; + rev = "v${version}"; + sha256= "k+OEwrA/saupP/wX6Ii5My0vffiJ0X9xMCTrliMSMik="; + }; + + nativeBuildInputs = [ cmake ]; + + meta = with lib; { + description = " molecular point group symmetry lib"; + homepage = "https://github.com/mcodev31/libmsym"; + license = licenses.mit; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/libvdwxc/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/libvdwxc/default.nix new file mode 100644 index 000000000000..c0da65e7c788 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/libvdwxc/default.nix @@ -0,0 +1,52 @@ +{ stdenv +, lib +, fetchFromGitLab +, gfortran +, autoreconfHook +, fftwMpi +, mpi +}: + +stdenv.mkDerivation rec { + pname = "libvdwxc"; + # Stable version has non-working MPI detection. + version = "unstable-24.02.2020"; + + src = fetchFromGitLab { + owner = "libvdwxc"; + repo = pname; + rev = "92f4910c6ac88e111db2fb3a518089d0510c53b0"; + sha256 = "1c7pjrvifncbdyngs2bv185imxbcbq64nka8gshhp8n2ns6fids6"; + }; + + nativeBuildInputs = [ autoreconfHook gfortran ]; + + propagatedBuildInputs = [ mpi fftwMpi ]; + + preConfigure = '' + mkdir build && cd build + + export PATH=$PATH:${mpi}/bin + configureFlagsArray+=( + --with-mpi=${lib.getDev mpi} + CC=mpicc + FC=mpif90 + MPICC=mpicc + MPIFC=mpif90 + ) + ''; + + configureScript = "../configure"; + + hardeningDisable = [ "format" ]; + + doCheck = true; + + meta = with lib; { + description = "Portable C library of density functionals with van der Waals interactions for density functional theory"; + license = with licenses; [ lgpl3Plus bsd3 ]; + homepage = "https://libvdwxc.org/"; + platforms = platforms.unix; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix new file mode 100644 index 000000000000..a3726ea5e5dd --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix @@ -0,0 +1,46 @@ +{ stdenv +, lib +, fetchFromGitHub +, gfortran +, pkg-config +, json-fortran +, cmake +}: + +stdenv.mkDerivation rec { + pname = "mctc-lib"; + version = "0.3.1"; + + src = fetchFromGitHub { + owner = "grimme-lab"; + repo = pname; + rev = "v${version}"; + hash = "sha256-AXjg/ZsitdDf9fNoGVmVal1iZ4/sxjJb7A9W4yye/rg="; + }; + + nativeBuildInputs = [ gfortran pkg-config cmake ]; + + buildInputs = [ json-fortran ]; + + outputs = [ "out" "dev" ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + doCheck = true; + + meta = with lib; { + description = "Modular computation tool chain library"; + homepage = "https://github.com/grimme-lab/mctc-lib"; + license = licenses.asl20; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix new file mode 100644 index 000000000000..a93b8f32cef2 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix @@ -0,0 +1,25 @@ +{ stdenv, lib, fetchFromGitHub, cmake, msgpack } : + +stdenv.mkDerivation rec { + pname = "mmtf-cpp"; + version = "1.1.0"; + + src = fetchFromGitHub { + owner = "rcsb"; + repo = pname; + rev = "v${version}"; + hash = "sha256-8JrNobvekMggS8L/VORKA32DNUdXiDrYMObjd29wQmc="; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ msgpack ]; + + meta = with lib; { + description = "A library of exchange-correlation functionals with arbitrary-order derivatives"; + homepage = "https://github.com/rcsb/mmtf-cpp"; + license = licenses.mit; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix new file mode 100644 index 000000000000..b560ac16c698 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/molequeue/default.nix @@ -0,0 +1,34 @@ +{ lib, stdenv, fetchFromGitHub, cmake, qttools, wrapQtAppsHook }: + +stdenv.mkDerivation rec { + pname = "molequeue"; + version = "0.9.0"; + + src = fetchFromGitHub { + owner = "OpenChemistry"; + repo = pname; + rev = version; + hash = "sha256-+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg="; + }; + + nativeBuildInputs = [ + cmake + wrapQtAppsHook + ]; + + buildInputs = [ qttools ]; + + # Fix the broken CMake files to use the correct paths + postInstall = '' + substituteInPlace $out/lib/cmake/${pname}/MoleQueueConfig.cmake \ + --replace "$out/" "" + ''; + + meta = with lib; { + description = "Desktop integration of high performance computing resources"; + maintainers = with maintainers; [ sheepforce ]; + homepage = "https://github.com/OpenChemistry/molequeue"; + platforms = platforms.linux; + license = licenses.bsd3; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix new file mode 100644 index 000000000000..948d11435461 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix @@ -0,0 +1,43 @@ +{ stdenv +, lib +, fetchFromGitHub +, cmake +, gfortran +, mctc-lib +}: + +stdenv.mkDerivation rec { + pname = "mstore"; + version = "0.2.0"; + + src = fetchFromGitHub { + owner = "grimme-lab"; + repo = pname; + rev = "v${version}"; + hash = "sha256-dN2BulLS/ENRFVdJIrZRxgBV8S4d5+7BjTCGnhBbf4I="; + }; + + nativeBuildInputs = [ cmake gfortran ]; + + buildInputs = [ mctc-lib ]; + + outputs = [ "out" "dev" ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + meta = with lib; { + description = "Molecular structure store for testing"; + license = licenses.asl20; + homepage = "https://github.com/grimme-lab/mstore"; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix new file mode 100644 index 000000000000..b90f073a4f2e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix @@ -0,0 +1,53 @@ +{ stdenv +, lib +, fetchFromGitHub +, cmake +, gfortran +, blas +, lapack +, mctc-lib +, mstore +}: + +assert !blas.isILP64 && !lapack.isILP64; + +stdenv.mkDerivation rec { + pname = "multicharge"; + version = "0.2.0"; + + src = fetchFromGitHub { + owner = "grimme-lab"; + repo = pname; + rev = "v${version}"; + hash = "sha256-oUI5x5/Gd0EZBb1w+0jlJUF9X51FnkHFu8H7KctqXl0="; + }; + + nativeBuildInputs = [ cmake gfortran ]; + + buildInputs = [ blas lapack mctc-lib mstore ]; + + outputs = [ "out" "dev" ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + doCheck = true; + preCheck = '' + export OMP_NUM_THREADS=2 + ''; + + meta = with lib; { + description = "Electronegativity equilibration model for atomic partial charges"; + license = licenses.asl20; + homepage = "https://github.com/grimme-lab/multicharge"; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/openmm/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/openmm/default.nix new file mode 100644 index 000000000000..9b37f14f1403 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/openmm/default.nix @@ -0,0 +1,108 @@ +{ stdenv +, lib +, fetchFromGitHub +, cmake +, gfortran +, fftwSinglePrec +, doxygen +, swig +, enablePython ? false +, python3Packages +, enableOpencl ? true +, opencl-headers +, ocl-icd +, config +, enableCuda ? config.cudaSupport +, cudaPackages +, addOpenGLRunpath +}: + +stdenv.mkDerivation rec { + pname = "openmm"; + version = "8.1.1"; + + src = fetchFromGitHub { + owner = "openmm"; + repo = pname; + rev = version; + hash = "sha256-pYWBniV1J+UZBOPPjuUxVevONHaclo+GvGBEpr7Zmxg="; + }; + + # "This test is stochastic and may occassionally fail". It does. + postPatch = '' + rm \ + platforms/*/tests/Test*BrownianIntegrator.* \ + platforms/*/tests/Test*LangevinIntegrator.* \ + serialization/tests/TestSerializeIntegrator.cpp + ''; + + nativeBuildInputs = [ + cmake + gfortran + swig + doxygen + python3Packages.python + ] ++ lib.optional enableCuda addOpenGLRunpath; + + buildInputs = [ fftwSinglePrec ] + ++ lib.optionals enableOpencl [ ocl-icd opencl-headers ] + ++ lib.optional enableCuda cudaPackages.cudatoolkit; + + propagatedBuildInputs = lib.optionals enablePython (with python3Packages; [ + setuptools + python + numpy + cython + ]); + + cmakeFlags = [ + "-DBUILD_TESTING=ON" + "-DOPENMM_BUILD_AMOEBA_PLUGIN=ON" + "-DOPENMM_BUILD_CPU_LIB=ON" + "-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=ON" + "-DOPENMM_BUILD_DRUDE_PLUGIN=ON" + "-DOPENMM_BUILD_PME_PLUGIN=ON" + "-DOPENMM_BUILD_RPMD_PLUGIN=ON" + "-DOPENMM_BUILD_SHARED_LIB=ON" + ] ++ lib.optionals enablePython [ + "-DOPENMM_BUILD_PYTHON_WRAPPERS=ON" + ] ++ lib.optionals enableOpencl [ + "-DOPENMM_BUILD_OPENCL_LIB=ON" + "-DOPENMM_BUILD_AMOEBA_OPENCL_LIB=ON" + "-DOPENMM_BUILD_DRUDE_OPENCL_LIB=ON" + "-DOPENMM_BUILD_RPMD_OPENCL_LIB=ON" + ] ++ lib.optionals enableCuda [ + "-DCUDA_SDK_ROOT_DIR=${cudaPackages.cudatoolkit}" + "-DOPENMM_BUILD_AMOEBA_CUDA_LIB=ON" + "-DOPENMM_BUILD_CUDA_LIB=ON" + "-DOPENMM_BUILD_DRUDE_CUDA_LIB=ON" + "-DOPENMM_BUILD_RPMD_CUDA_LIB=ON" + "-DCMAKE_LIBRARY_PATH=${cudaPackages.cudatoolkit}/lib64/stubs" + ]; + + postInstall = lib.strings.optionalString enablePython '' + export OPENMM_LIB_PATH=$out/lib + export OPENMM_INCLUDE_PATH=$out/include + cd python + ${python3Packages.python.pythonOnBuildForHost.interpreter} setup.py build + ${python3Packages.python.pythonOnBuildForHost.interpreter} setup.py install --prefix=$out + mv $out/lib/python*/site-packages/OpenMM*.egg/{openmm,simtk} $out/lib/python*/site-packages/. + ''; + + postFixup = '' + for lib in $out/lib/plugins/*CUDA.so $out/lib/plugins/*Cuda*.so; do + addOpenGLRunpath "$lib" + done + ''; + + # Couldn't get CUDA to run properly in the sandbox + doCheck = !enableCuda && !enableOpencl; + + meta = with lib; { + description = "Toolkit for molecular simulation using high performance GPU code"; + homepage = "https://openmm.org/"; + license = with licenses; [ gpl3Plus lgpl3Plus mit ]; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/plumed/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/plumed/default.nix new file mode 100644 index 000000000000..b825c8270d62 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/plumed/default.nix @@ -0,0 +1,34 @@ +{ stdenv +, lib +, fetchFromGitHub +, blas +}: + +assert !blas.isILP64; + +stdenv.mkDerivation rec { + pname = "plumed"; + version = "2.9.0"; + + src = fetchFromGitHub { + owner = "plumed"; + repo = "plumed2"; + rev = "v${version}"; + hash = "sha256-yL+59f908IhbxGIylI1ydi1BPZwAapjK/vP4/h5gcHk="; + }; + + postPatch = '' + patchShebangs . + ''; + + buildInputs = [ blas ]; + + enableParallelBuilding = true; + + meta = with lib; { + description = "Molecular metadynamics library"; + homepage = "https://github.com/plumed/plumed2"; + license = licenses.lgpl3Only; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix new file mode 100644 index 000000000000..ae5e30d73608 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix @@ -0,0 +1,52 @@ +{ stdenv +, lib +, fetchFromGitHub +, gfortran +, cmake +, mctc-lib +, mstore +, toml-f +, blas +}: + +assert !blas.isILP64; + +stdenv.mkDerivation rec { + pname = "simple-dftd3"; + version = "1.0.0"; + + src = fetchFromGitHub { + owner = "dftd3"; + repo = pname; + rev = "v${version}"; + hash = "sha256-dfXiKKCGJ69aExSKpVC3Bp//COy256R9PDyxCNmDsfo="; + }; + + nativeBuildInputs = [ cmake gfortran ]; + + buildInputs = [ mctc-lib mstore toml-f blas ]; + + outputs = [ "out" "dev" ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + doCheck = true; + preCheck = '' + export OMP_NUM_THREADS=2 + ''; + + meta = with lib; { + description = "Reimplementation of the DFT-D3 program"; + license = with licenses; [ lgpl3Only gpl3Only ]; + homepage = "https://github.com/dftd3/simple-dftd3"; + platforms = [ "x86_64-linux" ]; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix new file mode 100644 index 000000000000..74f24e10f55f --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix @@ -0,0 +1,42 @@ +{ buildPythonPackage +, pkg-config +, meson +, simple-dftd3 +, cffi +, numpy +, toml +, qcengine +, pyscf +, ase +, pytestCheckHook +}: + +buildPythonPackage { + inherit (simple-dftd3) pname version src meta; + + # pytest is also required for installation, not only testing + nativeBuildInputs = [ pytestCheckHook ]; + + buildInputs = [ simple-dftd3 ]; + + propagatedBuildInputs = [ + cffi + numpy + toml + ]; + + checkInputs = [ + ase + qcengine + pyscf + ]; + + preConfigure = '' + cd python + ''; + + # The compiled CFFI is not placed correctly before pytest invocation + preCheck = '' + find . -name "_libdftd3*" -exec cp {} ./dftd3/. \; + ''; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/0001-fix-multicharge-dep-needed-for-static-compilation.patch b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/0001-fix-multicharge-dep-needed-for-static-compilation.patch new file mode 100644 index 000000000000..d2d84f42e09f --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/0001-fix-multicharge-dep-needed-for-static-compilation.patch @@ -0,0 +1,31 @@ +From 1885a2349102742e33c5c97a8ab4bcacc032fc70 Mon Sep 17 00:00:00 2001 +From: Ryan Swart <ryan@talosystems.com> +Date: Thu, 30 Mar 2023 15:50:23 +0800 +Subject: [PATCH] fix: multicharge dep needed for static compilation + +--- + config/meson.build | 8 ++++++++ + 1 file changed, 8 insertions(+) + +diff --git a/config/meson.build b/config/meson.build +index 4f76160..629fa5e 100644 +--- a/config/meson.build ++++ b/config/meson.build +@@ -136,6 +136,14 @@ sdftd3_dep = dependency( + ) + lib_deps += sdftd3_dep + ++# Create multicharge library as subproject ++multicharge_dep = dependency( ++ 'multicharge', ++ fallback: ['multicharge'], ++ default_options: ['default_library=static', 'api=false', 'python=false'], ++) ++lib_deps += multicharge_dep ++ + # Create TOML Fortran as subproject + tomlf_dep = dependency( + 'toml-f', +-- +2.39.2 + diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix new file mode 100644 index 000000000000..bea5793addbf --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix @@ -0,0 +1,75 @@ +{ stdenv +, lib +, fetchFromGitHub +, fetchpatch +, cmake +, gfortran +, blas +, lapack +, mctc-lib +, mstore +, toml-f +, multicharge +, dftd4 +, simple-dftd3 +}: + +assert !blas.isILP64 && !lapack.isILP64; + +stdenv.mkDerivation rec { + pname = "tblite"; + version = "0.3.0"; + + src = fetchFromGitHub { + owner = "tblite"; + repo = pname; + rev = "v${version}"; + hash = "sha256-R7CAFG/x55k5Ieslxeq+DWq1wPip4cI+Yvn1cBbeVNs="; + }; + + patches = [ + # toml-f 0.4 compatibility + (fetchpatch { + url = "https://github.com/tblite/tblite/commit/da759fd02b8fbf470a5c6d3df9657cca6b1d0a9a.diff"; + hash = "sha256-VaeA2VyK+Eas432HMSpJ0lXxHBBNGpfkUO1eHeWpYl0="; + }) + ]; + + # Fix the Pkg-Config files for doubled store paths + postPatch = '' + substituteInPlace config/template.pc \ + --replace "\''${prefix}/" "" + ''; + + nativeBuildInputs = [ cmake gfortran ]; + + buildInputs = [ + blas + lapack + mctc-lib + mstore + toml-f + multicharge + dftd4 + simple-dftd3 + ]; + + outputs = [ "out" "dev" ]; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}" + ]; + + doCheck = true; + preCheck = '' + export OMP_NUM_THREADS=2 + ''; + + meta = with lib; { + description = "Light-weight tight-binding framework"; + license = with licenses; [ gpl3Plus lgpl3Plus ]; + homepage = "https://github.com/tblite/tblite"; + platforms = platforms.linux; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix new file mode 100644 index 000000000000..3a72cfaaa6a3 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix @@ -0,0 +1,61 @@ +{ buildPythonPackage +, fetchpatch +, meson +, ninja +, pkg-config +, tblite +, numpy +, simple-dftd3 +, cffi +, gfortran +, blas +, lapack +, mctc-lib +, mstore +, toml-f +, multicharge +, dftd4 +}: + +buildPythonPackage { + inherit (tblite) pname version src meta; + + nativeBuildInputs = [ + tblite + meson + ninja + pkg-config + gfortran + mctc-lib + ]; + + buildInputs = [ + tblite + simple-dftd3 + blas + lapack + mctc-lib + mstore + toml-f + multicharge + dftd4 + ]; + + propagatedBuildInputs = [ tblite simple-dftd3 cffi numpy ]; + + + patches = [ + # Add multicharge to the meson deps; otherwise we get missing mod_multicharge errors + ./0001-fix-multicharge-dep-needed-for-static-compilation.patch + + # Toml-f 0.4.0 compatibility https://github.com/tblite/tblite/pull/108 + (fetchpatch { + url = "https://github.com/tblite/tblite/commit/e4255519b58a5198a5fa8f3073bef1c78a4bbdbe.diff"; + hash = "sha256-BMwYsdWfK+vG3BFgzusLYfwo0WXrYSPxJoEJIyOvbPg="; + }) + ]; + + format = "other"; + pythonImportsCheck = [ "tblite" "tblite.interface" ]; + mesonFlags = [ "-Dpython=true" ]; +} diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix new file mode 100644 index 000000000000..0534c7b46b03 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/chemistry/xcfun/default.nix @@ -0,0 +1,30 @@ +{ stdenv, lib, fetchFromGitHub, cmake, gfortran, python3 } : + +stdenv.mkDerivation rec { + pname = "xcfun"; + version = "2.1.1"; + + src = fetchFromGitHub { + owner = "dftlibs"; + repo = pname; + rev = "v${version}"; + sha256 = "1bj70cnhbh6ziy02x988wwl7cbwaq17ld7qwhswqkgnnx8rpgxid"; + }; + + nativeBuildInputs = [ + cmake + gfortran + ]; + + propagatedBuildInputs = [ (python3.withPackages (p: with p; [ pybind11 ])) ]; + + cmakeFlags = [ "-DXCFUN_MAX_ORDER=3" ]; + + meta = with lib; { + description = "A library of exchange-correlation functionals with arbitrary-order derivatives"; + homepage = "https://github.com/dftlibs/xcfun"; + license = licenses.mpl20; + platforms = platforms.unix; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/electronics/coloquinte/default.nix b/nixpkgs/pkgs/development/libraries/science/electronics/coloquinte/default.nix new file mode 100644 index 000000000000..6946080c100e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/electronics/coloquinte/default.nix @@ -0,0 +1,38 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, lemon-graph +, eigen +, boost +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "coloquinte"; + version = "0.3.1"; + + src = fetchFromGitHub { + owner = "coloquinte"; + repo = "PlaceRoute"; + rev = finalAttrs.version; + hash = "sha256-bPDXaNZCNBM0qiu+46cL/zH/41lwqHPqfqTzJaERgVQ="; + }; + + nativeBuildInputs = [ + cmake + ]; + + buildInputs = [ + lemon-graph + eigen + boost + ]; + + meta = { + description = "Placement library for electronic circuits"; + homepage = "https://github.com/Coloquinte/PlaceRoute"; + license = lib.licenses.mit; + platforms = lib.platforms.linux; + maintainers = [ lib.maintainers.coloquinte ]; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix b/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix new file mode 100644 index 000000000000..6ac453aec2c0 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix @@ -0,0 +1,47 @@ +{ lib +, mkDerivation +, fetchFromGitHub +, cmake +, csxcad +, tinyxml +, vtkWithQt5 +, qtbase +}: + +mkDerivation { + pname = "qcsxcad"; + version = "unstable-2023-01-06"; + + src = fetchFromGitHub { + owner = "thliebig"; + repo = "QCSXCAD"; + rev = "1cde9d560a5000f4c24c249d2dd5ccda12de38b6"; + hash = "sha256-kc9Vnx6jGiQC2K88ZH00b61D/DbWxAIZZwYCsINqtrY="; + }; + + outputs = [ "out" "dev" ]; + + nativeBuildInputs = [ + cmake + ]; + + cmakeFlags = [ + "-DCSXCAD_ROOT_DIR=${csxcad}" + "-DENABLE_RPATH=OFF" + ]; + + buildInputs = [ + csxcad + tinyxml + vtkWithQt5 + qtbase + ]; + + 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/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix new file mode 100644 index 000000000000..f67d68d768a0 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix @@ -0,0 +1,33 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +}: + +stdenv.mkDerivation { + pname = "quadprogpp"; + version = "unstable-2023-01-20"; + + src = fetchFromGitHub { + owner = "liuq"; + repo = "QuadProgpp"; + rev = "4c51d91deb5af251957edf9454bfb74279a4544e"; + hash = "sha256-uozwuTAOPsRwYM9KyG3V0hwcmaPpfZPID9Wdd4olsvY="; + }; + + nativeBuildInputs = [ + cmake + ]; + + meta = with lib; { + description = "A C++ library for Quadratic Programming"; + longDescription = '' + QuadProg++ is a C++ library for Quadratic Programming which implements + the Goldfarb-Idnani active-set dual method. + ''; + homepage = "https://github.com/liuq/QuadProgpp"; + license = licenses.mit; + maintainers = with maintainers; [ wegank ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix new file mode 100644 index 000000000000..17838ab37390 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix @@ -0,0 +1,72 @@ +{ lib, stdenv +, fetchFromGitHub +, perl +, python3 + +# Enable BLAS interface with 64-bit integer width. +, blas64 ? false + +# Target architecture. "amdzen" compiles kernels for all Zen +# generations. To build kernels for specific Zen generations, +# use "zen", "zen2", "zen3", or "zen4". +, withArchitecture ? "amdzen" + +# Enable OpenMP-based threading. +, withOpenMP ? true +}: + +let + threadingSuffix = lib.optionalString withOpenMP "-mt"; + blasIntSize = if blas64 then "64" else "32"; + +in stdenv.mkDerivation rec { + pname = "amd-blis"; + version = "4.2"; + + src = fetchFromGitHub { + owner = "amd"; + repo = "blis"; + rev = version; + hash = "sha256-mLigzaA2S7qFCQT8UWC6bHWAvBjgpqvtgabPyFWBYT0="; + }; + + inherit blas64; + + nativeBuildInputs = [ + perl + python3 + ]; + + # Tests currently fail with non-Zen CPUs due to a floating point + # exception in one of the generic kernels. Try to re-enable the + # next release. + doCheck = false; + + enableParallelBuilding = true; + + configureFlags = [ + "--enable-cblas" + "--blas-int-size=${blasIntSize}" + ] ++ lib.optionals withOpenMP [ "--enable-threading=openmp" ] + ++ [ withArchitecture ]; + + postPatch = '' + patchShebangs configure build/flatten-headers.py + ''; + + postInstall = '' + ls $out/lib + ln -s $out/lib/libblis${threadingSuffix}.so $out/lib/libblas.so.3 + ln -s $out/lib/libblis${threadingSuffix}.so $out/lib/libcblas.so.3 + ln -s $out/lib/libblas.so.3 $out/lib/libblas.so + ln -s $out/lib/libcblas.so.3 $out/lib/libcblas.so + ''; + + meta = with lib; { + description = "BLAS-compatible library optimized for AMD CPUs"; + homepage = "https://developer.amd.com/amd-aocl/blas-library/"; + license = licenses.bsd3; + maintainers = [ maintainers.markuskowa ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix new file mode 100644 index 000000000000..0ca1c4950541 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix @@ -0,0 +1,62 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, gfortran +, python3 +, amd-blis +, aocl-utils + +, withOpenMP ? true +, blas64 ? false +, withAMDOpt ? true +}: + +stdenv.mkDerivation rec { + pname = "amd-libflame"; + version = "4.2"; + + src = fetchFromGitHub { + owner = "amd"; + repo = "libflame"; + rev = version; + hash = "sha256-eiH2eq+nKUjlB1bZTZNRW1+efCHZ68UOSFy0NpcY1FI="; + }; + + postPatch = '' + patchShebangs build + + # Enforce reproducible build compiler flags + substituteInPlace CMakeLists.txt --replace '-mtune=native' "" + ''; + + passthru = { inherit blas64; }; + + nativeBuildInputs = [ cmake gfortran python3 ]; + + buildInputs = [ amd-blis aocl-utils ]; + + cmakeFlags = [ + "-DLIBAOCLUTILS_LIBRARY_PATH=${lib.getLib aocl-utils}/lib/libaoclutils${stdenv.hostPlatform.extensions.sharedLibrary}" + "-DLIBAOCLUTILS_INCLUDE_PATH=${lib.getDev aocl-utils}/include" + "-DENABLE_BUILTIN_LAPACK2FLAME=ON" + "-DENABLE_CBLAS_INTERFACES=ON" + "-DENABLE_EXT_LAPACK_INTERFACE=ON" + ] + ++ lib.optional (!withOpenMP) "-DENABLE_MULTITHREADING=OFF" + ++ lib.optional blas64 "-DENABLE_ILP64=ON" + ++ lib.optional withAMDOpt "-DENABLE_AMD_OPT=ON"; + + postInstall = '' + ln -s $out/lib/libflame.so $out/lib/liblapack.so.3 + ln -s $out/lib/libflame.so $out/lib/liblapacke.so.3 + ''; + + meta = with lib; { + description = "LAPACK-compatible linear algebra library optimized for AMD CPUs"; + homepage = "https://developer.amd.com/amd-aocl/blas-library/"; + license = licenses.bsd3; + maintainers = [ maintainers.markuskowa ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix new file mode 100644 index 000000000000..744d565eddcd --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix @@ -0,0 +1,68 @@ +{ lib, stdenv, fetchFromGitHub, cmake +, gfortran, blas, lapack, eigen +, useMpi ? false +, mpi +, openssh +, igraph +}: + +# MPI version can only be built with LP64 interface. +# See https://github.com/opencollab/arpack-ng#readme +assert useMpi -> !blas.isILP64; + +stdenv.mkDerivation rec { + pname = "arpack"; + version = "3.9.1"; + + src = fetchFromGitHub { + owner = "opencollab"; + repo = "arpack-ng"; + rev = version; + sha256 = "sha256-HCvapLba8oLqx9I5+KDAU0s/dTmdWOEilS75i4gyfC0="; + }; + + nativeBuildInputs = [ cmake gfortran ]; + buildInputs = assert (blas.isILP64 == lapack.isILP64); [ + blas + lapack + eigen + ] ++ lib.optional useMpi mpi; + + nativeCheckInputs = lib.optional useMpi openssh; + + doCheck = true; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=ON" + "-DINTERFACE64=${if blas.isILP64 then "1" else "0"}" + "-DMPI=${if useMpi then "ON" else "OFF"}" + ]; + + preCheck = '' + # Prevent tests from using all cores + export OMP_NUM_THREADS=2 + ''; + + postFixup = lib.optionalString stdenv.isDarwin '' + install_name_tool -change libblas.dylib ${blas}/lib/libblas.dylib $out/lib/libarpack.dylib + ''; + + passthru = { + inherit (blas) isILP64; + tests = { + inherit igraph; + }; + }; + + meta = { + homepage = "https://github.com/opencollab/arpack-ng"; + changelog = "https://github.com/opencollab/arpack-ng/blob/${src.rev}/CHANGES"; + description = '' + A collection of Fortran77 subroutines to solve large scale eigenvalue + problems. + ''; + license = lib.licenses.bsd3; + maintainers = with lib.maintainers; [ ttuegel dotlambda ]; + platforms = lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix new file mode 100644 index 000000000000..4431ab63c7b7 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix @@ -0,0 +1,44 @@ +{ lib, stdenv, fetchurl, cmake, gfortran +# Whether to build with ILP64 interface +, blas64 ? false +}: + +stdenv.mkDerivation rec { + pname = "blas"; + version = "3.12.0"; + + src = fetchurl { + url = "http://www.netlib.org/blas/${pname}-${version}.tgz"; + sha256 = "sha256-zMQbXQiOUNsAMDF66bDJrzdXEME5KsrR/iCWAtpaWq0="; + }; + + passthru = { inherit blas64; }; + + nativeBuildInputs = [ cmake gfortran ]; + + cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" ] + ++ lib.optional blas64 "-DBUILD_INDEX64=ON"; + + postInstall = let + canonicalExtension = if stdenv.hostPlatform.isLinux + then "${stdenv.hostPlatform.extensions.sharedLibrary}.${lib.versions.major version}" + else stdenv.hostPlatform.extensions.sharedLibrary; + in lib.optionalString blas64 '' + ln -s $out/lib/libblas64${canonicalExtension} $out/lib/libblas${canonicalExtension} + ''; + + preFixup = lib.optionalString stdenv.isDarwin '' + for fn in $(find $out/lib -name "*.so*"); do + if [ -L "$fn" ]; then continue; fi + install_name_tool -id "$fn" "$fn" + done + ''; + + meta = with lib; { + description = "Basic Linear Algebra Subprograms"; + license = licenses.publicDomain; + maintainers = [ maintainers.markuskowa ]; + homepage = "http://www.netlib.org/blas/"; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix new file mode 100644 index 000000000000..2c9aa745ba12 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix @@ -0,0 +1,64 @@ +{ lib, stdenv +, fetchFromGitHub +, perl +, python3 + +# Enable BLAS interface with 64-bit integer width. +, blas64 ? false + +# Target architecture. x86_64 builds Intel and AMD kernels. +, withArchitecture ? "x86_64" + +# Enable OpenMP-based threading. +, withOpenMP ? true +}: + +let + blasIntSize = if blas64 then "64" else "32"; +in stdenv.mkDerivation rec { + pname = "blis"; + version = "0.9.0"; + + src = fetchFromGitHub { + owner = "flame"; + repo = "blis"; + rev = version; + sha256 = "sha256-1aHIdt5wCDrT1hBPnaUVThwjwDkJQ0G0+tao2iFXYpM="; + }; + + inherit blas64; + + nativeBuildInputs = [ + perl + python3 + ]; + + doCheck = true; + + enableParallelBuilding = true; + + configureFlags = [ + "--enable-cblas" + "--blas-int-size=${blasIntSize}" + ] ++ lib.optionals withOpenMP [ "--enable-threading=openmp" ] + ++ [ withArchitecture ]; + + postPatch = '' + patchShebangs configure build/flatten-headers.py + ''; + + postInstall = '' + ln -s $out/lib/libblis.so.4 $out/lib/libblas.so.3 + ln -s $out/lib/libblis.so.4 $out/lib/libcblas.so.3 + ln -s $out/lib/libblas.so.3 $out/lib/libblas.so + ln -s $out/lib/libcblas.so.3 $out/lib/libcblas.so + ''; + + meta = with lib; { + description = "BLAS-compatible linear algebra library"; + homepage = "https://github.com/flame/blis"; + license = licenses.bsd3; + maintainers = [ ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/bonmin/default.nix b/nixpkgs/pkgs/development/libraries/science/math/bonmin/default.nix new file mode 100644 index 000000000000..5a736f976957 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/bonmin/default.nix @@ -0,0 +1,53 @@ +{ lib +, stdenv +, fetchFromGitHub +, gfortran +, pkg-config +, blas +, bzip2 +, cbc +, clp +, ipopt +, lapack +, libamplsolver +, zlib +}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + pname = "bonmin"; + version = "1.8.9"; + + src = fetchFromGitHub { + owner = "coin-or"; + repo = "Bonmin"; + rev = "releases/${version}"; + sha256 = "sha256-nqjAQ1NdNJ/T4p8YljEWRt/uy2aDwyBeAsag0TmRc5Q="; + }; + + nativeBuildInputs = [ + gfortran + pkg-config + ]; + buildInputs = [ + blas + bzip2 + cbc + clp + ipopt + lapack + libamplsolver + zlib + ]; + + meta = with lib; { + description = "An open-source code for solving general MINLP (Mixed Integer NonLinear Programming) problems"; + homepage = "https://github.com/coin-or/Bonmin"; + license = licenses.epl10; + platforms = platforms.unix; + maintainers = with maintainers; [ aanderse ]; + # never built on aarch64-darwin, x86_64-darwin since first introduction in nixpkgs + broken = stdenv.isDarwin; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix new file mode 100644 index 000000000000..6ec28ba1c226 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix @@ -0,0 +1,46 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +, pkg-config +, boost +, m4ri +, gd +}: + +stdenv.mkDerivation rec { + version = "1.2.12"; + pname = "brial"; + + src = fetchFromGitHub { + owner = "BRiAl"; + repo = "BRiAl"; + rev = version; + sha256 = "sha256-y6nlqRBJRWohGDAKe/F37qBP1SgtFHR1HD+erFJReOM="; + }; + + # FIXME package boost-test and enable checks + doCheck = false; + + configureFlags = [ + "--with-boost-unit-test-framework=no" + ]; + + buildInputs = [ + boost + m4ri + gd + ]; + + nativeBuildInputs = [ + autoreconfHook + pkg-config + ]; + + meta = with lib; { + homepage = "https://github.com/BRiAl/BRiAl"; + description = "Legacy version of PolyBoRi maintained by sagemath developers"; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix new file mode 100644 index 000000000000..311ffefcfaad --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix @@ -0,0 +1,35 @@ +{ lib, stdenv, fetchFromGitHub, gfortran, suitesparse, blas, lapack }: +stdenv.mkDerivation rec { + pname = "cholmod-extra"; + version = "1.2.0"; + + src = fetchFromGitHub { + repo = pname; + owner = "jluttine"; + rev = version; + sha256 = "0hz1lfp0zaarvl0dv0zgp337hyd8np41kmdpz5rr3fc6yzw7vmkg"; + }; + + nativeBuildInputs = [ gfortran ]; + buildInputs = [ suitesparse blas lapack ]; + + makeFlags = [ + "BLAS=-lcblas" + ]; + + installFlags = [ + "INSTALL_LIB=$(out)/lib" + "INSTALL_INCLUDE=$(out)/include" + ]; + + doCheck = true; + + meta = with lib; { + homepage = "https://github.com/jluttine/cholmod-extra"; + description = "A set of additional routines for SuiteSparse CHOLMOD Module"; + license = with licenses; [ gpl2Plus ]; + maintainers = with maintainers; [ jluttine ]; + platforms = with platforms; unix; + }; + +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix new file mode 100644 index 000000000000..a87d107b3a17 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix @@ -0,0 +1,68 @@ +{ lib, stdenv +, fetchFromGitHub +, cmake +, gfortran +, blas +, boost +, python3 +, ocl-icd +, opencl-headers +, Accelerate, CoreGraphics, CoreVideo, OpenCL +}: + +stdenv.mkDerivation rec { + pname = "clblas"; + version = "2.12"; + + src = fetchFromGitHub { + owner = "clMathLibraries"; + repo = "clBLAS"; + rev = "v${version}"; + sha256 = "154mz52r5hm0jrp5fqrirzzbki14c1jkacj75flplnykbl36ibjs"; + }; + + patches = [ ./platform.patch ]; + + postPatch = '' + sed -i -re 's/(set\(\s*Boost_USE_STATIC_LIBS\s+).*/\1OFF\ \)/g' src/CMakeLists.txt + ''; + + preConfigure = '' + cd src + ''; + + cmakeFlags = [ + "-DBUILD_TEST=OFF" + ]; + + nativeBuildInputs = [ cmake gfortran ]; + buildInputs = [ + blas + python3 + boost + ] ++ lib.optionals (!stdenv.isDarwin) [ + ocl-icd + opencl-headers + ] ++ lib.optionals stdenv.isDarwin [ + Accelerate + CoreGraphics + CoreVideo + ]; + propagatedBuildInputs = lib.optionals stdenv.isDarwin [ + OpenCL + ]; + + strictDeps = true; + + meta = with lib; { + homepage = "https://github.com/clMathLibraries/clBLAS"; + description = "A software library containing BLAS functions written in OpenCL"; + longDescription = '' + This package contains a library of BLAS functions on top of OpenCL. + ''; + license = licenses.asl20; + maintainers = with maintainers; [ artuuge ]; + platforms = platforms.unix; + }; + +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/clblas/platform.patch b/nixpkgs/pkgs/development/libraries/science/math/clblas/platform.patch new file mode 100644 index 000000000000..87404a426a4b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/clblas/platform.patch @@ -0,0 +1,34 @@ +diff --git a/src/library/tools/ktest/config.cpp b/src/library/tools/ktest/config.cpp +index 8b20128..faf9bde 100644 +--- a/src/library/tools/ktest/config.cpp ++++ b/src/library/tools/ktest/config.cpp +@@ -24,8 +24,6 @@ + + using namespace clMath; + +-static const char DEFAULT_PLATFORM_NAME[] = "AMD Accelerated Parallel Processing"; +- + Config::Config() : + defaultConfig_(""), + cpp_("ktest.cpp"), +@@ -35,7 +33,10 @@ Config::Config() : + hasFuncID_(false), hasSubdims_(false), + skipAccuracy_(false) + { +- setPlatform(DEFAULT_PLATFORM_NAME); ++ platform_ = NULL; ++ setPlatform(""); ++ ++ device_ = NULL; + setDevice(""); + + memset(&kargs_, 0, sizeof(kargs_)); +@@ -262,7 +263,7 @@ Config::setPlatform(const std::string& name) + continue; + } + if (name.empty()) { +- found = (strcmp(pname, DEFAULT_PLATFORM_NAME) == 0); ++ found = true; + } + else { + found = (strcmp(pname, name.c_str()) == 0); diff --git a/nixpkgs/pkgs/development/libraries/science/math/clblast/default.nix b/nixpkgs/pkgs/development/libraries/science/math/clblast/default.nix new file mode 100644 index 000000000000..e4bbd09a7586 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/clblast/default.nix @@ -0,0 +1,44 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, ninja +, opencl-headers +, ocl-icd +}: + +stdenv.mkDerivation rec { + pname = "clblast"; + version = "1.6.2"; + + src = fetchFromGitHub { + owner = "CNugteren"; + repo = "CLBlast"; + rev = version; + hash = "sha256-S25g25Il6rzkpU9IqOFDDeEr3uYyt/uewZZAl09YSts="; + }; + + nativeBuildInputs = [ + cmake + ninja + ]; + + buildInputs = [ + opencl-headers + ocl-icd + ]; + + cmakeFlags = [ + # https://github.com/NixOS/nixpkgs/issues/144170 + "-DCMAKE_INSTALL_INCLUDEDIR=include" + "-DCMAKE_INSTALL_LIBDIR=lib" + ]; + + meta = with lib; { + description = "The tuned OpenCL BLAS library"; + homepage = "https://github.com/CNugteren/CLBlast"; + license = licenses.asl20; + maintainers = with maintainers; [ Tungsten842 ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix new file mode 100644 index 000000000000..55a1b9dcb4c9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix @@ -0,0 +1,39 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +}: + +stdenv.mkDerivation rec { + version = "1.22"; + pname = "cliquer"; + + # autotoolized version of the original cliquer + src = fetchFromGitHub { + owner = "dimpase"; + repo = "autocliquer"; + rev = "v${version}"; + sha256 = "00gcmrhi2fjn8b246w5a3b0pl7p6haxy5wjvd9kcqib1xanz59z4"; + }; + + doCheck = true; + + nativeBuildInputs = [ + autoreconfHook + ]; + + meta = with lib; { + description = "Routines for clique searching"; + longDescription = '' + Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. + It uses an exact branch-and-bound algorithm developed by Patric Östergård. + It is designed with the aim of being efficient while still being flexible and + easy to use. + ''; + homepage = "https://users.aalto.fi/~pat/cliquer.html"; + downloadPage = src.meta.homepage; # autocliquer + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + mainProgram = "cl"; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix b/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix new file mode 100644 index 000000000000..c5efbb757df8 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix @@ -0,0 +1,73 @@ +{ lib, stdenv, fetchurl, gfortran, opencl-headers, clblas, ocl-icd, mkl, intel-ocl }: + +let + incfile = builtins.toFile "make.inc.custom" '' + CC = g++ + FORT = gfortran + + ARCH = ar + ARCHFLAGS = cr + RANLIB = ranlib + + OPTS = -fPIC -O3 -DADD_ -Wall + FOPTS = -fPIC -O3 -DADD_ -Wall -x f95-cpp-input + F77OPTS = -fPIC -O3 -DADD_ -Wall + LDOPTS = -fPIC + + -include make.check-mkl + -include make.check-clblas + + # Gnu mkl is not available I guess? + #LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lpthread -lm -fopenmp + LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lm -fopenmp + LIB += -lclBLAS -lOpenCL + + LIBDIR = -L$(MKLROOT)/lib/intel64 \ + -L$(MKLROOT)/../compiler/lib/intel64 \ + -L$(clBLAS)/lib64 + + INC = -I$(clBLAS)/include + #-I$(AMDAPP)/include + ''; +in stdenv.mkDerivation rec { + pname = "clmagma"; + version = "1.3.0"; + src = fetchurl { + url = "https://icl.cs.utk.edu/projectsfiles/magma/cl/clmagma-${version}.tar.gz"; + sha256 = "1n27ny0xhwirw2ydn46pfcwy53gzia9zbam4irx44fd4d7f9ydv7"; + name = "clmagma-${version}.tar.gz"; + }; + + buildInputs = [ + gfortran + clblas + opencl-headers + ocl-icd + mkl + intel-ocl + ]; + + enableParallelBuilding=true; + + MKLROOT = "${mkl}"; + clBLAS = "${clblas}"; + + # Otherwise build looks for it in /run/opengl-driver/etc/OpenCL/vendors, + # which is not available. + OPENCL_VENDOR_PATH="${intel-ocl}/etc/OpenCL/vendors"; + + preBuild = '' + # By default it tries to use GPU, and thus fails for CPUs + sed -i "s/CL_DEVICE_TYPE_GPU/CL_DEVICE_TYPE_DEFAULT/" interface_opencl/clmagma_runtime.cpp + sed -i "s%/usr/local/clmagma%/$out%" Makefile.internal + cp ${incfile} make.inc + ''; + + meta = with lib; { + description = "Matrix Algebra on GPU and Multicore Architectures, OpenCL port"; + license = licenses.bsd3; + homepage = "https://icl.cs.utk.edu/magma/index.html"; + platforms = platforms.linux; + maintainers = with maintainers; [ volhovm ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/coin-utils/default.nix b/nixpkgs/pkgs/development/libraries/science/math/coin-utils/default.nix new file mode 100644 index 000000000000..60b9de0ab33a --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/coin-utils/default.nix @@ -0,0 +1,31 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch }: + +stdenv.mkDerivation rec { + version = "2.11.10"; + pname = "coinutils"; + + src = fetchFromGitHub { + owner = "coin-or"; + repo = "CoinUtils"; + rev = "releases/${version}"; + hash = "sha256-Rbm45HRbRKQ6Cdup+gvKJ1xkK1HKG3irR5AIjhLer7g="; + }; + + patches = [ + (fetchpatch { + url = "https://github.com/coin-or/CoinUtils/commit/1700ed92c2bc1562aabe65dee3b4885bd5c87fb9.patch"; + stripLen = 1; + extraPrefix = "CoinUtils/"; + hash = "sha256-8S6XteZvoJlL+5MWiOrW7HXsdcnzpuEFTyzX9qg7OUY="; + }) + ]; + + doCheck = true; + + meta = with lib; { + license = licenses.epl20; + homepage = "https://github.com/coin-or/CoinUtils"; + description = "Collection of classes and helper functions that are generally useful to multiple COIN-OR projects"; + maintainers = with maintainers; [ tmarkus ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/dbcsr/default.nix b/nixpkgs/pkgs/development/libraries/science/math/dbcsr/default.nix new file mode 100644 index 000000000000..2c576a190026 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/dbcsr/default.nix @@ -0,0 +1,81 @@ +{ stdenv +, lib +, fetchFromGitHub +, cmake +, mpiCheckPhaseHook +, pkg-config +, fypp +, gfortran +, blas +, lapack +, python3 +, libxsmm +, mpi +, openssh +}: + +stdenv.mkDerivation rec { + pname = "dbcsr"; + version = "2.6.0"; + + src = fetchFromGitHub { + owner = "cp2k"; + repo = "dbcsr"; + rev = "v${version}"; + hash = "sha256-+xSxfrzsxBdb424F/3mIETleEPoETxU0LB0OBJrR7gw="; + }; + + postPatch = '' + patchShebangs . + + # Force build of shared library, otherwise just static. + substituteInPlace src/CMakeLists.txt \ + --replace 'add_library(dbcsr ''${DBCSR_SRCS})' 'add_library(dbcsr SHARED ''${DBCSR_SRCS})' \ + --replace 'add_library(dbcsr_c ''${DBCSR_C_SRCS})' 'add_library(dbcsr_c SHARED ''${DBCSR_C_SRCS})' + + # Avoid calling the fypp wrapper script with python again. The nix wrapper took care of that. + substituteInPlace cmake/fypp-sources.cmake \ + --replace 'COMMAND ''${Python_EXECUTABLE} ''${FYPP_EXECUTABLE}' 'COMMAND ''${FYPP_EXECUTABLE}' + ''; + + nativeBuildInputs = [ + gfortran + python3 + cmake + pkg-config + fypp + ]; + + buildInputs = [ blas lapack libxsmm ]; + + propagatedBuildInputs = [ mpi ]; + + preConfigure = '' + export PKG_CONFIG_PATH=${libxsmm}/lib + ''; + + cmakeFlags = [ + "-DUSE_OPENMP=ON" + "-DUSE_SMM=libxsmm" + "-DWITH_C_API=ON" + "-DBUILD_TESTING=ON" + "-DTEST_OMP_THREADS=2" + "-DTEST_MPI_RANKS=2" + "-DENABLE_SHARED=ON" + "-DUSE_MPI=ON" + ]; + + checkInputs = [ + openssh + mpiCheckPhaseHook + ]; + + doCheck = true; + + meta = with lib; { + description = "Distributed Block Compressed Sparse Row matrix library"; + license = licenses.gpl2Only; + homepage = "https://github.com/cp2k/dbcsr"; + maintainers = [ maintainers.sheepforce ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix new file mode 100644 index 000000000000..b60bd1fe76c1 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix @@ -0,0 +1,38 @@ +{ lib, stdenv, fetchFromGitHub }: + +stdenv.mkDerivation rec { + pname = "ecos"; + version = "2.0.7"; + + src = fetchFromGitHub { + owner = "embotech"; + repo = "ecos"; + rev = version; + sha256 = "1hsndim5kjvcwk5svqa4igawzahj982180xj1d7yd0dbjlgxc7w7"; + }; + + buildPhase = '' + make all shared + ''; + + doCheck = true; + checkPhase = '' + make test + ./runecos + ''; + + installPhase = '' + mkdir -p $out/lib + cp lib*.a lib*.so $out/lib + cp -r include $out/ + ''; + + meta = with lib; { + description = "A lightweight conic solver for second-order cone programming"; + homepage = "https://www.embotech.com/ECOS"; + downloadPage = "https://github.com/embotech/ecos/releases"; + license = licenses.gpl3; + platforms = platforms.all; + maintainers = with maintainers; [ bhipple ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/faiss/default.nix b/nixpkgs/pkgs/development/libraries/science/math/faiss/default.nix new file mode 100644 index 000000000000..25ac539e05f2 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/faiss/default.nix @@ -0,0 +1,153 @@ +{ lib +, config +, fetchFromGitHub +, symlinkJoin +, stdenv +, cmake +, cudaPackages ? { } +, cudaSupport ? config.cudaSupport +, pythonSupport ? true +, pythonPackages +, llvmPackages +, boost +, blas +, swig +, addOpenGLRunpath +, optLevel ? let + optLevels = + lib.optionals stdenv.hostPlatform.avx2Support [ "avx2" ] + ++ lib.optionals stdenv.hostPlatform.sse4_1Support [ "sse4" ] + ++ [ "generic" ]; + in + # Choose the maximum available optimization level + builtins.head optLevels +, faiss # To run demos in the tests +, runCommand +}@inputs: + +let + pname = "faiss"; + version = "1.7.4"; + + inherit (cudaPackages) cudaFlags backendStdenv; + inherit (cudaFlags) cudaCapabilities dropDot; + + stdenv = if cudaSupport then backendStdenv else inputs.stdenv; + + cudaJoined = symlinkJoin { + name = "cuda-packages-unsplit"; + paths = with cudaPackages; [ + cuda_cudart # cuda_runtime.h + libcublas + libcurand + cuda_cccl + ] ++ lib.optionals (cudaPackages ? cuda_profiler_api) [ + cuda_profiler_api # cuda_profiler_api.h + ] ++ lib.optionals (!(cudaPackages ? cuda_profiler_api)) [ + cuda_nvprof # cuda_profiler_api.h + ]; + }; +in +stdenv.mkDerivation { + inherit pname version; + + outputs = [ "out" "demos" ]; + + src = fetchFromGitHub { + owner = "facebookresearch"; + repo = pname; + rev = "v${version}"; + hash = "sha256-WSce9X6sLZmGM5F0ZkK54VqpIy8u1VB0e9/l78co29M="; + }; + + buildInputs = [ + blas + swig + ] ++ lib.optionals pythonSupport [ + pythonPackages.setuptools + pythonPackages.pip + pythonPackages.wheel + ] ++ lib.optionals stdenv.cc.isClang [ + llvmPackages.openmp + ] ++ lib.optionals cudaSupport [ + cudaJoined + ]; + + propagatedBuildInputs = lib.optionals pythonSupport [ + pythonPackages.numpy + ]; + + nativeBuildInputs = [ cmake ] ++ lib.optionals cudaSupport [ + cudaPackages.cuda_nvcc + addOpenGLRunpath + ] ++ lib.optionals pythonSupport [ + pythonPackages.python + ]; + + passthru.extra-requires.all = [ + pythonPackages.numpy + ]; + + cmakeFlags = [ + "-DFAISS_ENABLE_GPU=${if cudaSupport then "ON" else "OFF"}" + "-DFAISS_ENABLE_PYTHON=${if pythonSupport then "ON" else "OFF"}" + "-DFAISS_OPT_LEVEL=${optLevel}" + ] ++ lib.optionals cudaSupport [ + "-DCMAKE_CUDA_ARCHITECTURES=${builtins.concatStringsSep ";" (map dropDot cudaCapabilities)}" + "-DCUDAToolkit_INCLUDE_DIR=${cudaJoined}/include" + ]; + + + # pip wheel->pip install commands copied over from opencv4 + + buildPhase = '' + make -j faiss + make demo_ivfpq_indexing + '' + lib.optionalString pythonSupport '' + make -j swigfaiss + (cd faiss/python && + python -m pip wheel --verbose --no-index --no-deps --no-clean --no-build-isolation --wheel-dir dist .) + ''; + + installPhase = '' + make install + mkdir -p $demos/bin + cp ./demos/demo_ivfpq_indexing $demos/bin/ + '' + lib.optionalString pythonSupport '' + mkdir -p $out/${pythonPackages.python.sitePackages} + (cd faiss/python && python -m pip install dist/*.whl --no-index --no-warn-script-location --prefix="$out" --no-cache) + ''; + + fixupPhase = lib.optionalString (pythonSupport && cudaSupport) '' + addOpenGLRunpath $out/${pythonPackages.python.sitePackages}/faiss/*.so + addOpenGLRunpath $demos/bin/* + ''; + + # Need buildPythonPackage for this one + # pythonImportsCheck = [ + # "faiss" + # ]; + + passthru = { + inherit cudaSupport cudaPackages pythonSupport; + + tests = { + runDemos = runCommand "${pname}-run-demos" + { buildInputs = [ faiss.demos ]; } + # There are more demos, we run just the one that documentation mentions + '' + demo_ivfpq_indexing && touch $out + ''; + } // lib.optionalAttrs pythonSupport { + pytest = pythonPackages.callPackage ./tests.nix { }; + }; + }; + + meta = with lib; { + description = "A library for efficient similarity search and clustering of dense vectors by Facebook Research"; + homepage = "https://github.com/facebookresearch/faiss"; + license = licenses.mit; + platforms = platforms.unix; + maintainers = with maintainers; [ SomeoneSerge ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/faiss/tests.nix b/nixpkgs/pkgs/development/libraries/science/math/faiss/tests.nix new file mode 100644 index 000000000000..858a980bfeaf --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/faiss/tests.nix @@ -0,0 +1,37 @@ +{ lib +, buildPythonPackage +, faiss +, scipy +, pytestCheckHook +}: + +assert faiss.pythonSupport; + +buildPythonPackage { + pname = "faiss-pytest-suite"; + inherit (faiss) version; + + format = "other"; + + src = "${faiss.src}/tests"; + + dontBuild = true; + dontInstall = true; + + # Tests that need GPUs and would fail in the sandbox + disabledTestPaths = lib.optionals faiss.cudaSupport [ + "test_contrib.py" + ]; + + disabledTests = [ + # https://github.com/facebookresearch/faiss/issues/2836 + "test_update_codebooks_with_double" + ]; + + nativeCheckInputs = [ + faiss + pytestCheckHook + scipy + ] ++ + faiss.extra-requires.all; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix new file mode 100644 index 000000000000..c5426ed67fc7 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix @@ -0,0 +1,40 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +, gmp +}: + +stdenv.mkDerivation rec { + version = "1.0"; + pname = "flintqs"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "FlintQS"; + rev = "v${version}"; + sha256 = "1f0lnayz6j6qgasx8pbq61d2fqam0wwhsmh6h15l4vq58l1vvbwj"; + }; + + preAutoreconf = '' + touch ChangeLog + ''; + + buildInputs = [ + gmp + ]; + + nativeBuildInputs = [ + autoreconfHook + ]; + + doCheck = true; + + meta = with lib; { + description = "Highly optimized multi-polynomial quadratic sieve for integer factorization"; + homepage = "https://github.com/sagemath/FlintQS"; + license = with licenses; [ gpl2 ]; + maintainers = teams.sage.members; + mainProgram = "QuadraticSieve"; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix new file mode 100644 index 000000000000..a76c2f878ba7 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix @@ -0,0 +1,43 @@ +{ lib +, stdenv +, fetchFromGitHub +, pkg-config +, blas +, lapack +, gfortran +, enableAMPL ? true, libamplsolver +}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + pname = "ipopt"; + version = "3.14.14"; + + src = fetchFromGitHub { + owner = "coin-or"; + repo = "Ipopt"; + rev = "releases/${version}"; + sha256 = "sha256-qMPdJVLIXFePhTA6qRr1Pth/BjJ62cj9y8C1HKQJGDQ="; + }; + + CXXDEFS = [ "-DHAVE_RAND" "-DHAVE_CSTRING" "-DHAVE_CSTDIO" ]; + + configureFlags = [ + "--with-asl-cflags=-I${libamplsolver}/include" + "--with-asl-lflags=-lamplsolver" + ]; + + nativeBuildInputs = [ pkg-config gfortran ]; + buildInputs = [ blas lapack ] ++ lib.optionals enableAMPL [ libamplsolver ]; + + enableParallelBuilding = true; + + meta = with lib; { + description = "A software package for large-scale nonlinear optimization"; + homepage = "https://projects.coin-or.org/Ipopt"; + license = licenses.epl10; + platforms = platforms.unix; + maintainers = with maintainers; [ abbradar ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix new file mode 100644 index 000000000000..639497bb1f8c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix @@ -0,0 +1,53 @@ +{ lib, stdenv +, fetchurl +, cmake +, gtest +, blas +, fftw +, liblapack +, gfortran +}: + +stdenv.mkDerivation rec { + pname = "it++"; + version = "4.3.1"; + + src = fetchurl { + url = "mirror://sourceforge/itpp/itpp-${version}.tar.bz2"; + sha256 = "0xxqag9wi0lg78xgw7b40rp6wxqp5grqlbs9z0ifvdfzqlhpcwah"; + }; + + nativeBuildInputs = [ cmake gfortran ]; + buildInputs = [ + fftw + liblapack + + # NOTE: OpenBLAS doesn't work here because IT++ doesn't pass aligned + # buffers, which causes segfaults in the optimized kernels :-( + blas + ]; + + cmakeFlags = [ + "-DCMAKE_CXX_FLAGS=-std=c++14" + "-DBLAS_FOUND:BOOL=TRUE" + "-DBLAS_LIBRARIES:STRING=${blas}/lib/libblas.so" + "-DLAPACK_FOUND:BOOL=TRUE" + "-DLAPACK_LIBRARIES:STRING=${liblapack}/lib/liblapack.so" + "-DGTEST_DIR:PATH=${gtest.src}/googletest" + ]; + + doCheck = true; + + checkPhase = '' + ./gtests/itpp_gtests + ''; + + meta = with lib; { + description = "IT++ is a C++ library of mathematical, signal processing and communication classes and functions"; + homepage = "https://itpp.sourceforge.net/"; + license = licenses.gpl3; + platforms = platforms.unix; + maintainers = with maintainers; [ andrew-d ]; + broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/itpp.x86_64-darwin + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/latte-integrale/default.nix b/nixpkgs/pkgs/development/libraries/science/math/latte-integrale/default.nix new file mode 100644 index 000000000000..7eb485974ff2 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/latte-integrale/default.nix @@ -0,0 +1,41 @@ +{ lib +, stdenv +, fetchurl +, fetchpatch +, gmp +, ntl +, cddlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "latte-integrale"; + version = "1.7.6"; + + src = fetchurl { + url = "https://github.com/latte-int/latte/releases/download/version_${lib.replaceStrings ["."] ["_"] finalAttrs.version}/latte-int-${finalAttrs.version}.tar.gz"; + sha256 = "sha256-AGwQ6+XVv9ybFZy6YmSkQyhh/nY84F/oIWJKt9P8IXA="; + }; + + patches = [ + # C++17 compat + (fetchpatch { + url = "https://github.com/latte-int/latte/commit/6dbf7f07d5c9e1f3afe793f782d191d4465088ae.patch"; + excludes = [ "code/latte/sqlite/IntegrationDB.h" ]; + sha256 = "sha256-i7c11y54OLuJ0m7PBnhEoAzJzxC842JU7A6TOtTz06k="; + }) + ]; + + buildInputs = [ + gmp + ntl + cddlib + ]; + + meta = { + description = "Software for counting lattice points and integration over convex polytopes"; + homepage = "https://www.math.ucdavis.edu/~latte/"; + license = lib.licenses.gpl2; + maintainers = with lib.maintainers; [ amesgen ]; + platforms = lib.platforms.unix; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix new file mode 100644 index 000000000000..b1896917658c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix @@ -0,0 +1,41 @@ +{ lib, stdenv +, autoreconfHook +, gengetopt +, pkg-config +, fetchFromGitLab +, pari +}: + +stdenv.mkDerivation rec { + version = "2.0.5"; + pname = "lcalc"; + + src = fetchFromGitLab { + owner = "sagemath"; + repo = pname; + rev = version; + sha256 = "sha256-RxWZ7T0I9zV7jUVnL6jV/PxEoU32KY7Q1UsOL5Lonuc="; + }; + + nativeBuildInputs = [ + autoreconfHook + gengetopt + pkg-config + ]; + + buildInputs = [ + pari + ]; + + configureFlags = [ + "--with-pari" + ]; + + meta = with lib; { + homepage = "https://gitlab.com/sagemath/lcalc"; + description = "A program for calculating with L-functions"; + license = with licenses; [ gpl2 ]; + maintainers = teams.sage.members; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/default.nix new file mode 100644 index 000000000000..a40091bac8b5 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/default.nix @@ -0,0 +1,39 @@ +{ lib, stdenv, substitute, fetchurl, fetchpatch }: + +stdenv.mkDerivation rec { + pname = "libamplsolver"; + version = "20211109"; + + src = fetchurl { + url = "https://ampl.com/netlib/ampl/solvers.tgz"; + sha256 = "sha256-LVmScuIvxmZzywPSBl9T9YcUBJP7UFAa3eWs9r4q3JM="; + }; + + patches = [ + (substitute { + src = ./libamplsolver-sharedlib.patch; + substitutions = [ "--replace" "@sharedlibext@" "${stdenv.hostPlatform.extensions.sharedLibrary}" ]; + }) + ]; + + installPhase = '' + runHook preInstall + pushd sys.$(uname -m).$(uname -s) + install -D -m 0644 *.h -t $out/include + install -D -m 0644 *${stdenv.hostPlatform.extensions.sharedLibrary}* -t $out/lib + install -D -m 0644 *.a -t $out/lib + popd + '' + lib.optionalString stdenv.isDarwin '' + install_name_tool -id $out/lib/libamplsolver.dylib $out/lib/libamplsolver.dylib + '' + '' + runHook postInstall + ''; + + meta = with lib; { + description = "A library of routines that help solvers work with AMPL"; + homepage = "https://ampl.com/netlib/ampl/"; + license = [ licenses.mit ]; + platforms = platforms.unix; + maintainers = with maintainers; [ aanderse ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/libamplsolver-sharedlib.patch b/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/libamplsolver-sharedlib.patch new file mode 100644 index 000000000000..f2af2910e89c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libamplsolver/libamplsolver-sharedlib.patch @@ -0,0 +1,39 @@ +Authors: Andrei Rozanski and Grace Dinh +Last-Update: 2022-08-23 +Description: fix makefile.u in order to get libamplsover.so (Linux) or libamplsolver.dylib (Mac) + +--- a/makefile.u ++++ b/makefile.u + +@@ -26,8 +26,9 @@ + + .SUFFIXES: .c .o + CC = cc +-CFLAGS = -O ++CFLAGS := $(CFLAGS) -pipe -DASL_BUILD -fPIC -DPIC + SHELL=/bin/sh ++OFILES=$(addsuffix .o,$(basename $(a))) + + # Add -DNO_RUSAGE to the CFLAGS assignment if your system + # lacks getrusage(). This only matters for compiling xectim.c. +@@ -86,7 +87,7 @@ + .c.o: + $(CC) -c $(CFLAGS) $*.c + +-all: arith.h stdio1.h amplsolver.a funcadd0.o ++all: arith.h stdio1.h amplsolver.a funcadd0.o libamplsolver@sharedlibext@ + + a = \ + asldate.c \ +@@ -189,6 +190,11 @@ + # search path, e.g. + # exec true + # or just comment out the ranlib invocation above. ++libamplsolver.so: $(OFILES) ++ $(CC) $^ -shared -Wl,-soname,libamplsolver.so.0 $(LDFLAGS) -o $@.0 ++ ln -s $@.0 $@ ++libamplsolver.dylib: amplsolver.a ++ $(CC) -fpic -shared -Wl,-all_load amplsolver.a $(LDFLAGS) -o libamplsolver.dylib + + Aslh = arith.h asl.h funcadd.h stdio1.h + auxinfo.o libnamsave.o: funcadd.h stdio1.h \ No newline at end of file diff --git a/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix new file mode 100644 index 000000000000..2ee2e831f6e6 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix @@ -0,0 +1,34 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +}: + +stdenv.mkDerivation rec { + version = "1.2"; + pname = "libbraiding"; + + src = fetchFromGitHub { + owner = "miguelmarco"; + repo = "libbraiding"; + rev = version; + sha256 = "sha256-cgg6rvlOvFqGjgbw6i7QXS+tqvfFd1MkPCEjnW/FyFs="; + }; + + nativeBuildInputs = [ + autoreconfHook + ]; + + # no tests included for now (2018-08-05), but can't hurt to activate + doCheck = true; + + meta = with lib; { + homepage = "https://github.com/miguelmarco/libbraiding/"; + description = "C++ library for computations on braid groups"; + longDescription = '' + A library to compute several properties of braids, including centralizer and conjugacy check. + ''; + license = licenses.gpl3; + maintainers = teams.sage.members; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix new file mode 100644 index 000000000000..d0f09290c3c7 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix @@ -0,0 +1,35 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +, boehmgc +}: + +stdenv.mkDerivation rec { + version = "1.02r6"; + pname = "libhomfly"; + + src = fetchFromGitHub { + owner = "miguelmarco"; + repo = "libhomfly"; + rev = version; + sha256 = "sha256-s1Hgy6S9+uREKsgjOVQdQfnds6oSLo5UWTrt5DJnY2s="; + }; + + buildInputs = [ + boehmgc + ]; + + nativeBuildInputs = [ + autoreconfHook + ]; + + doCheck = true; + + meta = with lib; { + homepage = "https://github.com/miguelmarco/libhomfly/"; + description = "Library to compute the homfly polynomial of knots and links"; + license = licenses.unlicense; + maintainers = teams.sage.members; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix new file mode 100644 index 000000000000..595ba2aa5713 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix @@ -0,0 +1,83 @@ +{ lib +, stdenv +, fetchFromGitHub +, gfortran +, cmake +, shared ? true +# Compile with ILP64 interface +, blas64 ? false +, testers +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "liblapack"; + version = "3.12.0"; + + src = fetchFromGitHub { + owner = "Reference-LAPACK"; + repo = "lapack"; + rev = "v${finalAttrs.version}"; + sha256 = "sha256-xn9HL4YF8JPka1gwet5bGGo2k505H3RfWpxkUIYNecQ="; + }; + + nativeBuildInputs = [ gfortran cmake ]; + + # Configure stage fails on aarch64-darwin otherwise, due to either clang 11 or gfortran 10. + hardeningDisable = lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [ "stackprotector" ]; + + cmakeFlags = [ + "-DCMAKE_Fortran_FLAGS=-fPIC" + "-DLAPACKE=ON" + "-DCBLAS=ON" + "-DBUILD_TESTING=ON" + ] ++ lib.optional shared "-DBUILD_SHARED_LIBS=ON" + ++ lib.optional blas64 "-DBUILD_INDEX64=ON" + # Tries to run host platform binaries during the build + # Will likely be disabled by default in 3.12, see: + # https://github.com/Reference-LAPACK/lapack/issues/757 + ++ lib.optional (!stdenv.buildPlatform.canExecute stdenv.hostPlatform) "-DTEST_FORTRAN_COMPILER=OFF"; + + passthru = { inherit blas64; }; + + postInstall = let + canonicalExtension = if stdenv.hostPlatform.isLinux + then "${stdenv.hostPlatform.extensions.sharedLibrary}.${lib.versions.major finalAttrs.version}" + else stdenv.hostPlatform.extensions.sharedLibrary; + in lib.optionalString blas64 '' + ln -s $out/lib/liblapack64${canonicalExtension} $out/lib/liblapack${canonicalExtension} + ln -s $out/lib/liblapacke64${canonicalExtension} $out/lib/liblapacke${canonicalExtension} + ''; + + doCheck = true; + + # Some CBLAS related tests fail on Darwin: + # 14 - CBLAS-xscblat2 (Failed) + # 15 - CBLAS-xscblat3 (Failed) + # 17 - CBLAS-xdcblat2 (Failed) + # 18 - CBLAS-xdcblat3 (Failed) + # 20 - CBLAS-xccblat2 (Failed) + # 21 - CBLAS-xccblat3 (Failed) + # 23 - CBLAS-xzcblat2 (Failed) + # 24 - CBLAS-xzcblat3 (Failed) + # + # Upstream issue to track: + # * https://github.com/Reference-LAPACK/lapack/issues/440 + ctestArgs = lib.optionalString stdenv.isDarwin "-E '^(CBLAS-(x[sdcz]cblat[23]))$'"; + + checkPhase = '' + runHook preCheck + ctest ${finalAttrs.ctestArgs} + runHook postCheck + ''; + + passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage; + + meta = with lib; { + description = "Linear Algebra PACKage"; + homepage = "http://www.netlib.org/lapack/"; + maintainers = with maintainers; [ markuskowa ]; + license = licenses.bsd3; + pkgConfigModules = [ "lapack" ]; + platforms = platforms.all; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix new file mode 100644 index 000000000000..26a1932bd192 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix @@ -0,0 +1,19 @@ +{ lib, stdenv, fetchurl }: +stdenv.mkDerivation rec { + pname = "liblbfgs"; + version = "1.10"; + + configureFlags = [ "--enable-sse2" ]; + src = fetchurl { + url = "https://github.com/downloads/chokkan/liblbfgs/liblbfgs-${version}.tar.gz"; + sha256 = "1kv8d289rbz38wrpswx5dkhr2yh4fg4h6sszkp3fawxm09sann21"; + }; + + meta = { + broken = (stdenv.isLinux && stdenv.isAarch64); + description = "Library of Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)"; + homepage = "http://www.chokkan.org/software/liblbfgs/"; + license = lib.licenses.mit; + platforms = lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix new file mode 100644 index 000000000000..47a6249ebdc6 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix @@ -0,0 +1,104 @@ +{ callPackage +, stdenv +, fetchzip +, lib +, libcxx + +, addOpenGLRunpath +, patchelf +, fixDarwinDylibNames + +, cudaSupport +}: + +let + # The binary libtorch distribution statically links the CUDA + # toolkit. This means that we do not need to provide CUDA to + # this derivation. However, we should ensure on version bumps + # that the CUDA toolkit for `passthru.tests` is still + # up-to-date. + version = "2.0.0"; + device = if cudaSupport then "cuda" else "cpu"; + srcs = import ./binary-hashes.nix version; + unavailable = throw "libtorch is not available for this platform"; + libcxx-for-libtorch = if stdenv.hostPlatform.system == "x86_64-darwin" then libcxx else stdenv.cc.cc.lib; +in stdenv.mkDerivation { + inherit version; + pname = "libtorch"; + + src = fetchzip srcs."${stdenv.hostPlatform.system}-${device}" or unavailable; + + nativeBuildInputs = + if stdenv.isDarwin then [ fixDarwinDylibNames ] + else [ patchelf ] ++ lib.optionals cudaSupport [ addOpenGLRunpath ]; + + dontBuild = true; + dontConfigure = true; + dontStrip = true; + + installPhase = '' + # Copy headers and CMake files. + mkdir -p $dev + cp -r include $dev + cp -r share $dev + + install -Dm755 -t $out/lib lib/*${stdenv.hostPlatform.extensions.sharedLibrary}* + + # 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 + rpath = lib.makeLibraryPath [ stdenv.cc.cc.lib ]; + in lib.optionalString stdenv.isLinux '' + find $out/lib -type f \( -name '*.so' -or -name '*.so.*' \) | while read lib; do + echo "setting rpath for $lib..." + patchelf --set-rpath "${rpath}:$out/lib" "$lib" + ${lib.optionalString cudaSupport '' + addOpenGLRunpath "$lib" + ''} + done + '' + lib.optionalString stdenv.isDarwin '' + for f in $out/lib/*.dylib; do + otool -L $f + done + for f in $out/lib/*.dylib; do + install_name_tool -id $out/lib/$(basename $f) $f || true + for rpath in $(otool -L $f | grep rpath | awk '{print $1}');do + install_name_tool -change $rpath $out/lib/$(basename $rpath) $f + done + if otool -L $f | grep /usr/lib/libc++ >& /dev/null; then + install_name_tool -change /usr/lib/libc++.1.dylib ${libcxx-for-libtorch.outPath}/lib/libc++.1.0.dylib $f + fi + done + for f in $out/lib/*.dylib; do + otool -L $f + done + ''; + + outputs = [ "out" "dev" ]; + + passthru.tests.cmake = callPackage ./test { + inherit cudaSupport; + }; + + meta = with lib; { + description = "C++ API of the PyTorch machine learning framework"; + homepage = "https://pytorch.org/"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; + # Includes CUDA and Intel MKL, but redistributions of the binary are not limited. + # https://docs.nvidia.com/cuda/eula/index.html + # https://www.intel.com/content/www/us/en/developer/articles/license/onemkl-license-faq.html + license = licenses.bsd3; + maintainers = with maintainers; [ junjihashimoto ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix new file mode 100644 index 000000000000..83533d89b1e8 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/binary-hashes.nix @@ -0,0 +1,19 @@ +version : builtins.getAttr version { + "2.0.0" = { + x86_64-darwin-cpu = { + name = "libtorch-macos-2.0.0.zip"; + url = "https://download.pytorch.org/libtorch/cpu/libtorch-macos-2.0.0.zip"; + hash = "sha256-u6y5IeYoiOC0yQ/k6JCChDs9lXWccLxUorgR8L62lkM="; + }; + x86_64-linux-cpu = { + name = "libtorch-cxx11-abi-shared-with-deps-2.0.0-cpu.zip"; + url = "https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip"; + hash = "sha256-BoZQ2MC1CDVVGfX3SHC3mEpLGWO8XK7AcLcHJXDsXuc="; + }; + x86_64-linux-cuda = { + name = "libtorch-cxx11-abi-shared-with-deps-2.0.0-cu118.zip"; + url = "https://download.pytorch.org/libtorch/cu118/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcu118.zip"; + hash = "sha256-Dpw9kQdA1NI9EOT7JBKwQP4wZT6lizcnKKTQ8WVJCZc="; + }; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/prefetch.sh b/nixpkgs/pkgs/development/libraries/science/math/libtorch/prefetch.sh new file mode 100755 index 000000000000..5c6d60ae8b20 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/prefetch.sh @@ -0,0 +1,38 @@ +#!/usr/bin/env nix-shell +#!nix-shell -i bash -p nix-prefetch-scripts + +set -eou pipefail + +version=$1 + +bucket="https://download.pytorch.org/libtorch" +CUDA_VERSION=cu116 + +url_and_key_list=( + "x86_64-darwin-cpu $bucket/cpu/libtorch-macos-${version}.zip libtorch-macos-${version}.zip" + "x86_64-linux-cpu $bucket/cpu/libtorch-cxx11-abi-shared-with-deps-${version}%2Bcpu.zip libtorch-cxx11-abi-shared-with-deps-${version}-cpu.zip" + "x86_64-linux-cuda $bucket/${CUDA_VERSION}/libtorch-cxx11-abi-shared-with-deps-${version}%2B${CUDA_VERSION}.zip libtorch-cxx11-abi-shared-with-deps-${version}-${CUDA_VERSION}.zip" +) + +hashfile="binary-hashes-$version.nix" +echo " \"$version\" = {" >> $hashfile + +for url_and_key in "${url_and_key_list[@]}"; do + key=$(echo "$url_and_key" | cut -d' ' -f1) + url=$(echo "$url_and_key" | cut -d' ' -f2) + name=$(echo "$url_and_key" | cut -d' ' -f3) + + echo "prefetching ${url}..." + hash=$(nix hash to-sri --type sha256 $(nix-prefetch-url --unpack "$url" --name "$name")) + + echo " $key = {" >> $hashfile + echo " name = \"$name\";" >> $hashfile + echo " url = \"$url\";" >> $hashfile + echo " hash = \"$hash\";" >> $hashfile + echo " };" >> $hashfile + + echo +done + +echo " };" >> $hashfile +echo "done." diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt new file mode 100644 index 000000000000..4e96704a4c17 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/CMakeLists.txt @@ -0,0 +1,5 @@ +cmake_minimum_required(VERSION 3.0) +find_package(Torch REQUIRED) +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") +add_executable(test test.cpp) +target_link_libraries(test "${TORCH_LIBRARIES}") diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix new file mode 100644 index 000000000000..a7940cd1db8d --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/default.nix @@ -0,0 +1,51 @@ +{ lib +, stdenv +, cmake +, libtorch-bin +, linkFarm +, symlinkJoin + +, cudaSupport +, cudaPackages ? {} +}: +let + inherit (cudaPackages) cudatoolkit cudnn; + + cudatoolkit_joined = symlinkJoin { + name = "${cudatoolkit.name}-unsplit"; + paths = [ cudatoolkit.out cudatoolkit.lib ]; + }; + + # We do not have access to /run/opengl-driver/lib in the sandbox, + # so use a stub instead. + cudaStub = linkFarm "cuda-stub" [{ + name = "libcuda.so.1"; + path = "${cudatoolkit}/lib/stubs/libcuda.so"; + }]; + +in stdenv.mkDerivation { + pname = "libtorch-test"; + version = libtorch-bin.version; + + src = ./.; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ libtorch-bin ] ++ + lib.optionals cudaSupport [ cudnn ]; + + cmakeFlags = lib.optionals cudaSupport + [ "-DCUDA_TOOLKIT_ROOT_DIR=${cudatoolkit_joined}" ]; + + doCheck = true; + + installPhase = '' + touch $out + ''; + + checkPhase = lib.optionalString cudaSupport '' + LD_LIBRARY_PATH=${cudaStub}''${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH \ + '' + '' + ./test + ''; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp new file mode 100644 index 000000000000..ca238fba521d --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/test/test.cpp @@ -0,0 +1,20 @@ +#undef NDEBUG +#include <cassert> + +#include <iostream> + +#include <torch/torch.h> + +int main() { + torch::Tensor tensor = torch::eye(3); + + 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/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix new file mode 100644 index 000000000000..6fa8567355a9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix @@ -0,0 +1,26 @@ +{ lib, stdenv, fetchurl, gmp }: + +stdenv.mkDerivation { + pname = "lrs"; + version = "7.2"; + + src = fetchurl { + url = "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-072.tar.gz"; + sha256 = "1w1jsnfgny8cihndr5gfm99pvwp48qsvxkqfsi2q87gd3m57aj7w"; + }; + + buildInputs = [ gmp ]; + + makeFlags = [ + "prefix=${placeholder "out"}" + "CC:=$(CC)" + ]; + + meta = { + description = "Implementation of the reverse search algorithm for vertex enumeration/convex hull problems"; + license = lib.licenses.gpl2; + maintainers = [ lib.maintainers.raskin ]; + platforms = lib.platforms.linux; + homepage = "http://cgm.cs.mcgill.ca/~avis/C/lrs.html"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix new file mode 100644 index 000000000000..26e26e4ffdbc --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv +, fetchFromBitbucket +, autoreconfHook +}: + +stdenv.mkDerivation rec { + version = "20200125"; + pname = "m4ri"; + + src = fetchFromBitbucket { + owner = "malb"; + repo = "m4ri"; + rev = "release-${version}"; + sha256 = "1dxgbv6zdyki3h61qlv7003wzhy6x14zmcaz9x19md1i7ng07w1k"; + }; + + doCheck = true; + + nativeBuildInputs = [ + autoreconfHook + ]; + + meta = with lib; { + homepage = "https://malb.bitbucket.io/m4ri/"; + description = "Library to do fast arithmetic with dense matrices over F_2"; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix new file mode 100644 index 000000000000..214f27046527 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix @@ -0,0 +1,41 @@ +{ lib, stdenv +, fetchFromBitbucket +, autoreconfHook +, m4ri +}: + +stdenv.mkDerivation rec { + version = "20200125"; + pname = "m4rie"; + + src = fetchFromBitbucket { + owner = "malb"; + repo = "m4rie"; + rev = "release-${version}"; + sha256 = "sha256-bjAcxfXsC6+jPYC472CN78jm4UljJQlkWyvsqckCDh0="; + }; + + doCheck = true; + + buildInputs = [ + m4ri + ]; + + nativeBuildInputs = [ + autoreconfHook + ]; + + meta = with lib; { + homepage = "https://malb.bitbucket.io/m4rie/"; + description = "Library for matrix multiplication, reduction and inversion over GF(2^k) for 2 <= k <= 10"; + longDescription = '' + M4RIE is a library for fast arithmetic with dense matrices over small finite fields of even characteristic. + It uses the M4RI library, implementing the same operations over the finite field F2. + ''; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + platforms = platforms.unix; + # never built on aarch64-darwin since first introduction in nixpkgs + broken = stdenv.isDarwin && stdenv.isAarch64; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix new file mode 100644 index 000000000000..9eb410595974 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix @@ -0,0 +1,53 @@ +args@{ callPackage +, lib +, ... +}: + +# Type aliases +# Release = { +# version: String +# hash: String +# supportedGpuTargets: List String +# } + +let + inherit (lib) lists strings trivial; + + computeName = version: "magma_${strings.replaceStrings [ "." ] [ "_" ] version}"; + + # buildMagmaPackage :: Release -> Derivation + buildMagmaPackage = magmaRelease: callPackage ./generic.nix ( + (builtins.removeAttrs args [ "callPackage" ]) // { + inherit magmaRelease; + } + ); + + # Reverse the list to have the latest release first + # magmaReleases :: List Release + magmaReleases = lists.reverseList (builtins.import ./releases.nix); + + # The latest release is the first element of the list and will be our default choice + # latestReleaseName :: String + latestReleaseName = computeName (builtins.head magmaReleases).version; + + # Function to transform our releases into build attributes + # toBuildAttrs :: Release -> { name: String, value: Derivation } + toBuildAttrs = release: { + name = computeName release.version; + value = buildMagmaPackage release; + }; + + # Add all supported builds as attributes + # allBuilds :: AttrSet String Derivation + allBuilds = builtins.listToAttrs (lists.map toBuildAttrs magmaReleases); + + # The latest release will be our default build + # defaultBuild :: AttrSet String Derivation + defaultBuild.magma = allBuilds.${latestReleaseName}; + + # builds :: AttrSet String Derivation + builds = allBuilds // defaultBuild; +in + +builds + diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix new file mode 100644 index 000000000000..7ef60e0418ed --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix @@ -0,0 +1,173 @@ +# Type aliases +# Release = { +# version: String +# hash: String +# supportedGpuTargets: List String +# } + +{ blas +, cmake +, cudaPackages +, cudaSupport ? config.cudaSupport +, fetchurl +, gfortran +, cudaCapabilities ? cudaPackages.cudaFlags.cudaCapabilities +, gpuTargets ? [ ] # Non-CUDA targets, that is HIP +, rocmPackages +, lapack +, lib +, libpthreadstubs +, magmaRelease +, ninja +, config + # At least one back-end has to be enabled, + # and we can't default to CUDA since it's unfree +, rocmSupport ? !cudaSupport +, static ? stdenv.hostPlatform.isStatic +, stdenv +, symlinkJoin +}: + + +let + inherit (lib) lists strings trivial; + inherit (cudaPackages) backendStdenv cudaFlags cudaVersion; + inherit (magmaRelease) version hash supportedGpuTargets; + + # NOTE: The lists.subtractLists function is perhaps a bit unintuitive. It subtracts the elements + # of the first list *from* the second list. That means: + # lists.subtractLists a b = b - a + + # For ROCm + # NOTE: The hip.gpuTargets are prefixed with "gfx" instead of "sm" like cudaFlags.realArches. + # For some reason, Magma's CMakeLists.txt file does not handle the "gfx" prefix, so we must + # remove it. + rocmArches = lists.map (x: strings.removePrefix "gfx" x) rocmPackages.clr.gpuTargets; + supportedRocmArches = lists.intersectLists rocmArches supportedGpuTargets; + unsupportedRocmArches = lists.subtractLists supportedRocmArches rocmArches; + + supportedCustomGpuTargets = lists.intersectLists gpuTargets supportedGpuTargets; + unsupportedCustomGpuTargets = lists.subtractLists supportedCustomGpuTargets gpuTargets; + + # Use trivial.warnIf to print a warning if any unsupported GPU targets are specified. + gpuArchWarner = supported: unsupported: + trivial.throwIf (supported == [ ]) + ( + "No supported GPU targets specified. Requested GPU targets: " + + strings.concatStringsSep ", " unsupported + ) + supported; + + gpuTargetString = strings.concatStringsSep "," ( + if gpuTargets != [ ] then + # If gpuTargets is specified, it always takes priority. + gpuArchWarner supportedCustomGpuTargets unsupportedCustomGpuTargets + else if rocmSupport then + gpuArchWarner supportedRocmArches unsupportedRocmArches + else if cudaSupport then + [ ] # It's important we pass explicit -DGPU_TARGET to reset magma's defaults + else + throw "No GPU targets specified" + ); + + # E.g. [ "80" "86" "90" ] + cudaArchitectures = (builtins.map cudaFlags.dropDot cudaCapabilities); + + cudaArchitecturesString = strings.concatStringsSep ";" cudaArchitectures; + minArch = + let + minArch' = builtins.head (builtins.sort strings.versionOlder cudaArchitectures); + in + # "75" -> "750" Cf. https://bitbucket.org/icl/magma/src/f4ec79e2c13a2347eff8a77a3be6f83bc2daec20/CMakeLists.txt#lines-273 + "${minArch'}0"; + +in + +assert (builtins.match "[^[:space:]]*" gpuTargetString) != null; + +stdenv.mkDerivation { + pname = "magma"; + inherit version; + + src = fetchurl { + name = "magma-${version}.tar.gz"; + url = "https://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-${version}.tar.gz"; + inherit hash; + }; + + nativeBuildInputs = [ + cmake + ninja + gfortran + ] ++ lists.optionals cudaSupport [ + cudaPackages.cuda_nvcc + ]; + + buildInputs = [ + libpthreadstubs + lapack + blas + ] ++ lists.optionals cudaSupport (with cudaPackages; [ + cuda_cudart.dev # cuda_runtime.h + cuda_cudart.lib # cudart + cuda_cudart.static # cudart_static + libcublas.dev # cublas_v2.h + libcublas.lib # cublas + libcusparse.dev # cusparse.h + libcusparse.lib # cusparse + ] ++ lists.optionals (strings.versionOlder cudaVersion "11.8") [ + cuda_nvprof.dev # <cuda_profiler_api.h> + ] ++ lists.optionals (strings.versionAtLeast cudaVersion "11.8") [ + cuda_profiler_api.dev # <cuda_profiler_api.h> + ] ++ lists.optionals (strings.versionAtLeast cudaVersion "12.0") [ + cuda_cccl.dev # <nv/target> + ]) ++ lists.optionals rocmSupport [ + rocmPackages.clr + rocmPackages.hipblas + rocmPackages.hipsparse + rocmPackages.llvm.openmp + ]; + + cmakeFlags = [ + "-DGPU_TARGET=${gpuTargetString}" + (lib.cmakeBool "MAGMA_ENABLE_CUDA" cudaSupport) + (lib.cmakeBool "MAGMA_ENABLE_HIP" rocmSupport) + ] ++ lists.optionals static [ + "-DBUILD_SHARED_LIBS=OFF" + ] ++ lists.optionals cudaSupport [ + "-DCMAKE_CUDA_ARCHITECTURES=${cudaArchitecturesString}" + "-DMIN_ARCH=${minArch}" # Disarms magma's asserts + "-DCMAKE_C_COMPILER=${backendStdenv.cc}/bin/cc" + "-DCMAKE_CXX_COMPILER=${backendStdenv.cc}/bin/c++" + ] ++ lists.optionals rocmSupport [ + "-DCMAKE_C_COMPILER=${rocmPackages.clr}/bin/hipcc" + "-DCMAKE_CXX_COMPILER=${rocmPackages.clr}/bin/hipcc" + ] ++ lists.optionals (cudaPackages.cudaAtLeast "12.0.0") [ + (lib.cmakeBool "USE_FORTRAN" false) + ]; + + buildFlags = [ + "magma" + "magma_sparse" + ]; + + doCheck = false; + + passthru = { + inherit cudaPackages cudaSupport rocmSupport gpuTargets; + }; + + meta = with lib; { + description = "Matrix Algebra on GPU and Multicore Architectures"; + license = licenses.bsd3; + homepage = "http://icl.cs.utk.edu/magma/index.html"; + platforms = platforms.linux; + maintainers = with maintainers; [ connorbaker ]; + + # Cf. https://bitbucket.org/icl/magma/src/fcfe5aa61c1a4c664b36a73ebabbdbab82765e9f/CMakeLists.txt#lines-20 + broken = + !(cudaSupport || rocmSupport) # At least one back-end enabled + || (cudaSupport && rocmSupport) # Mutually exclusive + || (cudaSupport && strings.versionOlder cudaVersion "9"); + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/releases.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/releases.nix new file mode 100644 index 000000000000..59f495d67109 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/magma/releases.nix @@ -0,0 +1,69 @@ +# NOTE: Order matters! Put the oldest version first, and the newest version last. +# NOTE: Make sure the supportedGpuTargets are in order of oldest to newest. +# You can update the supportedGpuTargets by looking at the CMakeLists.txt file. +# HIP is here: https://bitbucket.org/icl/magma/src/f4ec79e2c13a2347eff8a77a3be6f83bc2daec20/CMakeLists.txt#lines-386 +# CUDA works around magma's wrappers and uses FindCUDAToolkit directly +[ + { + version = "2.6.2"; + hash = "sha256-dbVU2rAJA+LRC5cskT5Q5/iMvGLzrkMrWghsfk7aCnE="; + supportedGpuTargets = [ + "700" + "701" + "702" + "703" + "704" + "705" + "801" + "802" + "803" + "805" + "810" + "900" + "902" + "904" + "906" + "908" + "909" + "90c" + "1010" + "1011" + "1012" + "1030" + "1031" + "1032" + "1033" + ]; + } + { + version = "2.7.2"; + hash = "sha256-cpvBpw5RinQi/no6VFN6R0EDWne+M0n2bqxcNiV21WA="; + supportedGpuTargets = [ + "700" + "701" + "702" + "703" + "704" + "705" + "801" + "802" + "803" + "805" + "810" + "900" + "902" + "904" + "906" + "908" + "909" + "90c" + "1010" + "1011" + "1012" + "1030" + "1031" + "1032" + "1033" + ]; + } +] diff --git a/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix new file mode 100644 index 000000000000..cd221e86b148 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix @@ -0,0 +1,25 @@ +{ lib, stdenv, fetchurl, unzip, cmake }: + +stdenv.mkDerivation rec { + pname = "metis"; + version = "5.1.0"; + + src = fetchurl { + url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-${version}.tar.gz"; + sha256 = "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"; + }; + + cmakeFlags = [ + "-DGKLIB_PATH=../GKlib" + # remove once updated past https://github.com/KarypisLab/METIS/commit/521a2c360dc21ace5c4feb6dc0b7992433e3cb0f + "-DCMAKE_SKIP_BUILD_RPATH=ON" + ]; + nativeBuildInputs = [ unzip cmake ]; + + meta = { + description = "Serial graph partitioning and fill-reducing matrix ordering"; + homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"; + license = lib.licenses.asl20; + platforms = lib.platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix new file mode 100644 index 000000000000..90e6c05da77d --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix @@ -0,0 +1,184 @@ +{ lib +, stdenv +, callPackage +, stdenvNoCC +, fetchurl +, rpmextract +, _7zz +, darwin +, validatePkgConfig +, enableStatic ? stdenv.hostPlatform.isStatic +}: + +/* + For details on using mkl as a blas provider for python packages such as numpy, + numexpr, scipy, etc., see the Python section of the NixPkgs manual. +*/ +let + # Release notes and download URLs are here: + # https://registrationcenter.intel.com/en/products/ + version = "${mklVersion}.${rel}"; + + mklVersion = "2023.1.0"; + rel = if stdenvNoCC.isDarwin then "43558" else "46342"; + + # Intel openmp uses its own versioning. + openmpVersion = "2023.1.0"; + openmpRel = "46305"; + + # Thread Building Blocks release. + tbbVersion = "2021.9.0"; + tbbRel = "43484"; + + shlibExt = stdenvNoCC.hostPlatform.extensions.sharedLibrary; + + oneapi-mkl = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-mkl-${mklVersion}-${mklVersion}-${rel}.x86_64.rpm"; + hash = "sha256-PGLPNnR+11AmmaNxldeze/l2Kw/4+mfjB+RqsPhP6oM="; + }; + + oneapi-mkl-common = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-mkl-common-${mklVersion}-${mklVersion}-${rel}.noarch.rpm"; + hash = "sha256-wztTE2R/IdG6ujGf7KFocpRmXzlZSnEKopTBOlPPlBw="; + }; + + oneapi-mkl-common-devel = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-mkl-common-devel-${mklVersion}-${mklVersion}-${rel}.noarch.rpm"; + hash = "sha256-MWa8mpyFM4zgDLup+EzFRM+N2Oxf0o6FBBRM8mAanbI="; + }; + + oneapi-mkl-devel = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-mkl-devel-${mklVersion}-${mklVersion}-${rel}.x86_64.rpm"; + hash = "sha256-Arq5kXktI92031XqfV0pkzQCHaFsTRKX05iOA/fPNOs="; + }; + + oneapi-openmp = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-openmp-${mklVersion}-${mklVersion}-${openmpRel}.x86_64.rpm"; + hash = "sha256-cyBD3P4AEvyreP4pP3BE+yyDB+ptblOQ9GYI8ysGsIM="; + }; + + oneapi-tbb = fetchurl { + url = "https://yum.repos.intel.com/oneapi/intel-oneapi-tbb-${tbbVersion}-${tbbVersion}-${tbbRel}.x86_64.rpm"; + hash = "sha256-pzJpQdiYVpcKDShePak2I0uEh7u08vJgX7OBF5p5yAM="; + }; + +in stdenvNoCC.mkDerivation ({ + pname = "mkl"; + inherit version; + + dontUnpack = stdenvNoCC.isLinux; + + sourceRoot = if stdenvNoCC.isDarwin then "." else null; + + nativeBuildInputs = [ validatePkgConfig ] ++ (if stdenvNoCC.isDarwin + then + [ _7zz darwin.cctools ] + else + [ rpmextract ]); + + buildPhase = if stdenvNoCC.isDarwin then '' + for f in bootstrapper.app/Contents/Resources/packages/*/cupPayload.cup; do + tar -xf $f + done + mkdir -p opt/intel + mv _installdir opt/intel/oneapi + '' else '' + rpmextract ${oneapi-mkl} + rpmextract ${oneapi-mkl-common} + rpmextract ${oneapi-mkl-common-devel} + rpmextract ${oneapi-mkl-devel} + rpmextract ${oneapi-openmp} + rpmextract ${oneapi-tbb} + ''; + + installPhase = '' + for f in $(find . -name 'mkl*.pc') ; do + bn=$(basename $f) + substituteInPlace $f \ + --replace $\{MKLROOT} "$out" \ + --replace "lib/intel64" "lib" + + sed -r -i "s|^prefix=.*|prefix=$out|g" $f + done + + for f in $(find opt/intel -name 'mkl*iomp.pc') ; do + substituteInPlace $f --replace "../compiler/lib" "lib" + done + + # License + install -Dm0655 -t $out/share/doc/mkl opt/intel/oneapi/mkl/${mklVersion}/licensing/license.txt + + # Dynamic libraries + mkdir -p $out/lib + cp -a opt/intel/oneapi/mkl/${mklVersion}/lib/${lib.optionalString stdenvNoCC.isLinux "intel64"}/*${shlibExt}* $out/lib + cp -a opt/intel/oneapi/compiler/${mklVersion}/${if stdenvNoCC.isDarwin then "mac" else "linux"}/compiler/lib/${lib.optionalString stdenvNoCC.isLinux "intel64_lin"}/*${shlibExt}* $out/lib + cp -a opt/intel/oneapi/tbb/${tbbVersion}/lib/${lib.optionalString stdenvNoCC.isLinux "intel64/gcc4.8"}/*${shlibExt}* $out/lib + + # Headers + cp -r opt/intel/oneapi/mkl/${mklVersion}/include $out/ + + # CMake config + cp -r opt/intel/oneapi/mkl/${mklVersion}/lib/cmake $out/lib + '' + + (if enableStatic then '' + install -Dm0644 -t $out/lib opt/intel/oneapi/mkl/${mklVersion}/lib/${lib.optionalString stdenvNoCC.isLinux "intel64"}/*.a + install -Dm0644 -t $out/lib/pkgconfig opt/intel/oneapi/mkl/${mklVersion}/lib/pkgconfig/*.pc + '' else '' + cp opt/intel/oneapi/mkl/${mklVersion}/lib/${lib.optionalString stdenvNoCC.isLinux "intel64"}/*${shlibExt}* $out/lib + install -Dm0644 -t $out/lib/pkgconfig opt/intel/oneapi/mkl/${mklVersion}/lib/pkgconfig/*dynamic*.pc + '') + '' + # Setup symlinks for blas / lapack + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/libblas${shlibExt} + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/libcblas${shlibExt} + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/liblapack${shlibExt} + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/liblapacke${shlibExt} + '' + lib.optionalString stdenvNoCC.hostPlatform.isLinux '' + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/libblas${shlibExt}".3" + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/libcblas${shlibExt}".3" + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/liblapack${shlibExt}".3" + ln -s $out/lib/libmkl_rt${shlibExt} $out/lib/liblapacke${shlibExt}".3" + ''; + + # 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 = 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.12.dylib $out/lib/libtbb.12.dylib $out/lib/libmkl_tbb_thread.dylib + install_name_tool -change @rpath/libtbbmalloc.2.dylib $out/lib/libtbbmalloc.2.dylib $out/lib/libtbbmalloc_proxy.dylib + ''; + + # Per license agreement, do not modify the binary + dontStrip = true; + dontPatchELF = true; + + passthru.tests = { + pkg-config-dynamic-iomp = callPackage ./test { enableStatic = false; execution = "iomp"; }; + pkg-config-static-iomp = callPackage ./test { enableStatic = true; execution = "iomp"; }; + pkg-config-dynamic-seq = callPackage ./test { enableStatic = false; execution = "seq"; }; + pkg-config-static-seq = callPackage ./test { enableStatic = true; execution = "seq"; }; + }; + + meta = with lib; { + description = "Intel OneAPI Math Kernel Library"; + longDescription = '' + Intel OneAPI Math Kernel Library (Intel oneMKL) optimizes code with minimal + effort for future generations of Intel processors. It is compatible with your + choice of compilers, languages, operating systems, and linking and + threading models. + ''; + homepage = "https://software.intel.com/en-us/mkl"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; + license = licenses.issl; + platforms = [ "x86_64-linux" "x86_64-darwin" ]; + maintainers = with maintainers; [ bhipple ]; + }; +} // lib.optionalAttrs stdenvNoCC.isDarwin { + src = fetchurl { + url = "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/087a9190-9d96-4b8c-bd2f-79159572ed89/m_onemkl_p_${mklVersion}.${rel}_offline.dmg"; + hash = "sha256-bUaaJPSaLr60fw0DzDCjPvY/UucHlLbCSLyQxyiAi04="; + }; +}) diff --git a/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix new file mode 100644 index 000000000000..cb3355260d12 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/mkl/test/default.nix @@ -0,0 +1,41 @@ +{ stdenv +, pkg-config +, mkl + +, enableStatic ? false +, execution ? "seq" +}: + +let + linkType = if enableStatic then "static" else "dynamic"; +in stdenv.mkDerivation { + pname = "mkl-test"; + version = mkl.version; + + src = ./.; + + nativeBuildInputs = [ pkg-config ]; + + buildInputs = [ (mkl.override { inherit enableStatic; }) ]; + + doCheck = true; + + buildPhase = '' + # Check regular Nix build. + gcc test.c -o test $(pkg-config --cflags --libs mkl-${linkType}-ilp64-${execution}) + + # Clear flags to ensure that we are purely relying on options + # provided by pkg-config. + NIX_CFLAGS_COMPILE="" \ + NIX_LDFLAGS="" \ + gcc test.c -o test $(pkg-config --cflags --libs mkl-${linkType}-ilp64-${execution}) + ''; + + installPhase = '' + touch $out + ''; + + checkPhase = '' + ./test + ''; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c b/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c new file mode 100644 index 000000000000..9413ac0c68e9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/mkl/test/test.c @@ -0,0 +1,12 @@ +#include <assert.h> + +#include <mkl_cblas.h> + +int main() { + float u[] = {1., 2., 3.}; + float v[] = {4., 5., 6.}; + + float dp = cblas_sdot(3, u, 1, v, 1); + + assert(dp == 32.); +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix new file mode 100644 index 000000000000..29b901277f61 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix @@ -0,0 +1,69 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, blas +, llvmPackages +}: + +let + suitesparseVersion = "7.6.0"; +in +stdenv.mkDerivation { + pname = "mongoose"; + version = "3.3.2"; + + outputs = [ "bin" "out" "dev" ]; + + src = fetchFromGitHub { + owner = "DrTimothyAldenDavis"; + repo = "SuiteSparse"; + rev = "v${suitesparseVersion}"; + hash = "sha256-zZXbUNXxVi4mpI4j4GjyVYraoPFWcuep9q5jl1XdqEo="; + }; + + nativeBuildInputs = [ + cmake + ]; + + buildInputs = [ + blas + ] ++ lib.optionals stdenv.cc.isClang [ + llvmPackages.openmp + ]; + + dontUseCmakeConfigure = true; + + cmakeFlags = [ + "-DBLAS_LIBRARIES=${blas}" + "-DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=ON" + ]; + + buildPhase = '' + runHook preConfigure + + for f in SuiteSparse_config Mongoose; do + (cd $f && cmakeConfigurePhase && make -j$NIX_BUILD_CORES) + done + + runHook postConfigure + ''; + + installPhase = '' + runHook preInstall + + for f in SuiteSparse_config Mongoose; do + (cd $f/build && make install -j$NIX_BUILD_CORES) + done + + runHook postInstall + ''; + + meta = with lib; { + description = "Graph Coarsening and Partitioning Library"; + homepage = "https://github.com/DrTimothyAldenDavis/SuiteSparse/tree/dev/Mongoose"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ wegank ]; + platforms = with platforms; unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix new file mode 100644 index 000000000000..7ecd6a88d13c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix @@ -0,0 +1,269 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch, perl, which +# Most packages depending on openblas expect integer width to match +# pointer width, but some expect to use 32-bit integers always +# (for compatibility with reference BLAS). +, blas64 ? null +# Multi-threaded applications must not call a threaded OpenBLAS +# (the only exception is when an application uses OpenMP as its +# *only* form of multi-threading). See +# https://github.com/OpenMathLib/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded +# https://github.com/OpenMathLib/OpenBLAS/issues/2543 +# This flag builds a single-threaded OpenBLAS using the flags +# stated in thre. +, singleThreaded ? false +, buildPackages +# Select a specific optimization target (other than the default) +# See https://github.com/OpenMathLib/OpenBLAS/blob/develop/TargetList.txt +, target ? null +# Select whether DYNAMIC_ARCH is enabled or not. +, dynamicArch ? null +# enable AVX512 optimized kernels. +# These kernels have been a source of trouble in the past. +# Use with caution. +, enableAVX512 ? false +, enableStatic ? stdenv.hostPlatform.isStatic +, enableShared ? !stdenv.hostPlatform.isStatic + +# for passthru.tests +, ceres-solver +, giac +, octave +, opencv +, python3 +, openmp ? null +}: + +let blas64_ = blas64; in + +let + setTarget = x: if target == null then x else target; + setDynamicArch = x: if dynamicArch == null then x else dynamicArch; + + # To add support for a new platform, add an element to this set. + configs = { + armv6l-linux = { + BINARY = 32; + TARGET = setTarget "ARMV6"; + DYNAMIC_ARCH = setDynamicArch false; + USE_OPENMP = true; + }; + + armv7l-linux = { + BINARY = 32; + TARGET = setTarget "ARMV7"; + DYNAMIC_ARCH = setDynamicArch false; + USE_OPENMP = true; + }; + + aarch64-darwin = { + BINARY = 64; + TARGET = setTarget "VORTEX"; + DYNAMIC_ARCH = setDynamicArch true; + USE_OPENMP = false; + MACOSX_DEPLOYMENT_TARGET = "11.0"; + }; + + aarch64-linux = { + BINARY = 64; + TARGET = setTarget "ARMV8"; + DYNAMIC_ARCH = setDynamicArch true; + USE_OPENMP = true; + }; + + i686-linux = { + BINARY = 32; + TARGET = setTarget "P2"; + DYNAMIC_ARCH = setDynamicArch true; + USE_OPENMP = true; + }; + + x86_64-darwin = { + BINARY = 64; + TARGET = setTarget "ATHLON"; + DYNAMIC_ARCH = setDynamicArch true; + NO_AVX512 = !enableAVX512; + USE_OPENMP = false; + MACOSX_DEPLOYMENT_TARGET = "10.7"; + }; + + x86_64-linux = { + BINARY = 64; + TARGET = setTarget "ATHLON"; + DYNAMIC_ARCH = setDynamicArch true; + NO_AVX512 = !enableAVX512; + USE_OPENMP = !stdenv.hostPlatform.isMusl; + }; + + powerpc64le-linux = { + BINARY = 64; + TARGET = setTarget "POWER5"; + DYNAMIC_ARCH = setDynamicArch true; + USE_OPENMP = !stdenv.hostPlatform.isMusl; + }; + + riscv64-linux = { + BINARY = 64; + TARGET = setTarget "RISCV64_GENERIC"; + DYNAMIC_ARCH = setDynamicArch false; + USE_OPENMP = true; + }; + + loongarch64-linux = { + BINARY = 64; + TARGET = setTarget "LOONGSONGENERIC"; + DYNAMIC_ARCH = setDynamicArch false; + USE_OPENMP = true; + }; + }; +in + +let + config = + configs.${stdenv.hostPlatform.system} + or (throw "unsupported system: ${stdenv.hostPlatform.system}"); +in + +let + blas64 = + if blas64_ != null + then blas64_ + else lib.hasPrefix "x86_64" stdenv.hostPlatform.system; + # Convert flag values to format OpenBLAS's build expects. + # `toString` is almost what we need other than bools, + # which we need to map {true -> 1, false -> 0} + # (`toString` produces empty string `""` for false instead of `0`) + mkMakeFlagValue = val: + if !builtins.isBool val then toString val + else if val then "1" else "0"; + mkMakeFlagsFromConfig = lib.mapAttrsToList (var: val: "${var}=${mkMakeFlagValue val}"); + + shlibExt = stdenv.hostPlatform.extensions.sharedLibrary; + +in +stdenv.mkDerivation rec { + pname = "openblas"; + version = "0.3.26"; + + outputs = [ "out" "dev" ]; + + src = fetchFromGitHub { + owner = "OpenMathLib"; + repo = "OpenBLAS"; + rev = "v${version}"; + hash = "sha256-AA3+x3SXkcg3g7bROZYLpWAbxnRedmQBZPe+rBJKxJ8="; + }; + + postPatch = '' + # cc1: error: invalid feature modifier 'sve2' in '-march=armv8.5-a+sve+sve2+bf16' + substituteInPlace Makefile.arm64 --replace "+sve2+bf16" "" + ''; + + inherit blas64; + + # Some hardening features are disabled due to sporadic failures in + # OpenBLAS-based programs. The problem may not be with OpenBLAS itself, but + # with how these flags interact with hardening measures used downstream. + # In either case, OpenBLAS must only be used by trusted code--it is + # inherently unsuitable for security-conscious applications--so there should + # be no objection to disabling these hardening measures. + hardeningDisable = [ + # don't modify or move the stack + "stackprotector" "pic" + # don't alter index arithmetic + "strictoverflow" + # don't interfere with dynamic target detection + "relro" "bindnow" + ]; + + nativeBuildInputs = [ + perl + which + ]; + + buildInputs = lib.optional (stdenv.cc.isClang && config.USE_OPENMP) openmp; + + depsBuildBuild = [ + buildPackages.gfortran + buildPackages.stdenv.cc + ]; + + enableParallelBuilding = true; + + makeFlags = mkMakeFlagsFromConfig (config // { + FC = "${stdenv.cc.targetPrefix}gfortran"; + CC = "${stdenv.cc.targetPrefix}${if stdenv.cc.isClang then "clang" else "cc"}"; + PREFIX = placeholder "out"; + OPENBLAS_INCLUDE_DIR = "${placeholder "dev"}/include"; + NUM_THREADS = 64; + INTERFACE64 = blas64; + NO_STATIC = !enableStatic; + NO_SHARED = !enableShared; + CROSS = stdenv.hostPlatform != stdenv.buildPlatform; + HOSTCC = "cc"; + # Makefile.system only checks defined status + # This seems to be a bug in the openblas Makefile: + # on x86_64 it expects NO_BINARY_MODE= + # but on aarch64 it expects NO_BINARY_MODE=0 + NO_BINARY_MODE = if stdenv.isx86_64 + then toString (stdenv.hostPlatform != stdenv.buildPlatform) + else stdenv.hostPlatform != stdenv.buildPlatform; + # This disables automatic build job count detection (which honours neither enableParallelBuilding nor NIX_BUILD_CORES) + # and uses the main make invocation's job count, falling back to 1 if no parallelism is used. + # https://github.com/OpenMathLib/OpenBLAS/blob/v0.3.20/getarch.c#L1781-L1792 + MAKE_NB_JOBS = 0; + } // (lib.optionalAttrs stdenv.cc.isClang { + LDFLAGS = "-L${lib.getLib buildPackages.gfortran.cc}/lib"; # contains `libgfortran.so`; building with clang needs this, gcc has it implicit + }) // (lib.optionalAttrs singleThreaded { + # As described on https://github.com/OpenMathLib/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded + USE_THREAD = false; + USE_LOCKING = true; # available with openblas >= 0.3.7 + USE_OPENMP = false; # openblas will refuse building with both USE_OPENMP=1 and USE_THREAD=0 + })); + + doCheck = true; + checkTarget = "tests"; + + postInstall = '' + # Write pkgconfig aliases. Upstream report: + # https://github.com/OpenMathLib/OpenBLAS/issues/1740 + for alias in blas cblas lapack; do + cat <<EOF > $out/lib/pkgconfig/$alias.pc +Name: $alias +Version: ${version} +Description: $alias provided by the OpenBLAS package. +Cflags: -I$dev/include +Libs: -L$out/lib -lopenblas +EOF + done + + # Setup symlinks for blas / lapack + '' + lib.optionalString enableShared '' + ln -s $out/lib/libopenblas${shlibExt} $out/lib/libblas${shlibExt} + ln -s $out/lib/libopenblas${shlibExt} $out/lib/libcblas${shlibExt} + ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapack${shlibExt} + ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapacke${shlibExt} + '' + lib.optionalString (stdenv.hostPlatform.isLinux && enableShared) '' + ln -s $out/lib/libopenblas${shlibExt} $out/lib/libblas${shlibExt}.3 + ln -s $out/lib/libopenblas${shlibExt} $out/lib/libcblas${shlibExt}.3 + ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapack${shlibExt}.3 + ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapacke${shlibExt}.3 + '' + lib.optionalString enableStatic '' + ln -s $out/lib/libopenblas.a $out/lib/libblas.a + ln -s $out/lib/libopenblas.a $out/lib/libcblas.a + ln -s $out/lib/libopenblas.a $out/lib/liblapack.a + ln -s $out/lib/libopenblas.a $out/lib/liblapacke.a + ''; + + passthru.tests = { + inherit (python3.pkgs) numpy scipy; + inherit ceres-solver giac octave opencv; + }; + + meta = with lib; { + description = "Basic Linear Algebra Subprograms"; + license = licenses.bsd3; + homepage = "https://github.com/OpenMathLib/OpenBLAS"; + platforms = attrNames configs; + maintainers = with maintainers; [ ttuegel ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix new file mode 100644 index 000000000000..4ee82bc0633e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix @@ -0,0 +1,23 @@ +{ lib, stdenv, fetchFromGitHub }: + +stdenv.mkDerivation rec { + pname = "openlibm"; + version = "0.8.2"; + + src = fetchFromGitHub { + owner = "JuliaLang"; + repo = "openlibm"; + rev = "v${version}"; + sha256 = "sha256-EnpwYtBpY+s5FVI2jhaFHTtAKHeaRlZVnWE/o2T1+FY="; + }; + + makeFlags = [ "prefix=$(out)" "CC=${stdenv.cc.targetPrefix}cc" ]; + + meta = { + description = "High quality system independent, portable, open source libm implementation"; + homepage = "https://openlibm.org/"; + license = lib.licenses.mit; + maintainers = [ lib.maintainers.ttuegel ]; + platforms = lib.platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix new file mode 100644 index 000000000000..14befd6d11fe --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix @@ -0,0 +1,24 @@ +{ lib, stdenv, fetchFromGitHub, gfortran }: + +stdenv.mkDerivation rec { + pname = "openspecfun"; + version = "0.5.6"; + src = fetchFromGitHub { + owner = "JuliaLang"; + repo = "openspecfun"; + rev = "v${version}"; + sha256 = "sha256-4MPoRMtDTkdvDfhNXKk/80pZjXRNEPcysLNTb5ohxWk="; + }; + + makeFlags = [ "prefix=$(out)" ]; + + nativeBuildInputs = [ gfortran ]; + + meta = { + description = "A collection of special mathematical functions"; + homepage = "https://github.com/JuliaLang/openspecfun"; + license = lib.licenses.mit; + maintainers = [ lib.maintainers.ttuegel ]; + platforms = lib.platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix new file mode 100644 index 000000000000..5cbc23589895 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix @@ -0,0 +1,126 @@ +{ abseil-cpp +, bzip2 +, cbc +, cmake +, eigen +, ensureNewerSourcesForZipFilesHook +, fetchFromGitHub +, fetchpatch +, glpk +, lib +, pkg-config +, protobuf +, python +, re2 +, stdenv +, swig4 +, unzip +, zlib +}: + +stdenv.mkDerivation rec { + pname = "or-tools"; + version = "9.4"; + + src = fetchFromGitHub { + owner = "google"; + repo = "or-tools"; + rev = "v${version}"; + sha256 = "sha256-joWonJGuxlgHhXLznRhC1MDltQulXzpo4Do9dec1bLY="; + }; + patches = [ + # Disable test that requires external input: https://github.com/google/or-tools/issues/3429 + (fetchpatch { + url = "https://github.com/google/or-tools/commit/7072ae92ec204afcbfce17d5360a5884c136ce90.patch"; + hash = "sha256-iWE+atp308q7pC1L1FD6sK8LvWchZ3ofxvXssguozbM="; + }) + # Fix test that broke in parallel builds: https://github.com/google/or-tools/issues/3461 + (fetchpatch { + url = "https://github.com/google/or-tools/commit/a26602f24781e7bfcc39612568aa9f4010bb9736.patch"; + hash = "sha256-gM0rW0xRXMYaCwltPK0ih5mdo3HtX6mKltJDHe4gbLc="; + }) + # Backport fix in cmake test configuration where pip installs newer version from PyPi over local build, + # breaking checkPhase: https://github.com/google/or-tools/issues/3260 + (fetchpatch { + url = "https://github.com/google/or-tools/commit/edd1544375bd55f79168db315151a48faa548fa0.patch"; + hash = "sha256-S//1YM3IoRCp3Ghg8zMF0XXgIpVmaw4gH8cVb9eUbqM="; + }) + # Don't use non-existent member of string_view. Partial patch from commit + # https://github.com/google/or-tools/commit/c5a2fa1eb673bf652cb9ad4f5049d054b8166e17.patch + ./fix-stringview-compile.patch + ]; + + # or-tools normally attempts to build Protobuf for the build platform when + # cross-compiling. Instead, just tell it where to find protoc. + postPatch = '' + echo "set(PROTOC_PRG $(type -p protoc))" > cmake/host.cmake + ''; + + cmakeFlags = [ + "-DBUILD_DEPS=OFF" + "-DBUILD_PYTHON=ON" + "-DBUILD_pybind11=OFF" + "-DFETCH_PYTHON_DEPS=OFF" + "-DUSE_GLPK=ON" + "-DUSE_SCIP=OFF" + "-DPython3_EXECUTABLE=${python.pythonOnBuildForHost.interpreter}" + ] ++ lib.optionals stdenv.isDarwin [ "-DCMAKE_MACOSX_RPATH=OFF" ]; + nativeBuildInputs = [ + cmake + ensureNewerSourcesForZipFilesHook + pkg-config + python.pythonOnBuildForHost + swig4 + unzip + ] ++ (with python.pythonOnBuildForHost.pkgs; [ + pip + mypy-protobuf + ]); + buildInputs = [ + bzip2 + cbc + eigen + glpk + python.pkgs.absl-py + python.pkgs.pybind11 + python.pkgs.setuptools + python.pkgs.wheel + re2 + zlib + ]; + propagatedBuildInputs = [ + abseil-cpp + protobuf + (python.pkgs.protobuf.override { protobuf = protobuf; }) + python.pkgs.numpy + ]; + nativeCheckInputs = [ + python.pkgs.matplotlib + python.pkgs.pandas + python.pkgs.virtualenv + ]; + + doCheck = true; + + # This extra configure step prevents the installer from littering + # $out/bin with sample programs that only really function as tests, + # and disables the upstream installation of a zipped Python egg that + # can’t be imported with our Python setup. + installPhase = '' + cmake . -DBUILD_EXAMPLES=OFF -DBUILD_PYTHON=OFF -DBUILD_SAMPLES=OFF + cmake --install . + pip install --prefix="$python" python/ + ''; + + outputs = [ "out" "python" ]; + + meta = with lib; { + homepage = "https://github.com/google/or-tools"; + license = licenses.asl20; + description = '' + Google's software suite for combinatorial optimization. + ''; + maintainers = with maintainers; [ andersk ]; + platforms = with platforms; linux ++ darwin; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch b/nixpkgs/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch new file mode 100644 index 000000000000..760ab80a38e4 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch @@ -0,0 +1,36 @@ +diff --git a/ortools/lp_data/lp_parser.cc b/ortools/lp_data/lp_parser.cc +index 58286306e5..bd26c019ab 100644 +--- a/ortools/lp_data/lp_parser.cc ++++ b/ortools/lp_data/lp_parser.cc +@@ -185,7 +185,7 @@ bool LPParser::ParseIntegerVariablesList(StringPiece line) { + + bool LPParser::ParseConstraint(StringPiece constraint) { + const StatusOr<ParsedConstraint> parsed_constraint_or_status = +- ::operations_research::glop::ParseConstraint(constraint.as_string()); ++ ::operations_research::glop::ParseConstraint(constraint); + if (!parsed_constraint_or_status.ok()) return false; + const ParsedConstraint& parsed_constraint = + parsed_constraint_or_status.value(); +@@ -342,10 +342,9 @@ TokenType LPParser::ConsumeToken(StringPiece* sp) { + + } // namespace + +-StatusOr<ParsedConstraint> ParseConstraint(absl::string_view constraint_view) { ++StatusOr<ParsedConstraint> ParseConstraint(absl::string_view constraint) { + ParsedConstraint parsed_constraint; + // Get the name, if present. +- StringPiece constraint{constraint_view}; + StringPiece constraint_copy{constraint}; + std::string consumed_name; + Fractional consumed_coeff; +@@ -413,8 +412,8 @@ StatusOr<ParsedConstraint> ParseConstraint(absl::string_view constraint_view) { + right_bound = consumed_coeff; + if (ConsumeToken(&constraint, &consumed_name, &consumed_coeff) != + TokenType::END) { +- return absl::InvalidArgumentError(absl::StrCat( +- "End of input was expected, found: ", constraint.as_string())); ++ return absl::InvalidArgumentError( ++ absl::StrCat("End of input was expected, found: ", constraint)); + } + } + diff --git a/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix new file mode 100644 index 000000000000..a6bc5a086251 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix @@ -0,0 +1,44 @@ +{ stdenv, lib, fetchFromGitHub, gfortran, pkg-config +, blas, zlib, bzip2, coin-utils +, withGurobi ? false, gurobi +, withCplex ? false, cplex }: + +stdenv.mkDerivation rec { + pname = "osi"; + version = "0.108.9"; + + src = fetchFromGitHub { + owner = "coin-or"; + repo = "Osi"; + rev = "releases/${version}"; + hash = "sha256-ueIa9CL4K5ygKpkMRvfuWR0emEG6omg65ZKCsConWsw="; + }; + + buildInputs = + [ blas zlib bzip2 coin-utils ] + ++ lib.optional withGurobi gurobi + ++ lib.optional withCplex cplex; + nativeBuildInputs = [ gfortran pkg-config ]; + configureFlags = + lib.optionals withGurobi [ "--with-gurobi-incdir=${gurobi}/include" "--with-gurobi-lib=-lgurobi${gurobi.libSuffix}" ] + ++ lib.optionals withCplex [ "--with-cplex-incdir=${cplex}/cplex/include/ilcplex" "--with-cplex-lib=-lcplex${cplex.libSuffix}" ]; + + NIX_LDFLAGS = + lib.optionalString withCplex "-L${cplex}/cplex/bin/${cplex.libArch}"; + + # Compile errors + env.NIX_CFLAGS_COMPILE = "-Wno-cast-qual"; + hardeningDisable = [ "format" ]; + + enableParallelBuilding = true; + + passthru = { inherit withGurobi withCplex; }; + + meta = with lib; { + description = "An abstract base class to a generic linear programming (LP) solver"; + homepage = "https://github.com/coin-or/Osi"; + license = licenses.epl20; + platforms = platforms.unix; + maintainers = with maintainers; [ abbradar ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix new file mode 100644 index 000000000000..bf22e1d74d93 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix @@ -0,0 +1,27 @@ +{ lib, stdenv +, fetchFromGitHub +, cmake +}: + +stdenv.mkDerivation rec { + pname = "osqp"; + version = "0.6.3"; + + src = fetchFromGitHub { + owner = "oxfordcontrol"; + repo = "osqp"; + rev = "v${version}"; + sha256 = "sha256-enkK5EFyAeLaUnHNYS3oq43HsHY5IuSLgsYP0k/GW8c="; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ cmake ]; + + meta = with lib; { + description = "A quadratic programming solver using operator splitting"; + homepage = "https://osqp.org"; + license = licenses.asl20; + maintainers = with maintainers; [ taktoa ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/p4est-sc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/p4est-sc/default.nix new file mode 100644 index 000000000000..bb5d212061f2 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/p4est-sc/default.nix @@ -0,0 +1,72 @@ +{ lib, stdenv, fetchFromGitHub, mpiCheckPhaseHook +, autoreconfHook, pkg-config +, p4est-sc-debugEnable ? true, p4est-sc-mpiSupport ? true +, mpi, openssh, zlib +}: + +let + dbg = lib.optionalString debugEnable "-dbg"; + debugEnable = p4est-sc-debugEnable; + mpiSupport = p4est-sc-mpiSupport; + isOpenmpi = mpiSupport && mpi.pname == "openmpi"; +in +stdenv.mkDerivation { + pname = "p4est-sc${dbg}"; + version = "unstable-2021-06-14"; + + # fetch an untagged snapshot of the prev3-develop branch + src = fetchFromGitHub { + owner = "cburstedde"; + repo = "libsc"; + rev = "1ae814e3fb1cc5456652e0d77550386842cb9bfb"; + sha256 = "14vm0b162jh8399pgpsikbwq4z5lkrw9vfzy3drqykw09n6nc53z"; + }; + + strictDeps = true; + nativeBuildInputs = [ autoreconfHook pkg-config ]; + propagatedNativeBuildInputs = lib.optional mpiSupport mpi + ++ lib.optional isOpenmpi openssh + ; + propagatedBuildInputs = [ zlib ]; + inherit debugEnable mpiSupport; + + postPatch = '' + echo "dist_scaclocal_DATA += config/sc_v4l2.m4" >> Makefile.am + ''; + preConfigure = '' + echo "2.8.0" > .tarball-version + ${lib.optionalString mpiSupport "unset CC"} + ''; + + configureFlags = [ "--enable-pthread=-pthread" ] + ++ lib.optional debugEnable "--enable-debug" + ++ lib.optional mpiSupport "--enable-mpi" + ; + + dontDisableStatic = true; + enableParallelBuilding = true; + makeFlags = [ "V=0" ]; + + nativeCheckInputs = lib.optionals mpiSupport [ + mpiCheckPhaseHook + openssh + ]; + + # disallow Darwin checks due to prototype incompatibility of qsort_r + # to be fixed in a future version of the source code + doCheck = !stdenv.isDarwin && stdenv.hostPlatform == stdenv.buildPlatform; + + meta = { + branch = "prev3-develop"; + description = "Support for parallel scientific applications"; + longDescription = '' + The SC library provides support for parallel scientific applications. + Its main purpose is to support the p4est software library, hence + this package is called p4est-sc, but it works standalone, too. + ''; + homepage = "https://www.p4est.org/"; + downloadPage = "https://github.com/cburstedde/libsc.git"; + license = lib.licenses.lgpl21Plus; + maintainers = [ lib.maintainers.cburstedde ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/p4est/default.nix b/nixpkgs/pkgs/development/libraries/science/math/p4est/default.nix new file mode 100644 index 000000000000..1218c695590e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/p4est/default.nix @@ -0,0 +1,64 @@ +{ lib +, stdenv +, fetchFromGitHub +, autoreconfHook +, pkg-config +, p4est-withMetis ? true, metis +, p4est-sc +}: + +let + inherit (p4est-sc) debugEnable mpiSupport; + dbg = lib.optionalString debugEnable "-dbg"; + withMetis = p4est-withMetis; +in +stdenv.mkDerivation { + pname = "p4est${dbg}"; + version = "unstable-2021-06-22"; + + # fetch an untagged snapshot of the prev3-develop branch + src = fetchFromGitHub { + owner = "cburstedde"; + repo = "p4est"; + rev = "7423ac5f2b2b64490a7a92e5ddcbd251053c4dee"; + sha256 = "0vffnf48rzw6d0as4c3x1f31b4kapmdzr1hfj5rz5ngah72gqrph"; + }; + + strictDeps = true; + nativeBuildInputs = [ autoreconfHook pkg-config ]; + propagatedBuildInputs = [ p4est-sc ]; + buildInputs = lib.optional withMetis metis; + inherit debugEnable mpiSupport withMetis; + + patches = [ ./p4est-metis.patch ]; + postPatch = '' + sed -i -e "s:\(^\s*ACLOCAL_AMFLAGS.*\)\s@P4EST_SC_AMFLAGS@\s*$:\1 -I ${p4est-sc}/share/aclocal:" Makefile.am + ''; + preAutoreconf = '' + echo "2.8.0" > .tarball-version + ''; + preConfigure = lib.optionalString mpiSupport '' + unset CC + ''; + + configureFlags = p4est-sc.configureFlags + ++ [ "--with-sc=${p4est-sc}" ] + ++ lib.optional withMetis "--with-metis" + ; + + inherit (p4est-sc) makeFlags dontDisableStatic enableParallelBuilding doCheck; + + meta = { + branch = "prev3-develop"; + description = "Parallel AMR on Forests of Octrees"; + longDescription = '' + The p4est software library provides algorithms for parallel AMR. + AMR refers to Adaptive Mesh Refinement, a technique in scientific + computing to cover the domain of a simulation with an adaptive mesh. + ''; + homepage = "https://www.p4est.org/"; + downloadPage = "https://github.com/cburstedde/p4est.git"; + license = lib.licenses.gpl2Plus; + maintainers = [ lib.maintainers.cburstedde ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/p4est/p4est-metis.patch b/nixpkgs/pkgs/development/libraries/science/math/p4est/p4est-metis.patch new file mode 100644 index 000000000000..46b8dc8af08c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/p4est/p4est-metis.patch @@ -0,0 +1,26 @@ +diff --git a/src/p4est_connectivity.c b/src/p4est_connectivity.c +index 95339136..c93528f2 100644 +--- a/src/p4est_connectivity.c ++++ b/src/p4est_connectivity.c +@@ -3715,6 +3715,7 @@ p4est_connectivity_reorder_newid (sc_MPI_Comm comm, int k, + sc_array_t * newid) + { + const int n = (int) conn->num_trees; ++ int metis_n; + int *xadj; + int *adjncy; + int *part; +@@ -3862,10 +3863,12 @@ p4est_connectivity_reorder_newid (sc_MPI_Comm comm, int k, + + P4EST_GLOBAL_INFO ("Entering metis\n"); + /* now call metis */ ++ metis_n = n; + P4EST_EXECUTE_ASSERT_INT +- (METIS_PartGraphRecursive (&n, &ncon, xadj, adjncy, NULL, NULL, ++ (METIS_PartGraphRecursive (&metis_n, &ncon, xadj, adjncy, NULL, NULL, + NULL, &k, NULL, NULL, NULL, &volume, part), + METIS_OK); ++ P4EST_ASSERT (metis_n == n); + P4EST_GLOBAL_INFO ("Done metis\n"); + + P4EST_GLOBAL_STATISTICSF ("metis volume %d\n", volume); diff --git a/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix new file mode 100644 index 000000000000..db70bf8dd7a4 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix @@ -0,0 +1,34 @@ +{ lib, stdenv +, fetchurl +, cmake +, mpi +}: + +stdenv.mkDerivation rec { + pname = "parmetis"; + version = "4.0.3"; + + src = fetchurl { + url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-${version}.tar.gz"; + sha256 = "0pvfpvb36djvqlcc3lq7si0c5xpb2cqndjg8wvzg35ygnwqs5ngj"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ mpi ]; + + # metis and GKlib are packaged with distribution + # AUR https://aur.archlinux.org/packages/parmetis/ has reported that + # it easier to build with the included packages as opposed to using the metis + # package. Compilation time is short. + configurePhase = '' + make config metis_path=$PWD/metis gklib_path=$PWD/metis/GKlib prefix=$out + ''; + + meta = with lib; { + 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; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix new file mode 100644 index 000000000000..c07250c660a3 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix @@ -0,0 +1,96 @@ +{ lib +, stdenv +, fetchurl +, darwin +, gfortran +, python3 +, blas +, lapack +, mpiSupport ? true +, mpi # generic mpi dependency +, openssh # required for openmpi tests +, petsc-withp4est ? false +, p4est +, zlib # propagated by p4est but required by petsc +, petsc-optimized ? false +, petsc-scalar-type ? "real" +, petsc-precision ? "double" +}: + +# This version of PETSc does not support a non-MPI p4est build +assert petsc-withp4est -> p4est.mpiSupport; + +stdenv.mkDerivation rec { + pname = "petsc"; + version = "3.19.4"; + + src = fetchurl { + url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; + sha256 = "sha256-fJQbcb5Sw7dkIU5JLfYBCdEvl/fYVMl6RN8MTZWLOQY="; + }; + + inherit mpiSupport; + withp4est = petsc-withp4est; + + strictDeps = true; + nativeBuildInputs = [ python3 gfortran ] + ++ lib.optional mpiSupport mpi + ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh + ; + buildInputs = [ blas lapack ] + ++ lib.optional withp4est p4est + ; + + prePatch = lib.optionalString stdenv.isDarwin '' + substituteInPlace config/install.py \ + --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool + ''; + + # Both OpenMPI and MPICH get confused by the sandbox environment and spew errors like this (both to stdout and stderr): + # [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery. + # [1684747490.391106] [localhost:14258:0] tcp_iface.c:837 UCX ERROR opendir(/sys/class/net) failed: No such file or directory + # These messages contaminate test output, which makes the quicktest suite to fail. The patch adds filtering for these messages. + patches = [ ./filter_mpi_warnings.patch ]; + + preConfigure = '' + patchShebangs ./lib/petsc/bin + configureFlagsArray=( + $configureFlagsArray + ${if !mpiSupport then '' + "--with-mpi=0" + '' else '' + "--CC=mpicc" + "--with-cxx=mpicxx" + "--with-fc=mpif90" + "--with-mpi=1" + ''} + ${lib.optionalString withp4est '' + "--with-p4est=1" + "--with-zlib-include=${zlib.dev}/include" + "--with-zlib-lib=-L${zlib}/lib -lz" + ''} + "--with-blas=1" + "--with-lapack=1" + "--with-scalar-type=${petsc-scalar-type}" + "--with-precision=${petsc-precision}" + ${lib.optionalString petsc-optimized '' + "--with-debugging=0" + COPTFLAGS='-g -O3' + FOPTFLAGS='-g -O3' + CXXOPTFLAGS='-g -O3' + ''} + ) + ''; + + configureScript = "python ./configure"; + + enableParallelBuilding = true; + doCheck = stdenv.hostPlatform == stdenv.buildPlatform; + + meta = with lib; { + description = "Portable Extensible Toolkit for Scientific computation"; + homepage = "https://www.mcs.anl.gov/petsc/index.html"; + license = licenses.bsd2; + maintainers = with maintainers; [ cburstedde ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch b/nixpkgs/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch new file mode 100644 index 000000000000..6a3c7bee051e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch @@ -0,0 +1,100 @@ +diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile +index 168febb34b6..71068469066 100644 +--- a/src/snes/tutorials/makefile ++++ b/src/snes/tutorials/makefile +@@ -13,6 +13,7 @@ include ${PETSC_DIR}/lib/petsc/conf/rules + # these tests are used by the makefile in PETSC_DIR for basic tests of the install and should not be removed + testex5f: ex5f.PETSc + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ + if (${DIFF} output/ex5f_1.testout ex5f_1.tmp > /dev/null 2>&1) then \ + echo "Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process"; \ + else \ +@@ -25,6 +26,7 @@ testex5f: ex5f.PETSc + ${MAKE} PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} ex5f.rm; + testex19: ex19.PETSc + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process"; \ + else \ +@@ -36,6 +38,7 @@ testex19: ex19.PETSc + ${RM} -f ex19_1.tmp; + testex19_mpi: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes"; \ + else \ +@@ -48,6 +51,7 @@ testex19_mpi: + #use unpreconditioned norm because HYPRE device installations use different AMG parameters + runex19_hypre: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre"; \ + else \ +@@ -57,6 +61,7 @@ runex19_hypre: + ${RM} -f ex19_1.tmp + runex19_hypre_cuda: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/cuda"; \ + else \ +@@ -66,6 +71,7 @@ runex19_hypre_cuda: + ${RM} -f ex19_1.tmp + runex19_hypre_hip: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/hip"; \ + else \ +@@ -75,6 +81,7 @@ runex19_hypre_hip: + ${RM} -f ex19_1.tmp + runex19_cuda: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -pc_gamg_esteig_ksp_max_it 10 -ksp_monitor -mg_levels_ksp_max_it 3 > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_cuda_1.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with cuda"; \ + else \ +@@ -84,6 +91,7 @@ runex19_cuda: + ${RM} -f ex19_1.tmp + runex19_ml: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_ml.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with ml"; \ + else \ +@@ -93,6 +101,7 @@ runex19_ml: + ${RM} -f ex19_1.tmp + runex19_fieldsplit_mumps: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ + if (${DIFF} output/ex19_fieldsplit_5.out ex19_6.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with mumps"; \ + else \ +@@ -102,6 +111,7 @@ runex19_fieldsplit_mumps: + ${RM} -f ex19_6.tmp + runex19_superlu_dist: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19.tmp; \ + if (${DIFF} output/ex19_superlu.out ex19.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with superlu_dist"; \ + else \ +@@ -111,6 +121,7 @@ runex19_superlu_dist: + ${RM} -f ex19.tmp + runex19_suitesparse: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_suitesparse.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with suitesparse"; \ + else \ +@@ -120,6 +131,7 @@ runex19_suitesparse: + ${RM} -f ex19_1.tmp + runex3k_kokkos: ex3k.PETSc + -@OMP_PROC_BIND=false ${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ + if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels"; \ + else \ diff --git a/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix b/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix new file mode 100644 index 000000000000..3b072fecde34 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv +, fetchFromGitHub +, autoreconfHook +}: + +stdenv.mkDerivation rec { + pname = "planarity"; + version = "3.0.2.0"; + + src = fetchFromGitHub { + owner = "graph-algorithms"; + repo = "edge-addition-planarity-suite"; + rev = "Version_${version}"; + sha256 = "sha256-cUAh2MXCSmtxFtV6iTHgSRgsq/26DjWwxhWJH1+367A="; + }; + + nativeBuildInputs = [ + autoreconfHook + ]; + + doCheck = true; + + meta = with lib; { + homepage = "https://github.com/graph-algorithms/edge-addition-planarity-suite"; + description = "A library for implementing graph algorithms"; + license = licenses.bsd3; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix b/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix new file mode 100644 index 000000000000..c00d579702cc --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix @@ -0,0 +1,27 @@ +{ lib, stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + pname = "rankwidth"; + version = "0.9"; + + src = fetchurl { + url = "mirror://sageupstream/rw/rw-${version}.tar.gz"; + sha256 = "sha256-weA1Bv4lzfy0KMBR/Fay0q/7Wwb7o/LOdWYxRmvvtEE="; + }; + + configureFlags = [ + "--enable-executable=no" # no igraph dependency + ]; + + # check phase is empty for now (as of version 0.9) + doCheck = true; + + meta = with lib; { + description = "Calculates rank-width and rank-decompositions"; + license = with licenses; [ gpl2Plus ]; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix new file mode 100644 index 000000000000..505457edd64f --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix @@ -0,0 +1,81 @@ +{ lib, stdenv +, fetchurl +, fetchpatch +, coreutils +}: + +stdenv.mkDerivation rec { + pname = "rubiks"; + version = "20070912"; + + src = fetchurl { + url = "mirror://sageupstream/rubiks/rubiks-${version}.tar.bz2"; + sha256 = "0zdmkb0j1kyspdpsszzb2k3279xij79jkx0dxd9f3ix1yyyg3yfq"; + }; + + preConfigure = '' + export INSTALL="${coreutils}/bin/install" + ''; + + # everything is done in `make install` + buildPhase = "true"; + + installFlags = [ + "PREFIX=$(out)" + ]; + + patches = [ + # Fix makefiles which use all the variables in all the wrong ways and + # hardcode values for some variables. + (fetchpatch { + url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-cu2-Makefile.patch"; + sha256 = "1ry3w1mk9q4jqd91zlaa1bdiiplld4hpfjaldbhlmzlgrrc99qmq"; + }) + (fetchpatch { + url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-mcube-Makefile.patch"; + sha256 = "0zsbh6k3kqdg82fv0kzghr1x7pafisv943gmssqscp107bhg77bz"; + }) + (fetchpatch { + url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-solver-Makefile.patch"; + sha256 = "0vhw70ylnmydgjhwx8jjlb2slccj4pfqn6vzirkyz1wp8apsmfhp"; + }) + (fetchpatch { + url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/reid-Makefile.patch"; + sha256 = "1r311sn012xs135s0d21qwsig2kld7rdcq19nm0zbnklviid57df"; + }) + ]; + + meta = with lib; { + homepage = "https://wiki.sagemath.org/spkg/rubiks"; + description = "Several programs for working with Rubik's cubes"; + # The individual websites are no longer available + longDescription = '' + There are several programs for working with Rubik's cubes, by three + different people. Look inside the directories under /src to see + specific info and licensing. In summary the three contributers are: + + + Michael Reid (GPL) http://www.math.ucf.edu/~reid/Rubik/optimal_solver.html + optimal - uses many pre-computed tables to find an optimal + solution to the 3x3x3 Rubik's cube + + + Dik T. Winter (MIT License) + cube - uses Kociemba's algorithm to iteratively find a short + solution to the 3x3x3 Rubik's cube + size222 - solves a 2x2x2 Rubik's cube + + + Eric Dietz (GPL) http://www.wrongway.org/?rubiksource + cu2 - A fast, non-optimal 2x2x2 solver + cubex - A fast, non-optimal 3x3x3 solver + mcube - A fast, non-optimal 4x4x4 solver + ''; + license = with licenses; [ + gpl2 # Michael Reid's and Eric Dietz software + mit # Dik T. Winter's software + ]; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix new file mode 100644 index 000000000000..85aa5c4a8736 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix @@ -0,0 +1,75 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake +, openssh, mpiCheckPhaseHook, mpi, blas, lapack +} : + +assert blas.isILP64 == lapack.isILP64; + +stdenv.mkDerivation rec { + pname = "scalapack"; + version = "2.2.1"; + + src = fetchFromGitHub { + owner = "Reference-ScaLAPACK"; + repo = pname; + rev = "v${version}"; + sha256 = "sha256-GNVGWrIWdfyTfbz7c31Vjt9eDlVzCd/aLHoWq2DMyX4="; + }; + + passthru = { inherit (blas) isILP64; }; + + # upstream patch, remove with next release + patches = [ (fetchpatch { + name = "gcc-10"; + url = "https://github.com/Reference-ScaLAPACK/scalapack/commit/a0f76fc0c1c16646875b454b7d6f8d9d17726b5a.patch"; + sha256 = "0civn149ikghakic30bynqg1bal097hr7i12cm4kq3ssrhq073bp"; + })]; + + # Required to activate ILP64. + # See https://github.com/Reference-ScaLAPACK/scalapack/pull/19 + postPatch = lib.optionalString passthru.isILP64 '' + sed -i 's/INTSZ = 4/INTSZ = 8/g' TESTING/EIG/* TESTING/LIN/* + sed -i 's/INTGSZ = 4/INTGSZ = 8/g' TESTING/EIG/* TESTING/LIN/* + + # These tests are not adapted to ILP64 + sed -i '/xssep/d;/xsgsep/d;/xssyevr/d' TESTING/CMakeLists.txt + ''; + + outputs = [ "out" "dev" ]; + + nativeBuildInputs = [ cmake ]; + nativeCheckInputs = [ openssh mpiCheckPhaseHook ]; + buildInputs = [ blas lapack ]; + propagatedBuildInputs = [ mpi ]; + hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ]; + + # xslu and xsllt tests seem to time out on x86_64-darwin. + # this line is left so those who force installation on x86_64-darwin can still build + doCheck = !(stdenv.isx86_64 && stdenv.isDarwin); + + preConfigure = '' + cmakeFlagsArray+=( + -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF + -DLAPACK_LIBRARIES="-llapack" + -DBLAS_LIBRARIES="-lblas" + -DCMAKE_Fortran_COMPILER=${lib.getDev mpi}/bin/mpif90 + ${lib.optionalString passthru.isILP64 '' + -DCMAKE_Fortran_FLAGS="-fdefault-integer-8" + -DCMAKE_C_FLAGS="-DInt=long" + ''} + ) + ''; + + # Increase individual test timeout from 1500s to 10000s because hydra's builds + # sometimes fail due to this + checkFlagsArray = [ "ARGS=--timeout 10000" ]; + + meta = with lib; { + homepage = "http://www.netlib.org/scalapack/"; + description = "Library of high-performance linear algebra routines for parallel distributed memory machines"; + license = licenses.bsd3; + platforms = platforms.unix; + maintainers = with maintainers; [ costrouc markuskowa gdinh ]; + # xslu and xsllt tests fail on x86 darwin + broken = stdenv.isDarwin && stdenv.isx86_64; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix new file mode 100644 index 000000000000..087f4787a53b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix @@ -0,0 +1,52 @@ +{ lib, stdenv, fetchFromGitHub, blas, lapack, gfortran, fixDarwinDylibNames }: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + pname = "scs"; + version = "3.2.3"; + + src = fetchFromGitHub { + owner = "cvxgrp"; + repo = "scs"; + rev = version; + sha256 = "sha256-0g0r3DNgkPZgag0qtz79Wk3Cre1I2yaabFi3OgUzgfc="; + }; + + # Actually link and add libgfortran to the rpath + postPatch = '' + substituteInPlace scs.mk \ + --replace "#-lgfortran" "-lgfortran" \ + --replace "gcc" "cc" + ''; + + nativeBuildInputs = lib.optional stdenv.isDarwin fixDarwinDylibNames; + + buildInputs = [ blas lapack gfortran.cc.lib ]; + + doCheck = true; + + # Test demo requires passing data and seed; numbers chosen arbitrarily. + postCheck = '' + ./out/demo_socp_indirect 42 0.42 0.42 42 + ''; + + installPhase = '' + runHook preInstall + mkdir -p $out/lib + cp -r include $out/ + cp out/*.a out/*.so out/*.dylib $out/lib/ + runHook postInstall + ''; + + meta = with lib; { + description = "Splitting Conic Solver"; + longDescription = '' + Numerical optimization package for solving large-scale convex cone problems + ''; + homepage = "https://github.com/cvxgrp/scs"; + license = licenses.mit; + platforms = platforms.all; + maintainers = [ maintainers.bhipple ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/spooles/allocate.patch b/nixpkgs/pkgs/development/libraries/science/math/spooles/allocate.patch new file mode 100644 index 000000000000..71f539711e7b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/spooles/allocate.patch @@ -0,0 +1,38 @@ +From cc153b180829c6b561765cbbb9b621d1142ff1cd Mon Sep 17 00:00:00 2001 +From: annalee <150648636+a-n-n-a-l-e-e@users.noreply.github.com> +Date: Tue, 28 Nov 2023 13:13:44 +0000 +Subject: [PATCH] use proper format specifier for size_t + +--- + Utilities/MM.h | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Utilities/MM.h b/Utilities/MM.h +index 11e86c5..301c3ec 100644 +--- a/Utilities/MM.h ++++ b/Utilities/MM.h +@@ -33,18 +33,18 @@ if ( (count) > 0 ) { \ + if ( (ptr = (type *)malloc((unsigned long)((count)*sizeof(type)))) \ + == NULL ) {\ + fprintf(stderr, \ +- "\n ALLOCATE failure : bytes %d, line %d, file %s", \ ++ "\n ALLOCATE failure : bytes %zu, line %d, file %s", \ + (count)*sizeof(type), __LINE__, __FILE__) ; \ + exit(-1) ; } \ + else if ( MEMORY_DEBUG > 0 ) { \ + fprintf(stderr, \ +- "\n ALLOCATE : address %p, bytes %d, line %d, file %s", \ ++ "\n ALLOCATE : address %p, bytes %zu, line %d, file %s", \ + ptr, (count)*sizeof(type), __LINE__, __FILE__) ; } } \ + else if ( (count) == 0 ) { \ + ptr = NULL ; } \ + else { \ + fprintf(stderr, \ +- "\n ALLOCATE error : bytes %d, line %d, file %s", \ ++ "\n ALLOCATE error : bytes %zu, line %d, file %s", \ + (count)*sizeof(type), __LINE__, __FILE__) ; \ + exit(-1) ; } + /* +-- +2.42.0 + diff --git a/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix b/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix new file mode 100644 index 000000000000..47738008b02d --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix @@ -0,0 +1,56 @@ +{ lib, stdenv, fetchurl, perl }: + +stdenv.mkDerivation rec { + pname = "spooles"; + version = "2.2"; + + src = fetchurl { + url = "http://www.netlib.org/linalg/spooles/spooles.${version}.tgz"; + sha256 = "1pf5z3vvwd8smbpibyabprdvcmax0grzvx2y0liy98c7x6h5jid8"; + }; + + sourceRoot = "."; + + patches = [ + ./spooles.patch + # fix compiler error where NULL is used as a zero parameter + ./transform.patch + # use proper format specifier for size_t + ./allocate.patch + ]; + + postPatch = lib.optionalString stdenv.hostPlatform.isDarwin '' + substituteInPlace makefile --replace "-Wl,-soname," "-Wl,-install_name,$out/lib/" + ''; + + buildPhase = '' + make lib + ''; + + installPhase = '' + mkdir -p $out/lib $out/include/spooles + cp libspooles.a libspooles.so.2.2 $out/lib/ + ln -s libspooles.so.2.2 $out/lib/libspooles.so.2 + ln -s libspooles.so.2 $out/lib/libspooles.so + for h in *.h; do + if [ $h != 'MPI.h' ]; then + cp $h $out/include/spooles + d=`basename $h .h` + if [ -d $d ]; then + mkdir $out/include/spooles/$d + cp $d/*.h $out/include/spooles/$d + fi + fi + done + ''; + + nativeBuildInputs = [ perl ]; + + meta = with lib; { + homepage = "http://www.netlib.org/linalg/spooles/"; + description = "Library for solving sparse real and complex linear systems of equations"; + license = licenses.publicDomain; + maintainers = with maintainers; [ gebner ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch b/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch new file mode 100644 index 000000000000..71fb4a7f44e1 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/spooles/spooles.patch @@ -0,0 +1,188 @@ +diff --git a/I2Ohash/src/util.c b/I2Ohash/src/util.c +index 72d082e..f32f667 100644 +--- a/I2Ohash/src/util.c ++++ b/I2Ohash/src/util.c +@@ -39,9 +39,10 @@ fflush(stdout) ; + */ + loc1 = (key1 + 1) % hashtable->nlist ; + loc2 = (key2 + 1) % hashtable->nlist ; +-loc = (loc1*loc2) % hashtable->nlist ; ++long int loc3 = (long int)loc1*(long int)loc2 % hashtable->nlist ; ++loc =(int) loc3; + #if MYDEBUG > 0 +-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ; ++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ; + fflush(stdout) ; + #endif + /* +@@ -158,9 +159,10 @@ fflush(stdout) ; + #endif + loc1 = (key1 + 1) % hashtable->nlist ; + loc2 = (key2 + 1) % hashtable->nlist ; +-loc = (loc1*loc2) % hashtable->nlist ; ++long int loc3 = (long int)loc1*(long int)loc2 % hashtable->nlist ; ++loc =(int) loc3; + #if MYDEBUG > 0 +-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ; ++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ; + fflush(stdout) ; + #endif + /* +diff --git a/MPI/makefile b/MPI/makefile +index 0c09f86..d25e70a 100644 +--- a/MPI/makefile ++++ b/MPI/makefile +@@ -2,7 +2,7 @@ all_drivers : + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMPI.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +diff --git a/MPI/src/makefile b/MPI/src/makefile +index f7650b7..71e4c49 100644 +--- a/MPI/src/makefile ++++ b/MPI/src/makefile +@@ -42,3 +42,8 @@ $(OBJ).a : \ + + clean : + - rm -f *.a *.o ++ ++makeLib : ++ perl ../../makeLib > makeG ++ make -f makeG ++ rm -f makeG +diff --git a/MT/makefile b/MT/makefile +index 9b86a32..d25e70a 100644 +--- a/MT/makefile ++++ b/MT/makefile +@@ -2,7 +2,7 @@ all_drivers : + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMT.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +diff --git a/Make.inc b/Make.inc +index f99eb8f..2de8a25 100644 +--- a/Make.inc ++++ b/Make.inc +@@ -12,7 +12,7 @@ + # for solaris + # + # CC = gcc +- CC = /usr/lang-4.0/bin/cc ++# CC = /usr/lang-4.0/bin/cc + # + # for sgi + # +@@ -28,7 +28,7 @@ + # + # OPTLEVEL = + # OPTLEVEL = -g -v +- OPTLEVEL = -O ++ OPTLEVEL = -O3 + # OPTLEVEL = -xO5 -v + # OPTLEVEL = -O3 + # OPTLEVEL = -O4 +@@ -43,7 +43,7 @@ + # set any load flags + # + # LDFLAGS = -Wl,+parallel -Wl,+tm,spp2000 # for hp exemplar +- LDFLAGS = ++# LDFLAGS = + # + #--------------------------------------------------------------------- + # +@@ -103,7 +103,7 @@ + # MPI install library + # + # MPI_INSTALL_DIR = +- MPI_INSTALL_DIR = /usr/local/mpich-1.0.13 ++# MPI_INSTALL_DIR = /usr/lib/openmpi + # + #--------------------------------------------------------------------- + # +@@ -142,6 +142,6 @@ + # MPI include path + # + # MPI_INCLUDE_DIR = +- MPI_INCLUDE_DIR = -I$(MPI_INSTALL_DIR)/include ++# MPI_INCLUDE_DIR = -I/usr/include/mpi + # + #--------------------------------------------------------------------- +diff --git a/Utilities/src/iohb.c b/Utilities/src/iohb.c +index ac38f7b..ac34034 100644 +--- a/Utilities/src/iohb.c ++++ b/Utilities/src/iohb.c +@@ -1725,7 +1725,7 @@ static void upcase(char* S) + + static void IOHBTerminate(char* message) + { +- fprintf(stderr,message); ++ fputs(message, stderr); + exit(1); + } + +diff --git a/makeLib b/makeLib +index 1780f39..7697b06 100755 +--- a/makeLib ++++ b/makeLib +@@ -64,14 +64,19 @@ foreach $src ( @srcnames ) { + $srcname = " \\\n " . $src ; + print $srcname ; + } ++print "\n\n.SUFFIXES: .c .o .lo .a .so" ; + print "\n\nOBJ_FILES = \$\{SRC:.c=.o\}" ; ++print "\n\nLOBJ_FILES = \$\{SRC:.c=.lo\}" ; + print "\n\n" ; + print <<'EOF' ; + .c.o : +- $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR) + +-../../spooles.a : ${OBJ_FILES} +- $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o ++.c.lo : ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR) ++ ++../../libspooles.a : ${OBJ_FILES} ${LOBJ_FILES} ++ $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o + rm -f $(OBJ)_*.o +- $(RANLIB) ../../spooles.a ++ $(RANLIB) ../../libspooles.a + EOF +diff --git a/makefile b/makefile +index f014c7d..7c8042a 100755 +--- a/makefile ++++ b/makefile +@@ -124,7 +124,9 @@ lib : + cd ZV ; make lib + cd misc ; make lib + #cd MPI ; make lib +-#cd MT ; make lib ++ cd MT ; make lib ++ $(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 : + cd A2/src ; make -f makeGlobalLib +diff --git a/timings.h b/timings.h +index 23df189..685800b 100644 +--- a/timings.h ++++ b/timings.h +@@ -2,9 +2,8 @@ + #define _TIMINGS_ + #include <sys/time.h> + static struct timeval TV ; +-static struct timezone TZ ; + #define MARKTIME(t) \ +- gettimeofday(&TV, &TZ) ; \ ++ gettimeofday(&TV, NULL) ; \ + t = (TV.tv_sec + 0.000001*TV.tv_usec) + #endif + diff --git a/nixpkgs/pkgs/development/libraries/science/math/spooles/transform.patch b/nixpkgs/pkgs/development/libraries/science/math/spooles/transform.patch new file mode 100644 index 000000000000..3be3babe9d65 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/spooles/transform.patch @@ -0,0 +1,43 @@ +From c5d0574182d76af3bf286dce0bb147ae3f098916 Mon Sep 17 00:00:00 2001 +From: annalee <150648636+a-n-n-a-l-e-e@users.noreply.github.com> +Date: Tue, 28 Nov 2023 12:57:18 +0000 +Subject: [PATCH] fix compiler error: use zero, not NULL, in calls to IVinit + +--- + ETree/src/transform.c | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/ETree/src/transform.c b/ETree/src/transform.c +index 1e36981..dbdfc70 100644 +--- a/ETree/src/transform.c ++++ b/ETree/src/transform.c +@@ -291,7 +291,7 @@ etree2 = ETree_compress(etree, mapIV) ; + remap the nzeros[] vector + ------------------------- + */ +-temp = IVinit(nfront, NULL) ; ++temp = IVinit(nfront, 0) ; + IVcopy(nfront, temp, nzeros) ; + IV_setSize(nzerosIV, nnew) ; + nzeros = IV_entries(nzerosIV) ; +@@ -453,7 +453,7 @@ etree2 = ETree_compress(etree, mapIV) ; + remap the nzeros[] vector + ------------------------- + */ +-temp = IVinit(nfront, NULL) ; ++temp = IVinit(nfront, 0) ; + IVcopy(nfront, temp, nzeros) ; + IV_setSize(nzerosIV, nnew) ; + nzeros = IV_entries(nzerosIV) ; +@@ -614,7 +614,7 @@ etree2 = ETree_compress(etree, mapIV) ; + remap the nzeros[] vector + ------------------------- + */ +-temp = IVinit(nfront, NULL) ; ++temp = IVinit(nfront, 0) ; + IVcopy(nfront, temp, nzeros) ; + IV_setSize(nzerosIV, nnew) ; + nzeros = IV_entries(nzerosIV) ; +-- +2.42.0 + diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix new file mode 100644 index 000000000000..ac08cb876253 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix @@ -0,0 +1,37 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, gnum4 +}: + +stdenv.mkDerivation rec { + pname = "suitesparse-graphblas"; + version = "9.0.3"; + + outputs = [ "out" "dev" ]; + + src = fetchFromGitHub { + owner = "DrTimothyAldenDavis"; + repo = "GraphBLAS"; + rev = "v${version}"; + hash = "sha256-qRRrxMshLLEltCzXFv/j6NgRi6x1SHlAuKG5NfLiBFs="; + }; + + nativeBuildInputs = [ + cmake + gnum4 + ]; + + preConfigure = '' + export HOME=$(mktemp -d) + ''; + + meta = with lib; { + description = "Graph algorithms in the language of linear algebra"; + homepage = "https://people.engr.tamu.edu/davis/GraphBLAS.html"; + license = licenses.asl20; + maintainers = with maintainers; [ wegank ]; + platforms = with platforms; unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix new file mode 100644 index 000000000000..b8ce3eca888c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix @@ -0,0 +1,43 @@ +{ lib, stdenv, fetchurl, gfortran, blas, lapack }: + +let + int_t = if blas.isILP64 then "int64_t" else "int32_t"; +in +stdenv.mkDerivation rec { + version = "4.2.1"; + pname = "suitesparse"; + src = fetchurl { + url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ; + sha256 = "1ga69637x7kdkiy3w3lq9dvva7220bdangv2lch2wx1hpi83h0p8"; + }; + + nativeBuildInputs = [ gfortran ]; + buildInputs = [ blas lapack ]; + + preConfigure = '' + mkdir -p $out/lib + mkdir -p $out/include + + sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ + -e 's/METIS .*$/METIS =/' \ + -e 's/METIS_PATH .*$/METIS_PATH =/' \ + -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \ + -e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/' + ''; + + makeFlags = [ + "PREFIX=\"$(out)\"" + "INSTALL_LIB=$(out)/lib" + "INSTALL_INCLUDE=$(out)/include" + "BLAS=-lblas" + "LAPACK=-llapack" + ]; + + meta = with lib; { + homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; + description = "A suite of sparse matrix algorithms"; + license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; + maintainers = with maintainers; [ ttuegel ]; + platforms = with platforms; unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix new file mode 100644 index 000000000000..cbc24b154656 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix @@ -0,0 +1,99 @@ +{ lib, stdenv, fetchurl, gfortran, blas, lapack +, config +, enableCuda ? config.cudaSupport, cudatoolkit +}: + +let + int_t = if blas.isILP64 then "int64_t" else "int32_t"; + SHLIB_EXT = stdenv.hostPlatform.extensions.sharedLibrary; +in +stdenv.mkDerivation rec { + version = "4.4.4"; + pname = "suitesparse"; + + src = fetchurl { + url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${version}.tar.gz"; + sha256 = "1zdn1y0ij6amj7smmcslkqgbqv9yy5cwmbyzqc9v6drzdzllgbpj"; + }; + + preConfigure = '' + mkdir -p $out/lib + mkdir -p $out/include + + sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ + -e 's/METIS .*$/METIS =/' \ + -e 's/METIS_PATH .*$/METIS_PATH =/' \ + -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \ + -e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/' + '' + + lib.optionalString stdenv.isDarwin '' + sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ + -e 's/^[[:space:]]*\(LIB = -lm\) -lrt/\1/' + '' + + lib.optionalString enableCuda '' + sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ + -e 's|^[[:space:]]*\(CUDA_ROOT =\)|CUDA_ROOT = ${cudatoolkit}|' \ + -e 's|^[[:space:]]*\(GPU_BLAS_PATH =\)|GPU_BLAS_PATH = $(CUDA_ROOT)|' \ + -e 's|^[[:space:]]*\(GPU_CONFIG =\)|GPU_CONFIG = -I$(CUDA_ROOT)/include -DGPU_BLAS -DCHOLMOD_OMP_NUM_THREADS=$(NIX_BUILD_CORES) |' \ + -e 's|^[[:space:]]*\(CUDA_PATH =\)|CUDA_PATH = $(CUDA_ROOT)|' \ + -e 's|^[[:space:]]*\(CUDART_LIB =\)|CUDART_LIB = $(CUDA_ROOT)/lib64/libcudart.so|' \ + -e 's|^[[:space:]]*\(CUBLAS_LIB =\)|CUBLAS_LIB = $(CUDA_ROOT)/lib64/libcublas.so|' \ + -e 's|^[[:space:]]*\(CUDA_INC_PATH =\)|CUDA_INC_PATH = $(CUDA_ROOT)/include/|' \ + -e 's|^[[:space:]]*\(NV20 =\)|NV20 = -arch=sm_20 -Xcompiler -fPIC|' \ + -e 's|^[[:space:]]*\(NV30 =\)|NV30 = -arch=sm_30 -Xcompiler -fPIC|' \ + -e 's|^[[:space:]]*\(NV35 =\)|NV35 = -arch=sm_35 -Xcompiler -fPIC|' \ + -e 's|^[[:space:]]*\(NVCC =\) echo|NVCC = $(CUDA_ROOT)/bin/nvcc|' \ + -e 's|^[[:space:]]*\(NVCCFLAGS =\)|NVCCFLAGS = $(NV20) -O3 -gencode=arch=compute_20,code=sm_20 -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_35,code=sm_35 -gencode=arch=compute_60,code=sm_60|' + ''; + + makeFlags = [ + "PREFIX=\"$(out)\"" + "INSTALL_LIB=$(out)/lib" + "INSTALL_INCLUDE=$(out)/include" + "BLAS=-lblas" + "LAPACK=-llapack" + ]; + + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin " -DNTIMER"; + + postInstall = '' + # Build and install shared library + ( + cd "$(mktemp -d)" + for i in "$out"/lib/lib*.a; do + ar -x $i + done + ${if enableCuda then cudatoolkit else stdenv.cc.outPath}/bin/${if enableCuda then "nvcc" else "cc"} *.o ${if stdenv.isDarwin then "-dynamiclib" else "--shared"} -o "$out/lib/libsuitesparse${SHLIB_EXT}" -lblas ${lib.optionalString enableCuda "-lcublas"} + ) + for i in umfpack cholmod amd camd colamd spqr; do + ln -s libsuitesparse${SHLIB_EXT} "$out"/lib/lib$i${SHLIB_EXT} + done + + # Install documentation + outdoc=$out/share/doc/suitesparse-${version} + mkdir -p $outdoc + cp -r AMD/Doc $outdoc/amd + cp -r BTF/Doc $outdoc/bft + cp -r CAMD/Doc $outdoc/camd + cp -r CCOLAMD/Doc $outdoc/ccolamd + cp -r CHOLMOD/Doc $outdoc/cholmod + cp -r COLAMD/Doc $outdoc/colamd + cp -r CXSparse/Doc $outdoc/cxsparse + cp -r KLU/Doc $outdoc/klu + cp -r LDL/Doc $outdoc/ldl + cp -r RBio/Doc $outdoc/rbio + cp -r SPQR/Doc $outdoc/spqr + cp -r UMFPACK/Doc $outdoc/umfpack + ''; + + nativeBuildInputs = [ gfortran ]; + buildInputs = [ blas lapack ]; + + meta = with lib; { + homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; + description = "A suite of sparse matrix algorithms"; + license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; + maintainers = with maintainers; [ ttuegel ]; + platforms = with platforms; unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix new file mode 100644 index 000000000000..9561cf2ed779 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix @@ -0,0 +1,94 @@ +{ lib, stdenv +, fetchFromGitHub +, gfortran +, blas, lapack +, metis +, fixDarwinDylibNames +, gmp +, mpfr +, config +, enableCuda ? config.cudaSupport +, cudaPackages +, openmp ? null +}: + +stdenv.mkDerivation rec { + pname = "suitesparse"; + version = "5.13.0"; + + outputs = [ "out" "dev" "doc" ]; + + src = fetchFromGitHub { + owner = "DrTimothyAldenDavis"; + repo = "SuiteSparse"; + rev = "v${version}"; + sha256 = "sha256-Anen1YtXsSPhk8DpA4JtADIz9m8oXFl9umlkb4iImf8="; + }; + + nativeBuildInputs = [ + ] ++ lib.optionals stdenv.isDarwin [ + fixDarwinDylibNames + ] ++ lib.optionals enableCuda [ + cudaPackages.cuda_nvcc + ]; + + # Use compatible indexing for lapack and blas used + buildInputs = assert (blas.isILP64 == lapack.isILP64); [ + blas lapack + metis + gfortran.cc.lib + gmp + mpfr + ] ++ lib.optionals stdenv.cc.isClang [ + openmp + ] ++ lib.optionals enableCuda [ + cudaPackages.cuda_cudart.dev + cudaPackages.cuda_cudart.lib + cudaPackages.cuda_cccl.dev + cudaPackages.libcublas.dev + cudaPackages.libcublas.lib + ]; + + preConfigure = '' + # Mongoose and GraphBLAS are packaged separately + sed -i "Makefile" -e '/GraphBLAS\|Mongoose/d' + ''; + + makeFlags = [ + "INSTALL=${placeholder "out"}" + "INSTALL_INCLUDE=${placeholder "dev"}/include" + "JOBS=$(NIX_BUILD_CORES)" + "MY_METIS_LIB=-lmetis" + ] ++ lib.optionals blas.isILP64 [ + "CFLAGS=-DBLAS64" + ] ++ lib.optionals enableCuda [ + "CUDA_PATH=${cudaPackages.cuda_nvcc}" + "CUDART_LIB=${cudaPackages.cuda_cudart.lib}/lib/libcudart.so" + "CUBLAS_LIB=${cudaPackages.libcublas.lib}/lib/libcublas.so" + ] ++ lib.optionals stdenv.isDarwin [ + # Unless these are set, the build will attempt to use `Accelerate` on darwin, see: + # https://github.com/DrTimothyAldenDavis/SuiteSparse/blob/v5.13.0/SuiteSparse_config/SuiteSparse_config.mk#L368 + "BLAS=-lblas" + "LAPACK=-llapack" + ] + ; + + env = lib.optionalAttrs stdenv.isDarwin { + # Ensure that there is enough space for the `fixDarwinDylibNames` hook to + # update the install names of the output dylibs. + NIX_LDFLAGS = "-headerpad_max_install_names"; + }; + + buildFlags = [ + # Build individual shared libraries, not demos + "library" + ]; + + meta = with lib; { + homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; + description = "A suite of sparse matrix algorithms"; + license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; + maintainers = with maintainers; [ ttuegel ]; + platforms = with platforms; unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/superlu/add-superlu-lib-as-dependency-for-the-unit-tests.patch b/nixpkgs/pkgs/development/libraries/science/math/superlu/add-superlu-lib-as-dependency-for-the-unit-tests.patch new file mode 100644 index 000000000000..29d86238af08 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/superlu/add-superlu-lib-as-dependency-for-the-unit-tests.patch @@ -0,0 +1,7 @@ +--- a/TESTING/MATGEN/CMakeLists.txt ++++ b/TESTING/MATGEN/CMakeLists.txt +@@ -97,3 +97,4 @@ if(enable_complex16) + endif() + + add_library(matgen ${sources}) ++target_link_libraries(matgen superlu) diff --git a/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix new file mode 100644 index 000000000000..f99e86ffe478 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix @@ -0,0 +1,44 @@ +{ lib, stdenv, fetchurl, cmake, + gfortran, blas, lapack}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + version = "5.2.1"; + pname = "superlu"; + + src = fetchurl { + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_${version}.tar.gz"; + sha256 = "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"; + }; + + nativeBuildInputs = [ cmake gfortran ]; + + propagatedBuildInputs = [ blas ]; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=true" + "-DUSE_XSDK_DEFAULTS=true" + ]; + + env = lib.optionalAttrs stdenv.cc.isClang { + NIX_CFLAGS_COMPILE = toString [ + "-Wno-error=implicit-function-declaration" + "-Wno-error=implicit-int" + ]; + }; + + patches = [ + ./add-superlu-lib-as-dependency-for-the-unit-tests.patch + ]; + + doCheck = true; + checkTarget = "test"; + + meta = { + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"; + license = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/License.txt"; + description = "A library for the solution of large, sparse, nonsymmetric systems of linear equations"; + platforms = lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/sympow/clean-extra-logfile-output-from-pari.patch b/nixpkgs/pkgs/development/libraries/science/math/sympow/clean-extra-logfile-output-from-pari.patch new file mode 100644 index 000000000000..cbcf18b4cdb2 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/sympow/clean-extra-logfile-output-from-pari.patch @@ -0,0 +1,39 @@ +commit 433a8b99da9d71e96434bd421c2468cbda29d37c +Author: Mauricio Collares <mauricio@collares.org> +Date: Tue Mar 2 22:07:11 2021 -0300 + + trim logfile information from pari 2.13 output + + Pari (since commit 609fb01faf827d91dfa9136849a647a3bbfe8036) prints + extra logfile information such as + + [logfile is "/tmp/nix-shell.2BquN9/home/.sympow/datafiles/P02HM.txt"] + + which messes up sympow's parsing. This commit reuses the same trimming + mechanism already in sympow to trim this new message. + +diff --git a/Configure b/Configure +index 1ef9756..776bec2 100755 +--- a/Configure ++++ b/Configure +@@ -322,7 +322,7 @@ echo "datafiles/param_data: \$(OTHERb)" >> $FILE + echo " \$(MKDIR) -p datafiles" >> $FILE + echo " \$(TOUCH) datafiles/param_data" >> $FILE + echo " \$(SH) armd.sh" >> $FILE +-echo " \$(SED) -i -e '/logfile =/d' datafiles/*.txt" >> $FILE ++echo " \$(SED) -i -e '/logfile /d' datafiles/*.txt" >> $FILE + echo "sympow.1: sympow" >> $FILE + echo " \$(HELP2MAN) \$(H2MFLAGS) -s 1 -n \"SYMPOW program\" -I sympow.h2m -o \$@ ./\$<" >> $FILE + echo "clean:" >> $FILE +diff --git a/generate.c b/generate.c +index dbb811f..783320c 100644 +--- a/generate.c ++++ b/generate.c +@@ -148,6 +148,7 @@ static void trimit(char *A) + " -e '" + "/^\?/d" ";" + "/^(/d" ";" ++ "/logfile /d" ";" + "/Warning:/d" ";" + "/^About to find TOO_BIG/d" ";" + "/^Now working backwards/d" ";" diff --git a/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix b/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix new file mode 100644 index 000000000000..09ca356ccdc5 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix @@ -0,0 +1,84 @@ +{ lib, stdenv +, fetchFromGitLab +, fetchpatch +, makeWrapper +, which +, autoconf +, help2man +, file +, pari +}: + +stdenv.mkDerivation rec { + version = "2.023.6"; + pname = "sympow"; + + src = fetchFromGitLab { + group = "rezozer"; + owner = "forks"; + repo = "sympow"; + rev = "v${version}"; + sha256 = "132l0xv00ld1svvv9wh99wfra4zzjv2885h2sq0dsl98wiyvi5zl"; + }; + + patches = [ + ./clean-extra-logfile-output-from-pari.patch + (fetchpatch { + name = "null-terminate-dupdirname.patch"; + url = "https://gitlab.com/rezozer/forks/sympow/-/merge_requests/5.diff"; + sha256 = "sha256-yKjio+qN9teL8L+mb7WOBN/iv545vRIxW20FJU37oO4="; + }) + ]; + + postUnpack = '' + patchShebangs . + ''; + + nativeBuildInputs = [ + makeWrapper + which + autoconf + help2man + file + pari + ]; + + configurePhase = '' + runHook preConfigure + export PREFIX="$out" + export VARPREFIX="$out" # see comment on postInstall + ./Configure # doesn't take any options + runHook postConfigure + ''; + + # Usually, sympow has 3 levels of caching: statically distributed in /usr/, + # shared in /var and per-user in ~/.sympow. The shared cache assumes trust in + # other users and a shared /var is not compatible with nix's approach, so we + # set VARPREFIX to the read-only $out. This effectively disables shared + # caching. See https://trac.sagemath.org/ticket/3360#comment:36 and sympow's + # README for more details on caching. + # sympow will complain at runtime about the lack of write-permissions on the + # shared cache. We pass the `-quiet` flag by default to disable this. + postInstall = '' + wrapProgram "$out/bin/sympow" --add-flags '-quiet' + ''; + + # Example from the README as a sanity check. + doInstallCheck = true; + installCheckPhase = '' + export HOME="$TMP/home" + mkdir -p "$HOME" + "$out/bin/sympow" -sp 2p16 -curve "[1,2,3,4,5]" | grep '8.3705' + ''; + + meta = with lib; { + description = "Compute special values of symmetric power elliptic curve L-functions"; + license = { + shortName = "sympow"; + fullName = "Custom, BSD-like. See COPYING file."; + free = true; + }; + maintainers = teams.sage.members; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix new file mode 100644 index 000000000000..1bee7f46d37c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix @@ -0,0 +1,108 @@ +{ stdenv +, bash +, buildPackages +, buildBazelPackage +, fetchFromGitHub +, lib +}: +let + buildPlatform = stdenv.buildPlatform; + hostPlatform = stdenv.hostPlatform; + pythonEnv = buildPackages.python3.withPackages (ps: [ ps.numpy ]); + bazelDepsSha256ByBuildAndHost = { + x86_64-linux = { + x86_64-linux = "sha256-61qmnAB80syYhURWYJOiOnoGOtNa1pPkxfznrFScPAo="; + aarch64-linux = "sha256-sOIYpp98wJRz3RGvPasyNEJ05W29913Lsm+oi/aq/Ag="; + }; + aarch64-linux = { + aarch64-linux = "sha256-MJU4y9Dt9xJWKgw7iKW+9Ur856rMIHeFD5u05s+Q7rQ="; + }; + }; + bazelHostConfigName.aarch64-linux = "elinux_aarch64"; + bazelDepsSha256ByHost = + bazelDepsSha256ByBuildAndHost.${buildPlatform.system} or + (throw "unsupported build system ${buildPlatform.system}"); + bazelDepsSha256 = bazelDepsSha256ByHost.${hostPlatform.system} or + (throw "unsupported host system ${hostPlatform.system} with build system ${buildPlatform.system}"); +in +buildBazelPackage rec { + name = "tensorflow-lite"; + version = "2.13.0"; + + src = fetchFromGitHub { + owner = "tensorflow"; + repo = "tensorflow"; + rev = "v${version}"; + hash = "sha256-Rq5pAVmxlWBVnph20fkAwbfy+iuBNlfFy14poDPd5h0="; + }; + + bazel = buildPackages.bazel_5; + + nativeBuildInputs = [ pythonEnv buildPackages.perl ]; + + bazelTargets = [ + "//tensorflow/lite:libtensorflowlite.so" + "//tensorflow/lite/c:tensorflowlite_c" + "//tensorflow/lite/tools/benchmark:benchmark_model" + "//tensorflow/lite/tools/benchmark:benchmark_model_performance_options" + ]; + + bazelFlags = [ + "--config=opt" + ] ++ lib.optionals (hostPlatform.system != buildPlatform.system) [ + "--config=${bazelHostConfigName.${hostPlatform.system}}" + ]; + + bazelBuildFlags = [ "--cxxopt=--std=c++17" ]; + + buildAttrs = { + installPhase = '' + mkdir -p $out/{bin,lib} + + # copy the libs and binaries into the output dir + cp ./bazel-bin/tensorflow/lite/c/libtensorflowlite_c.so $out/lib + cp ./bazel-bin/tensorflow/lite/libtensorflowlite.so $out/lib + cp ./bazel-bin/tensorflow/lite/tools/benchmark/benchmark_model $out/bin + cp ./bazel-bin/tensorflow/lite/tools/benchmark/benchmark_model_performance_options $out/bin + + find . -type f -name '*.h' | while read f; do + path="$out/include/''${f/.\//}" + install -D "$f" "$path" + + # remove executable bit from headers + chmod -x "$path" + done + ''; + }; + + fetchAttrs.sha256 = bazelDepsSha256; + + PYTHON_BIN_PATH = pythonEnv.interpreter; + + dontAddBazelOpts = true; + removeRulesCC = false; + + postPatch = '' + rm .bazelversion + + # Fix gcc-13 build failure by including missing include headers + sed -e '1i #include <cstdint>' -i \ + tensorflow/lite/kernels/internal/spectrogram.cc + ''; + + preConfigure = '' + patchShebangs configure + ''; + + # configure script freaks out when parameters are passed + dontAddPrefix = true; + configurePlatforms = []; + + meta = with lib; { + description = "An open source deep learning framework for on-device inference."; + homepage = "https://www.tensorflow.org/lite"; + license = licenses.asl20; + maintainers = with maintainers; [ mschwaig cpcloud ]; + platforms = [ "x86_64-linux" "aarch64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorrt/extension.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorrt/extension.nix new file mode 100644 index 000000000000..ffd9b672684c --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/tensorrt/extension.nix @@ -0,0 +1,156 @@ +final: prev: let + + inherit (final) callPackage; + inherit (prev) cudatoolkit cudaVersion lib pkgs; + + ### TensorRT + + buildTensorRTPackage = args: + callPackage ./generic.nix { } args; + + toUnderscore = str: lib.replaceStrings ["."] ["_"] str; + + majorMinorPatch = str: lib.concatStringsSep "." (lib.take 3 (lib.splitVersion str)); + + tensorRTPackages = with lib; let + # Check whether a file is supported for our cuda version + isSupported = fileData: elem cudaVersion fileData.supportedCudaVersions; + # Return the first file that is supported. In practice there should only ever be one anyway. + supportedFile = files: findFirst isSupported null files; + + # Compute versioned attribute name to be used in this package set + computeName = version: "tensorrt_${toUnderscore version}"; + + # Supported versions with versions as keys and file as value + supportedVersions = lib.recursiveUpdate + { + tensorrt = { + enable = false; + fileVersionCuda = null; + fileVersionCudnn = null; + fullVersion = "0.0.0"; + sha256 = null; + tarball = null; + supportedCudaVersions = [ ]; + }; + } + (mapAttrs' (version: attrs: nameValuePair (computeName version) attrs) + (filterAttrs (version: file: file != null) (mapAttrs (version: files: supportedFile files) tensorRTVersions))); + + # Add all supported builds as attributes + allBuilds = mapAttrs (name: file: buildTensorRTPackage (removeAttrs file ["fileVersionCuda"])) supportedVersions; + + # Set the default attributes, e.g. tensorrt = tensorrt_8_4; + defaultName = computeName tensorRTDefaultVersion; + defaultBuild = lib.optionalAttrs (allBuilds ? ${defaultName}) { tensorrt = allBuilds.${computeName tensorRTDefaultVersion}; }; + in { + inherit buildTensorRTPackage; + } // allBuilds // defaultBuild; + + tarballURL = + {fullVersion, fileVersionCuda, fileVersionCudnn ? null} : + "TensorRT-${fullVersion}.Linux.x86_64-gnu.cuda-${fileVersionCuda}" + + lib.optionalString (fileVersionCudnn != null) ".cudnn${fileVersionCudnn}" + + ".tar.gz"; + + tensorRTVersions = { + "8.6.1" = [ + rec { + fileVersionCuda = "12.0"; + fullVersion = "8.6.1.6"; + sha256 = "sha256-D4FXpfxTKZQ7M4uJNZE3M1CvqQyoEjnNrddYDNHrolQ="; + tarball = tarballURL { inherit fileVersionCuda fullVersion; }; + supportedCudaVersions = [ "12.0" "12.1" ]; + } + ]; + "8.5.3" = [ + rec { + fileVersionCuda = "11.8"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.3.1"; + sha256 = "sha256-BNeuOYvPTUAfGxI0DVsNrX6Z/FAB28+SE0ptuGu7YDY="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "11.0" "11.1" "11.2" "11.3" "11.4" "11.5" "11.6" "11.7" "11.8" ]; + } + rec { + fileVersionCuda = "10.2"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.3.1"; + sha256 = "sha256-WCt6yfOmFbrjqdYCj6AE2+s2uFpISwk6urP+2I0BnGQ="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "10.2" ]; + } + ]; + "8.5.2" = [ + rec { + fileVersionCuda = "11.8"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.2.2"; + sha256 = "sha256-Ov5irNS/JETpEz01FIFNMs9YVmjGHL7lSXmDpgCdgao="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "11.0" "11.1" "11.2" "11.3" "11.4" "11.5" "11.6" "11.7" "11.8" ]; + } + rec { + fileVersionCuda = "10.2"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.2.2"; + sha256 = "sha256-UruwQShYcHLY5d81lKNG7XaoUsZr245c+PUpUN6pC5E="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "10.2" ]; + } + ]; + "8.5.1" = [ + rec { + fileVersionCuda = "11.8"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.1.7"; + sha256 = "sha256-Ocx/B3BX0TY3lOj/UcTPIaXb7M8RFrACC6Da4PMGMHY="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "11.0" "11.1" "11.2" "11.3" "11.4" "11.5" "11.6" "11.7" "11.8" ]; + } + rec { + fileVersionCuda = "10.2"; + fileVersionCudnn = "8.6"; + fullVersion = "8.5.1.7"; + sha256 = "sha256-CcFGJhw7nFdPnSYYSxcto2MHK3F84nLQlJYjdIw8dPM="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "10.2" ]; + } + ]; + "8.4.0" = [ + rec { + fileVersionCuda = "11.6"; + fileVersionCudnn = "8.3"; + fullVersion = "8.4.0.6"; + sha256 = "sha256-DNgHHXF/G4cK2nnOWImrPXAkOcNW6Wy+8j0LRpAH/LQ="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "11.0" "11.1" "11.2" "11.3" "11.4" "11.5" "11.6" ]; + } + rec { + fileVersionCuda = "10.2"; + fileVersionCudnn = "8.3"; + fullVersion = "8.4.0.6"; + sha256 = "sha256-aCzH0ZI6BrJ0v+e5Bnm7b8mNltA7NNuIa8qRKzAQv+I="; + tarball = tarballURL { inherit fileVersionCuda fileVersionCudnn fullVersion; }; + supportedCudaVersions = [ "10.2" ]; + } + ]; + }; + + # Default attributes + tensorRTDefaultVersion = { + "10.2" = "8.4.0"; + "11.0" = "8.4.0"; + "11.1" = "8.4.0"; + "11.2" = "8.4.0"; + "11.3" = "8.4.0"; + "11.4" = "8.4.0"; + "11.5" = "8.4.0"; + "11.6" = "8.4.0"; + "11.7" = "8.5.3"; + "11.8" = "8.5.3"; + "12.0" = "8.6.1"; + "12.1" = "8.6.1"; + }.${cudaVersion} or "8.4.0"; + +in tensorRTPackages diff --git a/nixpkgs/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix b/nixpkgs/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix new file mode 100644 index 000000000000..2036c4c86253 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix @@ -0,0 +1,163 @@ +{ + cmake, + cudaPackages, + fetchFromGitHub, + lib, + ninja, + python3Packages ? {}, + pythonSupport ? false, + stdenv, + symlinkJoin, + which, +}: let + inherit (lib) lists strings; + inherit (cudaPackages) backendStdenv cudaFlags; + + cuda-common-redist = with cudaPackages; [ + cuda_cudart.dev # cuda_runtime.h + cuda_cudart.lib + cuda_cccl.dev # <nv/target> + libcublas.dev # cublas_v2.h + libcublas.lib + libcusolver.dev # cusolverDn.h + libcusolver.lib + libcusparse.dev # cusparse.h + libcusparse.lib + ]; + + cuda-native-redist = symlinkJoin { + name = "cuda-redist"; + paths = with cudaPackages; + [cuda_nvcc] + ++ cuda-common-redist; + }; + + cuda-redist = symlinkJoin { + name = "cuda-redist"; + paths = cuda-common-redist; + }; +in + stdenv.mkDerivation (finalAttrs: { + pname = "tiny-cuda-nn"; + version = "1.6"; + strictDeps = true; + + format = strings.optionalString pythonSupport "setuptools"; + + src = fetchFromGitHub { + owner = "NVlabs"; + repo = finalAttrs.pname; + rev = "v${finalAttrs.version}"; + fetchSubmodules = true; + hash = "sha256-qW6Fk2GB71fvZSsfu+mykabSxEKvaikZ/pQQZUycOy0="; + }; + + nativeBuildInputs = + [ + cmake + cuda-native-redist + ninja + which + ] + ++ lists.optionals pythonSupport (with python3Packages; [ + pip + setuptools + wheel + ]); + + buildInputs = + [ + cuda-redist + ] + ++ lib.optionals pythonSupport ( + with python3Packages; [ + pybind11 + python + ] + ); + + propagatedBuildInputs = lib.optionals pythonSupport ( + with python3Packages; [ + torch + ] + ); + + # NOTE: We cannot use pythonImportsCheck for this module because it uses torch to immediately + # initailize CUDA and GPU access is not allowed in the nix build environment. + # NOTE: There are no tests for the C++ library or the python bindings, so we just skip the check + # phase -- we're not missing anything. + doCheck = false; + + preConfigure = '' + export TCNN_CUDA_ARCHITECTURES="${ + strings.concatStringsSep ";" (lists.map cudaFlags.dropDot cudaFlags.cudaCapabilities) + }" + export CUDA_HOME="${cuda-native-redist}" + export LIBRARY_PATH="${cuda-native-redist}/lib/stubs:$LIBRARY_PATH" + export CC="${backendStdenv.cc}/bin/cc" + export CXX="${backendStdenv.cc}/bin/c++" + ''; + + # When building the python bindings, we cannot re-use the artifacts from the C++ build so we + # skip the CMake confurePhase and the buildPhase. + dontUseCmakeConfigure = pythonSupport; + + # The configurePhase usually puts you in the build directory, so for the python bindings we + # need to change directories to the source directory. + configurePhase = strings.optionalString pythonSupport '' + runHook preConfigure + mkdir -p "$NIX_BUILD_TOP/build" + cd "$NIX_BUILD_TOP/build" + runHook postConfigure + ''; + + buildPhase = strings.optionalString pythonSupport '' + runHook preBuild + python -m pip wheel \ + --no-build-isolation \ + --no-clean \ + --no-deps \ + --no-index \ + --verbose \ + --wheel-dir "$NIX_BUILD_TOP/build" \ + "$NIX_BUILD_TOP/source/bindings/torch" + runHook postBuild + ''; + + installPhase = + '' + runHook preInstall + mkdir -p "$out/lib" + '' + # Installing the C++ library just requires copying the static library to the output directory + + strings.optionalString (!pythonSupport) '' + cp libtiny-cuda-nn.a "$out/lib/" + '' + # Installing the python bindings requires building the wheel and installing it + + strings.optionalString pythonSupport '' + python -m pip install \ + --no-build-isolation \ + --no-cache-dir \ + --no-deps \ + --no-index \ + --no-warn-script-location \ + --prefix="$out" \ + --verbose \ + ./*.whl + '' + + '' + runHook postInstall + ''; + + passthru = { + inherit cudaPackages; + }; + + meta = with lib; { + description = "Lightning fast C++/CUDA neural network framework"; + homepage = "https://github.com/NVlabs/tiny-cuda-nn"; + license = licenses.bsd3; + maintainers = with maintainers; [connorbaker]; + platforms = platforms.linux; + }; + }) diff --git a/nixpkgs/pkgs/development/libraries/science/math/trilinos/default.nix b/nixpkgs/pkgs/development/libraries/science/math/trilinos/default.nix new file mode 100644 index 000000000000..1939b0a5307b --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/trilinos/default.nix @@ -0,0 +1,102 @@ +{ stdenv +, lib +, fetchFromGitHub +, blas +, boost +, cmake +, gfortran +, lapack +, mpi +, suitesparse +, swig +, withMPI ? false +}: + +# NOTE: Not all packages are enabled. We specifically enable the ones +# required to build Xyce. If the need comes, we can enable more of them. + +let + flagsBase = '' + -G "Unix Makefiles" + -DBUILD_SHARED_LIBS=ON + -DCMAKE_CXX_FLAGS="-O3 -fPIC" + -DCMAKE_C_FLAGS="-O3 -fPIC" + -DCMAKE_Fortran_FLAGS="-O3 -fPIC" + -DTrilinos_ENABLE_NOX=ON + -DNOX_ENABLE_LOCA=ON + -DTrilinos_ENABLE_EpetraExt=ON + -DEpetraExt_BUILD_BTF=ON + -DEpetraExt_BUILD_EXPERIMENTAL=ON + -DEpetraExt_BUILD_GRAPH_REORDERINGS=ON + -DTrilinos_ENABLE_TrilinosCouplings=ON + -DTrilinos_ENABLE_Ifpack=ON + -DTrilinos_ENABLE_AztecOO=ON + -DTrilinos_ENABLE_Belos=ON + -DTrilinos_ENABLE_Teuchos=ON + -DTeuchos_ENABLE_COMPLEX=ON + -DTrilinos_ENABLE_Amesos=ON + -DAmesos_ENABLE_KLU=ON + -DTrilinos_ENABLE_Amesos2=ON + -DAmesos2_ENABLE_KLU2=ON + -DAmesos2_ENABLE_Basker=ON + -DTrilinos_ENABLE_Sacado=ON + -DTrilinos_ENABLE_Stokhos=ON + -DTrilinos_ENABLE_Kokkos=ON + -DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES=OFF + -DTrilinos_ENABLE_CXX11=ON + -DTPL_ENABLE_AMD=ON + -DTPL_ENABLE_BLAS=ON + -DTPL_ENABLE_LAPACK=ON + ''; + flagsParallel = '' + -DCMAKE_C_COMPILER=mpicc + -DCMAKE_CXX_COMPILER=mpic++ + -DCMAKE_Fortran_COMPILER=mpif77 + -DTrilinos_ENABLE_Isorropia=ON + -DTrilinos_ENABLE_Zoltan=ON + -DTPL_ENABLE_MPI=ON + ''; +in +stdenv.mkDerivation rec { + pname = "trilinos"; + # Xyce 7.4 requires version 12.12.1 + # nixpkgs-update: no auto update + version = "12.12.1"; + + src = fetchFromGitHub { + owner = "trilinos"; + repo = "Trilinos"; + rev = "${pname}-release-${lib.replaceStrings [ "." ] [ "-" ] version}"; + sha256 = "sha256-Nqjr7RAlUHm6vs87a1P84Y7BIZEL0Vs/A1Z6dykfv+o="; + }; + + nativeBuildInputs = [ cmake gfortran swig ]; + + buildInputs = [ blas boost lapack suitesparse ] ++ lib.optionals withMPI [ mpi ]; + + preConfigure = + if withMPI then '' + cmakeFlagsArray+=(${flagsBase} ${flagsParallel}) + '' + else '' + cmakeFlagsArray+=(${flagsBase}) + ''; + + passthru = { + inherit withMPI; + }; + + meta = with lib; { + description = "Engineering and scientific problems algorithms"; + longDescription = '' + The Trilinos Project is an effort to develop algorithms and enabling + technologies within an object-oriented software framework for the + solution of large-scale, complex multi-physics engineering and scientific + problems. + ''; + homepage = "https://trilinos.org"; + license = licenses.bsd3; + maintainers = with maintainers; [ fbeffa ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/wcpg/default.nix b/nixpkgs/pkgs/development/libraries/science/math/wcpg/default.nix new file mode 100644 index 000000000000..8f14b940f383 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/wcpg/default.nix @@ -0,0 +1,44 @@ +{ lib +, stdenv +, fetchFromGitHub +, autoreconfHook +, blas +, gmp +, lapack +, libf2c +, mpfi +, mpfr +}: + +stdenv.mkDerivation rec { + pname = "wcpg"; + version = "0.9"; + + src = fetchFromGitHub { + owner = "fixif"; + repo = pname; + rev = version; + sha256 = "sha256-uA/ENjf4urEO+lqebkp/k54199o2434FYgPSmYCG4UA="; + }; + + nativeBuildInputs = [ + autoreconfHook + ]; + + buildInputs = [ + blas + gmp + lapack + libf2c + mpfi + mpfr + ]; + + meta = with lib; { + description = "Worst-Case Peak-Gain library"; + homepage = "https://github.com/fixif/WCPG"; + license = licenses.cecill-b; + platforms = platforms.unix; + maintainers = with maintainers; [ wegank ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix b/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix new file mode 100644 index 000000000000..bdaf6e6284ef --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/math/zn_poly/default.nix @@ -0,0 +1,64 @@ +{ stdenv +, lib +, fetchFromGitLab +, fetchpatch +, gmp +, python3 +, tune ? false # tune to hardware, impure +}: + +stdenv.mkDerivation rec { + version = "0.9.2"; + pname = "zn_poly"; + + # sage has picked up the maintenance (bug fixes and building, not development) + # from the original, now unmaintained project which can be found at + # http://web.maths.unsw.edu.au/~davidharvey/code/zn_poly/ + src = fetchFromGitLab { + owner = "sagemath"; + repo = "zn_poly"; + rev = version; + hash = "sha256-QBItcrrpOGj22/ShTDdfZjm63bGW2xY4c71R1q8abPE="; + }; + + buildInputs = [ + gmp + ]; + + nativeBuildInputs = [ + python3 # needed by ./configure to create the makefile + ]; + + # name of library file ("libzn_poly.so") + libbasename = "libzn_poly"; + libext = stdenv.hostPlatform.extensions.sharedLibrary; + + makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ]; + + # Tuning (either autotuning or with hand-written parameters) is possible + # but not implemented here. + # It seems buggy anyways (see homepage). + buildFlags = [ "all" "${libbasename}${libext}" ]; + + configureFlags = lib.optionals (!tune) [ + "--disable-tuning" + ]; + + # `make install` fails to install some header files and the lib file. + installPhase = '' + mkdir -p "$out/include/zn_poly" + mkdir -p "$out/lib" + cp "${libbasename}"*"${libext}" "$out/lib" + cp include/*.h "$out/include/zn_poly" + ''; + + doCheck = true; + + meta = with lib; { + homepage = "https://web.maths.unsw.edu.au/~davidharvey/code/zn_poly/"; + description = "Polynomial arithmetic over Z/nZ"; + license = with licenses; [ gpl3 ]; + maintainers = teams.sage.members; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix new file mode 100644 index 000000000000..fa6e5e48f846 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix @@ -0,0 +1,143 @@ +{ stdenv +, breakpointHook +, fetchFromGitLab +, python +, libxml2 +, sqlite + +, boost +, gtk3-x11 +, root +, glib +, gsl + +, cmake +, pkg-config + + +, libpcap + +, jansson + +, harfbuzz +, freetype + + # for binding generation +, castxml ? null +, cppyy ? null + + # can take a long time, generates > 30000 images/graphs +, enableDoxygen ? false + + # very long +, withManual ? false +, doxygen ? null +, graphviz ? null +, imagemagick ? null + # for manual, tetex is used to get the eps2pdf binary + # texlive to get latexmk. building manual still fails though +, dia +, tetex ? null +, ghostscript ? null +, texliveMedium ? null + + # generates python bindings +, pythonSupport ? true +, ncurses ? null + +, lib +}: + +let + pythonEnv = python.withPackages (ps: + lib.optional withManual ps.sphinx + ++ lib.optionals pythonSupport (with ps;[ pybindgen pygccxml cppyy]) + ); +in +stdenv.mkDerivation rec { + pname = "ns-3"; + version = "39"; + + src = fetchFromGitLab { + owner = "nsnam"; + repo = "ns-3-dev"; + rev = "ns-3.${version}"; + sha256 = "sha256-2d8xCCfxRpcCZgt7ne17F7cUo/wIxLyvjQs3izNUnmY="; + }; + + nativeBuildInputs = [ cmake pkg-config pythonEnv ]; + + outputs = [ "out" ]; + + # ncurses is a hidden dependency of waf when checking python + buildInputs = lib.optionals pythonSupport [ castxml ncurses ] + ++ lib.optionals enableDoxygen [ doxygen graphviz imagemagick ] + ++ lib.optionals withManual [ dia tetex ghostscript imagemagick texliveMedium ] + ++ [ + libxml2 + pythonEnv + sqlite.dev + gsl + boost + root + glib.out + glib.dev + libpcap + gtk3-x11.dev + harfbuzz + freetype + jansson + ]; + + propagatedBuildInputs = [ pythonEnv ]; + + preConfigure = '' + substituteInPlace src/tap-bridge/CMakeLists.txt \ + --replace '-DTAP_CREATOR="''${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/src/tap-bridge/' "-DTAP_CREATOR=\"$out/libexec/ns3/" + + substituteInPlace src/fd-net-device/CMakeLists.txt \ + --replace '-DRAW_SOCK_CREATOR="''${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/src/fd-net-device/' "-DRAW_SOCK_CREATOR=\"$out/libexec/ns3/" + + substituteInPlace src/fd-net-device/CMakeLists.txt \ + --replace '-DTAP_DEV_CREATOR="''${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/src/fd-net-device/' "-DTAP_DEV_CREATOR=\"$out/libexec/ns3/" + ''; + + doCheck = false; + + buildTargets = "build" + + lib.optionalString enableDoxygen " doxygen" + + lib.optionalString withManual "sphinx"; + + # to prevent fatal error: 'backward_warning.h' file not found + CXXFLAGS = "-D_GLIBCXX_PERMIT_BACKWARD_HASH"; + + # Make generated python bindings discoverable in customized python environment + passthru = { pythonModule = python; }; + + cmakeFlags = [ + "-DPython3_LIBRARY_DIRS=${pythonEnv}/lib" + "-DPython3_INCLUDE_DIRS=${pythonEnv}/include" + "-DPython3_EXECUTABLE=${pythonEnv}/bin/python" + "-DNS3_PYTHON_BINDINGS=ON" + "-DNS3_DES_METRICS=ON" + "-DNS3_BINDINGS_INSTALL_DIR=${pythonEnv.sitePackages}" + "-DNS3_LOG=ON" + "-DNS3_ASSERT=ON" + "-DNS3_GTK3=ON" + "-DGTK3_GLIBCONFIG_INCLUDE_DIR=${glib.out}/lib/glib-2.0/include" + ] + ++ lib.optional doCheck "-DNS3_TESTS=ON"; + + # strictoverflow prevents clang from discovering pyembed when bindings + hardeningDisable = [ "fortify" "strictoverflow" ]; + + meta = with lib; { + homepage = "http://www.nsnam.org"; + license = licenses.gpl3; + description = "A discrete time event network simulator"; + platforms = with platforms; unix; + maintainers = with maintainers; [ teto rgrunbla ]; + # never built on aarch64-darwin since first introduction in nixpkgs + broken = (stdenv.isDarwin && stdenv.isAarch64) || (stdenv.isLinux && stdenv.isAarch64); + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/robotics/edgetpu-compiler/default.nix b/nixpkgs/pkgs/development/libraries/science/robotics/edgetpu-compiler/default.nix new file mode 100644 index 000000000000..5e02398d1b4e --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/robotics/edgetpu-compiler/default.nix @@ -0,0 +1,59 @@ +{ autoPatchelfHook +, dpkg +, fetchurl +, lib +, libcxx +, stdenv +}: +stdenv.mkDerivation rec { + pname = "edgetpu-compiler"; + version = "15.0"; + + src = fetchurl rec { + url = "https://packages.cloud.google.com/apt/pool/${pname}_${version}_amd64_${sha256}.deb"; + sha256 = "ce03822053c2bddbb8640eaa988396ae66f9bc6b9d6d671914acd1727c2b445a"; + }; + + nativeBuildInputs = [ + autoPatchelfHook + dpkg + ]; + + buildInputs = [ + libcxx + ]; + + unpackPhase = '' + mkdir bin pkg + + dpkg -x $src pkg + + rm -r pkg/usr/share/lintian + + cp pkg/usr/bin/edgetpu_compiler_bin/edgetpu_compiler ./bin + cp -r pkg/usr/share . + + rm -r pkg + ''; + + dontConfigure = true; + dontBuild = true; + + installPhase = '' + runHook preInstall + + mkdir -p $out + cp -r ./{bin,share} $out + + runHook postInstall + ''; + + meta = with lib; { + description = "A command line tool that compiles a TensorFlow Lite model into an Edge TPU compatible file."; + homepage = "https://coral.ai/docs/edgetpu/compiler"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; + license = licenses.asl20; + maintainers = with maintainers; [ cpcloud ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix b/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix new file mode 100644 index 000000000000..28a38b7056dd --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix @@ -0,0 +1,26 @@ +{ lib, stdenv, fetchurl, cmake, boost }: + +stdenv.mkDerivation rec { + pname = "ispike"; + version = "2.1.1"; + + src = fetchurl { + url = "mirror://sourceforge/ispike/${pname}-${version}.tar.gz"; + sha256 = "0khrxp43bi5kisr8j4lp9fl4r5marzf7b4inys62ac108sfb28lp"; + }; + + postPatch = '' + sed -i "1i #include <map>" include/iSpike/YarpConnection.hpp + ''; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ boost ]; + + meta = { + description = "Spiking neural interface between iCub and a spiking neural simulator"; + homepage = "https://sourceforge.net/projects/ispike/"; + license = lib.licenses.lgpl3; + platforms = lib.platforms.unix; + maintainers = [ lib.maintainers.nico202 ]; + }; +} |