diff options
Diffstat (limited to 'pkgs/development/libraries/science/math')
19 files changed, 206 insertions, 443 deletions
diff --git a/pkgs/development/libraries/science/math/clblas/default.nix b/pkgs/development/libraries/science/math/clblas/default.nix index e5ad0e3e63d9c..910c40a4e0c03 100644 --- a/pkgs/development/libraries/science/math/clblas/default.nix +++ b/pkgs/development/libraries/science/math/clblas/default.nix @@ -42,10 +42,9 @@ stdenv.mkDerivation rec { "-DBUILD_TEST=OFF" ]; - nativeBuildInputs = [ cmake gfortran ]; + nativeBuildInputs = [ cmake gfortran python3 ]; buildInputs = [ blas - python3 boost ] ++ lib.optionals (!stdenv.isDarwin) [ ocl-icd diff --git a/pkgs/development/libraries/science/math/clblast/default.nix b/pkgs/development/libraries/science/math/clblast/default.nix index a7c8d8faee4c0..3bf38086ca2fa 100644 --- a/pkgs/development/libraries/science/math/clblast/default.nix +++ b/pkgs/development/libraries/science/math/clblast/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "clblast"; - version = "1.6.2"; + version = "1.6.3"; src = fetchFromGitHub { owner = "CNugteren"; repo = "CLBlast"; rev = version; - hash = "sha256-S25g25Il6rzkpU9IqOFDDeEr3uYyt/uewZZAl09YSts="; + hash = "sha256-fzenYFCAQ0B2NQgh5OaErv/yNEzjznB6ogRapqfL6P4="; }; nativeBuildInputs = [ diff --git a/pkgs/development/libraries/science/math/faiss/default.nix b/pkgs/development/libraries/science/math/faiss/default.nix index 5af73735fdf60..9d0dea3ff6a12 100644 --- a/pkgs/development/libraries/science/math/faiss/default.nix +++ b/pkgs/development/libraries/science/math/faiss/default.nix @@ -1,107 +1,112 @@ -{ 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 +{ + lib, + config, + fetchFromGitHub, + stdenv, + cmake, + cudaPackages ? { }, + cudaSupport ? config.cudaSupport, + pythonSupport ? true, + pythonPackages, + llvmPackages, + blas, + swig, + autoAddDriverRunpath, + 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"; + version = "1.8.0"; inherit (cudaPackages) flags backendStdenv; 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 - ]; - }; + cudaComponents = with cudaPackages; [ + cuda_cudart # cuda_runtime.h + libcublas + libcurand + cuda_cccl + + # cuda_profiler_api.h + (cudaPackages.cuda_profiler_api or cudaPackages.cuda_nvprof) + ]; in stdenv.mkDerivation { inherit pname version; - outputs = [ "out" "demos" ]; + outputs = [ + "out" + "demos" + "dist" + ]; src = fetchFromGitHub { owner = "facebookresearch"; repo = pname; rev = "v${version}"; - hash = "sha256-WSce9X6sLZmGM5F0ZkK54VqpIy8u1VB0e9/l78co29M="; + hash = "sha256-nS8nhkNGGb2oAJKfr/MIAZjAwMxBGbNd16/CkEtv67I="; }; - buildInputs = [ - blas - swig - ] ++ lib.optionals pythonSupport [ - pythonPackages.setuptools - pythonPackages.pip - pythonPackages.wheel - ] ++ lib.optionals stdenv.cc.isClang [ - llvmPackages.openmp - ] ++ lib.optionals cudaSupport [ - cudaJoined - ]; - - propagatedBuildInputs = lib.optionals pythonSupport [ - pythonPackages.numpy - ]; - - nativeBuildInputs = [ cmake ] ++ lib.optionals cudaSupport [ - cudaPackages.cuda_nvcc - addOpenGLRunpath - ] ++ lib.optionals pythonSupport [ - pythonPackages.python - ]; + # Remove the following substituteInPlace when updating + # to a release that contains change from PR + # https://github.com/facebookresearch/faiss/issues/3239 + # that fixes building faiss with swig 4.2.x + postPatch = '' + substituteInPlace faiss/python/swigfaiss.swig \ + --replace-fail '#ifdef SWIGWORDSIZE64' '#if (__SIZEOF_LONG__ == 8)' + ''; - passthru.extra-requires.all = [ - pythonPackages.numpy - ]; + nativeBuildInputs = + [ cmake ] + ++ lib.optionals cudaSupport [ + cudaPackages.cuda_nvcc + autoAddDriverRunpath + ] + ++ lib.optionals pythonSupport [ + pythonPackages.python + pythonPackages.setuptools + pythonPackages.pip + pythonPackages.wheel + ]; - cmakeFlags = [ - "-DFAISS_ENABLE_GPU=${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=${flags.cmakeCudaArchitecturesString}" - "-DCUDAToolkit_INCLUDE_DIR=${cudaJoined}/include" - ]; + buildInputs = + [ + blas + swig + ] + ++ lib.optionals pythonSupport [ pythonPackages.numpy ] + ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ] + ++ lib.optionals cudaSupport cudaComponents; + + cmakeFlags = + [ + (lib.cmakeBool "FAISS_ENABLE_GPU" cudaSupport) + (lib.cmakeBool "FAISS_ENABLE_PYTHON" pythonSupport) + (lib.cmakeFeature "FAISS_OPT_LEVEL" optLevel) + ] + ++ lib.optionals cudaSupport [ + (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" flags.cmakeCudaArchitecturesString) + ]; - buildFlags = [ - "faiss" - "demo_ivfpq_indexing" - ] ++ lib.optionals pythonSupport [ - "swigfaiss" - ]; + buildFlags = + [ "faiss" ] + # This is just a demo app used as a test. + # Disabled because linkage fails: + # https://github.com/facebookresearch/faiss/issues/3484 + ++ lib.optionals (!cudaSupport) [ "demo_ivfpq_indexing" ] + ++ lib.optionals pythonSupport [ "swigfaiss" ]; # pip wheel->pip install commands copied over from opencv4 @@ -110,36 +115,30 @@ stdenv.mkDerivation { python -m pip wheel --verbose --no-index --no-deps --no-clean --no-build-isolation --wheel-dir dist .) ''; - postInstall = '' - 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) - ''; - - postFixup = lib.optionalString (pythonSupport && cudaSupport) '' - addOpenGLRunpath $out/${pythonPackages.python.sitePackages}/faiss/*.so - addOpenGLRunpath $demos/bin/* - ''; - - # Need buildPythonPackage for this one - # pythonImportsCheck = [ - # "faiss" - # ]; + postInstall = + '' + mkdir -p $demos/bin + if [[ "$buildInputs" == *demo_ivfpq_indexing* ]] ; then + cp ./demos/demo_ivfpq_indexing $demos/bin/ + fi + '' + + lib.optionalString pythonSupport '' + mkdir "$dist" + cp faiss/python/dist/*.whl "$dist/" + ''; passthru = { inherit cudaSupport cudaPackages pythonSupport; tests = { - runDemos = runCommand "${pname}-run-demos" - { buildInputs = [ faiss.demos ]; } - # There are more demos, we run just the one that documentation mentions - '' - demo_ivfpq_indexing && touch $out - ''; - } // lib.optionalAttrs pythonSupport { - pytest = pythonPackages.callPackage ./tests.nix { }; + runDemos = + runCommand "${pname}-run-demos" { buildInputs = [ faiss.demos ]; } + # There are more demos, we run just the one that documentation mentions + '' + demo_ivfpq_indexing && touch $out + ''; + pythonFaiss = pythonPackages.faiss; + pytest = pythonPackages.faiss.tests.pytest; }; }; diff --git a/pkgs/development/libraries/science/math/faiss/tests.nix b/pkgs/development/libraries/science/math/faiss/tests.nix deleted file mode 100644 index 858a980bfeaf3..0000000000000 --- a/pkgs/development/libraries/science/math/faiss/tests.nix +++ /dev/null @@ -1,37 +0,0 @@ -{ lib -, buildPythonPackage -, faiss -, scipy -, pytestCheckHook -}: - -assert faiss.pythonSupport; - -buildPythonPackage { - pname = "faiss-pytest-suite"; - inherit (faiss) version; - - format = "other"; - - src = "${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/pkgs/development/libraries/science/math/itpp/default.nix b/pkgs/development/libraries/science/math/itpp/default.nix index d2f6b1ee8aec4..a1a1ed8a69bc0 100644 --- a/pkgs/development/libraries/science/math/itpp/default.nix +++ b/pkgs/development/libraries/science/math/itpp/default.nix @@ -48,7 +48,7 @@ stdenv.mkDerivation rec { homepage = "https://itpp.sourceforge.net/"; license = licenses.gpl3; platforms = platforms.unix; - maintainers = with maintainers; [ ]; + maintainers = [ ]; broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/itpp.x86_64-darwin }; } diff --git a/pkgs/development/libraries/science/math/lcalc/default.nix b/pkgs/development/libraries/science/math/lcalc/default.nix index ebab7c00809ad..6ea1ca8f8e6c0 100644 --- a/pkgs/development/libraries/science/math/lcalc/default.nix +++ b/pkgs/development/libraries/science/math/lcalc/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { owner = "sagemath"; repo = pname; rev = version; - sha256 = "sha256-RxWZ7T0I9zV7jUVnL6jV/PxEoU32KY7Q1UsOL5Lonuc="; + hash = "sha256-RxWZ7T0I9zV7jUVnL6jV/PxEoU32KY7Q1UsOL5Lonuc="; }; nativeBuildInputs = [ diff --git a/pkgs/development/libraries/science/math/libtorch/bin.nix b/pkgs/development/libraries/science/math/libtorch/bin.nix index 5b08cfa7dcf07..92050cd172834 100644 --- a/pkgs/development/libraries/science/math/libtorch/bin.nix +++ b/pkgs/development/libraries/science/math/libtorch/bin.nix @@ -4,12 +4,13 @@ , lib , libcxx , llvmPackages +, config -, addOpenGLRunpath +, addDriverRunpath , patchelf , fixDarwinDylibNames -, cudaSupport +, cudaSupport ? config.cudaSupport }: let @@ -31,7 +32,7 @@ in stdenv.mkDerivation { nativeBuildInputs = if stdenv.isDarwin then [ fixDarwinDylibNames ] - else [ patchelf ] ++ lib.optionals cudaSupport [ addOpenGLRunpath ]; + else [ patchelf ] ++ lib.optionals cudaSupport [ addDriverRunpath ]; dontBuild = true; dontConfigure = true; @@ -64,7 +65,7 @@ in stdenv.mkDerivation { echo "setting rpath for $lib..." patchelf --set-rpath "${rpath}:$out/lib" "$lib" ${lib.optionalString cudaSupport '' - addOpenGLRunpath "$lib" + addDriverRunpath "$lib" ''} done '' + lib.optionalString stdenv.isDarwin '' diff --git a/pkgs/development/libraries/science/math/magma/generic.nix b/pkgs/development/libraries/science/math/magma/generic.nix index a675142f361d4..08dac598f7d91 100644 --- a/pkgs/development/libraries/science/math/magma/generic.nix +++ b/pkgs/development/libraries/science/math/magma/generic.nix @@ -134,19 +134,15 @@ stdenv.mkDerivation { blas python3 ] ++ lists.optionals cudaSupport (with effectiveCudaPackages; [ - 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 + cuda_cudart # cuda_runtime.h + libcublas # cublas_v2.h + libcusparse # cusparse.h ] ++ lists.optionals (cudaOlder "11.8") [ - cuda_nvprof.dev # <cuda_profiler_api.h> + cuda_nvprof # <cuda_profiler_api.h> ] ++ lists.optionals (cudaAtLeast "11.8") [ - cuda_profiler_api.dev # <cuda_profiler_api.h> + cuda_profiler_api # <cuda_profiler_api.h> ] ++ lists.optionals (cudaAtLeast "12.0") [ - cuda_cccl.dev # <nv/target> + cuda_cccl # <nv/target> ]) ++ lists.optionals rocmSupport [ rocmPackages.clr rocmPackages.hipblas diff --git a/pkgs/development/libraries/science/math/mkl/default.nix b/pkgs/development/libraries/science/math/mkl/default.nix index 90e6c05da77d0..607b6c89e40d1 100644 --- a/pkgs/development/libraries/science/math/mkl/default.nix +++ b/pkgs/development/libraries/science/math/mkl/default.nix @@ -5,7 +5,7 @@ , fetchurl , rpmextract , _7zz -, darwin +, cctools , validatePkgConfig , enableStatic ? stdenv.hostPlatform.isStatic }: @@ -72,7 +72,7 @@ in stdenvNoCC.mkDerivation ({ nativeBuildInputs = [ validatePkgConfig ] ++ (if stdenvNoCC.isDarwin then - [ _7zz darwin.cctools ] + [ _7zz cctools ] else [ rpmextract ]); diff --git a/pkgs/development/libraries/science/math/mkl/test/default.nix b/pkgs/development/libraries/science/math/mkl/test/default.nix index cb3355260d127..1717e11e43d86 100644 --- a/pkgs/development/libraries/science/math/mkl/test/default.nix +++ b/pkgs/development/libraries/science/math/mkl/test/default.nix @@ -12,7 +12,9 @@ in stdenv.mkDerivation { pname = "mkl-test"; version = mkl.version; - src = ./.; + unpackPhase = '' + cp ${./test.c} test.c + ''; nativeBuildInputs = [ pkg-config ]; diff --git a/pkgs/development/libraries/science/math/or-tools/default.nix b/pkgs/development/libraries/science/math/or-tools/default.nix index acb0ece75463c..cb4670204d112 100644 --- a/pkgs/development/libraries/science/math/or-tools/default.nix +++ b/pkgs/development/libraries/science/math/or-tools/default.nix @@ -6,7 +6,7 @@ , eigen , ensureNewerSourcesForZipFilesHook , fetchFromGitHub -, fetchpatch +, substituteAll , glpk , lib , pkg-config @@ -19,53 +19,57 @@ , zlib }: +let + pybind11_protobuf = fetchFromGitHub { + owner = "pybind"; + repo = "pybind11_protobuf"; + rev = "b713501f1da56d9b76c42f89efd00b97c26c9eac"; + hash = "sha256-f6pzRWextH+7lm1xzyhx98wCIWH3lbhn59gSCcjsBVw="; + }; +in stdenv.mkDerivation rec { pname = "or-tools"; - version = "9.4"; + version = "9.7"; src = fetchFromGitHub { owner = "google"; repo = "or-tools"; rev = "v${version}"; - sha256 = "sha256-joWonJGuxlgHhXLznRhC1MDltQulXzpo4Do9dec1bLY="; + hash = "sha256-eHukf6TbY2dx7iEf8WfwfWsjDEubPtRO02ju0kHtASo="; }; + 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="; + (substituteAll { + src = ./offline.patch; + pybind11_protobuf = "../../pybind11_protobuf"; }) - # 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 + + cp -R ${pybind11_protobuf} pybind11_protobuf + chmod -R u+w pybind11_protobuf ''; cmakeFlags = [ "-DBUILD_DEPS=OFF" "-DBUILD_PYTHON=ON" "-DBUILD_pybind11=OFF" + "-DBUILD_pybind11_protobuf=ON" + "-DCMAKE_INSTALL_BINDIR=bin" + "-DCMAKE_INSTALL_INCLUDEDIR=include" + "-DCMAKE_INSTALL_LIBDIR=lib" "-DFETCH_PYTHON_DEPS=OFF" "-DUSE_GLPK=ON" "-DUSE_SCIP=OFF" "-DPython3_EXECUTABLE=${python.pythonOnBuildForHost.interpreter}" ] ++ lib.optionals stdenv.isDarwin [ "-DCMAKE_MACOSX_RPATH=OFF" ]; + + strictDeps = true; + nativeBuildInputs = [ cmake ensureNewerSourcesForZipFilesHook @@ -78,14 +82,18 @@ stdenv.mkDerivation rec { ] ++ (with python.pythonOnBuildForHost.pkgs; [ pip mypy-protobuf + mypy ]); buildInputs = [ + abseil-cpp bzip2 cbc eigen glpk python.pkgs.absl-py python.pkgs.pybind11 + python.pkgs.pytest + python.pkgs.scipy python.pkgs.setuptools python.pkgs.wheel re2 @@ -103,7 +111,19 @@ stdenv.mkDerivation rec { python.pkgs.virtualenv ]; - doCheck = true; + env.NIX_CFLAGS_COMPILE = toString [ + # fatal error: 'python/google/protobuf/proto_api.h' file not found + "-I${protobuf.src}" + # fatal error: 'pybind11_protobuf/native_proto_caster.h' file not found + "-I${pybind11_protobuf}" + ]; + + # some tests fail on linux and hang on darwin + doCheck = false; + + preCheck = '' + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}$PWD/lib + ''; # This extra configure step prevents the installer from littering # $out/bin with sample programs that only really function as tests, diff --git a/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch b/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch deleted file mode 100644 index 760ab80a38e4d..0000000000000 --- a/pkgs/development/libraries/science/math/or-tools/fix-stringview-compile.patch +++ /dev/null @@ -1,36 +0,0 @@ -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/pkgs/development/libraries/science/math/or-tools/offline.patch b/pkgs/development/libraries/science/math/or-tools/offline.patch new file mode 100644 index 0000000000000..1a2a4dbe3631b --- /dev/null +++ b/pkgs/development/libraries/science/math/or-tools/offline.patch @@ -0,0 +1,16 @@ +diff --git a/cmake/dependencies/CMakeLists.txt b/cmake/dependencies/CMakeLists.txt +index af3a28c113..ba92c3c55e 100644 +--- a/cmake/dependencies/CMakeLists.txt ++++ b/cmake/dependencies/CMakeLists.txt +@@ -177,9 +177,8 @@ if(BUILD_PYTHON AND BUILD_pybind11_protobuf) + list(APPEND CMAKE_MESSAGE_INDENT " ") + FetchContent_Declare( + pybind11_protobuf +- GIT_REPOSITORY "https://github.com/pybind/pybind11_protobuf.git" +- GIT_TAG "main" +- PATCH_COMMAND git apply --ignore-whitespace "${CMAKE_CURRENT_LIST_DIR}/../../patches/pybind11_protobuf.patch" ++ SOURCE_DIR @pybind11_protobuf@ ++ PATCH_COMMAND patch -p1 < "${CMAKE_CURRENT_LIST_DIR}/../../patches/pybind11_protobuf.patch" + ) + FetchContent_MakeAvailable(pybind11_protobuf) + list(POP_BACK CMAKE_MESSAGE_INDENT) diff --git a/pkgs/development/libraries/science/math/osqp/default.nix b/pkgs/development/libraries/science/math/osqp/default.nix index d308302e2c9f3..bcb1031684668 100644 --- a/pkgs/development/libraries/science/math/osqp/default.nix +++ b/pkgs/development/libraries/science/math/osqp/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { owner = "oxfordcontrol"; repo = "osqp"; rev = "v${version}"; - sha256 = "sha256-enkK5EFyAeLaUnHNYS3oq43HsHY5IuSLgsYP0k/GW8c="; + hash = "sha256-enkK5EFyAeLaUnHNYS3oq43HsHY5IuSLgsYP0k/GW8c="; fetchSubmodules = true; }; diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix deleted file mode 100644 index c07250c660a33..0000000000000 --- a/pkgs/development/libraries/science/math/petsc/default.nix +++ /dev/null @@ -1,96 +0,0 @@ -{ 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/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch b/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch deleted file mode 100644 index f3a34de9304e3..0000000000000 --- a/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch +++ /dev/null @@ -1,100 +0,0 @@ -diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile -index 672a62a..a5fd1c4 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 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -pc_gamg_esteig_ksp_max_it 10 -ksp_monitor -mg_levels_ksp_max_it 3 > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ - if (${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/pkgs/development/libraries/science/math/scalapack/default.nix b/pkgs/development/libraries/science/math/scalapack/default.nix index 2f8d3dbe15de3..f1e0f6cf5a128 100644 --- a/pkgs/development/libraries/science/math/scalapack/default.nix +++ b/pkgs/development/libraries/science/math/scalapack/default.nix @@ -52,10 +52,11 @@ stdenv.mkDerivation rec { -DLAPACK_LIBRARIES="-llapack" -DBLAS_LIBRARIES="-lblas" -DCMAKE_Fortran_COMPILER=${lib.getDev mpi}/bin/mpif90 - ${lib.optionalString passthru.isILP64 '' - -DCMAKE_Fortran_FLAGS="-fdefault-integer-8" - -DCMAKE_C_FLAGS="-DInt=long" - ''} + -DCMAKE_C_FLAGS="${lib.concatStringsSep " " [ + "-Wno-implicit-function-declaration" + (lib.optionalString passthru.isILP64 "-DInt=long") + ]}" + ${lib.optionalString passthru.isILP64 ''-DCMAKE_Fortran_FLAGS="-fdefault-integer-8"''} ) ''; diff --git a/pkgs/development/libraries/science/math/suitesparse/default.nix b/pkgs/development/libraries/science/math/suitesparse/default.nix index fcfd9b56a1b14..43623e8604b9b 100644 --- a/pkgs/development/libraries/science/math/suitesparse/default.nix +++ b/pkgs/development/libraries/science/math/suitesparse/default.nix @@ -36,17 +36,15 @@ stdenv.mkDerivation rec { buildInputs = assert (blas.isILP64 == lapack.isILP64); [ blas lapack metis - gfortran.cc.lib + (lib.getLib gfortran.cc) gmp mpfr ] ++ lib.optionals stdenv.cc.isClang [ openmp ] ++ lib.optionals enableCuda [ - cudaPackages.cuda_cudart.dev - cudaPackages.cuda_cudart.lib - cudaPackages.cuda_cccl.dev - cudaPackages.libcublas.dev - cudaPackages.libcublas.lib + cudaPackages.cuda_cudart + cudaPackages.cuda_cccl + cudaPackages.libcublas ]; preConfigure = '' @@ -63,8 +61,8 @@ stdenv.mkDerivation rec { "CFLAGS=-DBLAS64" ] ++ lib.optionals enableCuda [ "CUDA_PATH=${cudaPackages.cuda_nvcc}" - "CUDART_LIB=${cudaPackages.cuda_cudart.lib}/lib/libcudart.so" - "CUBLAS_LIB=${cudaPackages.libcublas.lib}/lib/libcublas.so" + "CUDART_LIB=${lib.getLib cudaPackages.cuda_cudart}/lib/libcudart.so" + "CUBLAS_LIB=${lib.getLib cudaPackages.libcublas}/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 diff --git a/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix b/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix index e9367d416e325..bea271b0cef15 100644 --- a/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix +++ b/pkgs/development/libraries/science/math/tiny-cuda-nn/default.nix @@ -14,15 +14,15 @@ inherit (cudaPackages) backendStdenv flags; 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 + (lib.getDev cuda_cudart) # cuda_runtime.h + (lib.getLib cuda_cudart) + (lib.getDev cuda_cccl) # <nv/target> + (lib.getDev libcublas) # cublas_v2.h + (lib.getLib libcublas) + (lib.getDev libcusolver) # cusolverDn.h + (lib.getLib libcusolver) + (lib.getDev libcusparse) # cusparse.h + (lib.getLib libcusparse) ]; cuda-native-redist = symlinkJoin { @@ -46,7 +46,7 @@ in src = fetchFromGitHub { owner = "NVlabs"; - repo = finalAttrs.pname; + repo = "tiny-cuda-nn"; rev = "v${finalAttrs.version}"; fetchSubmodules = true; hash = "sha256-qW6Fk2GB71fvZSsfu+mykabSxEKvaikZ/pQQZUycOy0="; |