diff options
Diffstat (limited to 'nixpkgs/pkgs/development/libraries/science/math')
9 files changed, 98 insertions, 109 deletions
diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix index 962e8e8e6ace..f6d00411221c 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix @@ -6,10 +6,10 @@ # Enable BLAS interface with 64-bit integer width. , blas64 ? false -# Target architecture. "amd64" compiles kernels for all Zen +# Target architecture. "amdzen" compiles kernels for all Zen # generations. To build kernels for specific Zen generations, -# use "zen", "zen2", or "zen3". -, withArchitecture ? "amd64" +# use "zen", "zen2", "zen3", or "zen4". +, withArchitecture ? "amdzen" # Enable OpenMP-based threading. , withOpenMP ? true @@ -18,15 +18,16 @@ let threadingSuffix = lib.optionalString withOpenMP "-mt"; blasIntSize = if blas64 then "64" else "32"; + in stdenv.mkDerivation rec { pname = "amd-blis"; - version = "3.0"; + version = "4.1"; src = fetchFromGitHub { owner = "amd"; repo = "blis"; rev = version; - hash = "sha256-bbbeo1yOKse9pzbsB6lQ7pULKdzu3G7zJzTUgPXiMZY="; + hash = "sha256-1vd4uBg/+Vufqsr+MnAWSUW/THkribHNSMeq1/is8K4="; }; inherit blas64; @@ -54,8 +55,9 @@ in stdenv.mkDerivation rec { ''; postInstall = '' - ln -s $out/lib/libblis${threadingSuffix}.so.3 $out/lib/libblas.so.3 - ln -s $out/lib/libblis${threadingSuffix}.so.3 $out/lib/libcblas.so.3 + 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 $out/lib/libcblas.so ''; diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/add-lapacke.diff b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/add-lapacke.diff deleted file mode 100644 index 3e3ef1e60ff5..000000000000 --- a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/add-lapacke.diff +++ /dev/null @@ -1,34 +0,0 @@ -diff --git a/Makefile b/Makefile -index 5549ce30..ac2ee51e 100644 ---- a/Makefile -+++ b/Makefile -@@ -583,14 +583,14 @@ endif - - # --- Shared library linker rules --- - --$(LIBFLAME_SO_PATH): $(MK_ALL_FLAMEC_OBJS) -+$(LIBFLAME_SO_PATH): $(MK_ALL_FLAMEC_OBJS) $(LAPACKE_A_PATH) - ifeq ($(ENABLE_VERBOSE),yes) - ifeq ($(FLA_ENABLE_MAX_ARG_LIST_HACK),yes) - $(CAT) $(AR_OBJ_LIST_FILE) | xargs -n$(AR_CHUNK_SIZE) $(AR) $(ARFLAGS) $(LIBFLAME_A) - ifeq ($(OS_NAME),Darwin) -- $(LINKER) $(SOFLAGS) -o $@ -Wl,-force_load,$(LIBFLAME_A) $(LDFLAGS) -+ $(LINKER) $(SOFLAGS) -o $@ -Wl,-force_load,$(LIBFLAME_A),$(LAPACKE_A_PATH) $(LDFLAGS) - else -- $(LINKER) $(SOFLAGS) -o $@ -Wl,--whole-archive,$(LIBFLAME_A),--no-whole-archive $(LDFLAGS) -+ $(LINKER) $(SOFLAGS) -o $@ -Wl,--whole-archive,$(LIBFLAME_A),$(LAPACKE_A_PATH)--no-whole-archive $(LDFLAGS) - endif - else - # NOTE: Can't use $^ automatic variable as long as $(AR_OBJ_LIST_FILE) is in -@@ -602,9 +602,9 @@ else - ifeq ($(FLA_ENABLE_MAX_ARG_LIST_HACK),yes) - @$(CAT) $(AR_OBJ_LIST_FILE) | xargs -n$(AR_CHUNK_SIZE) $(AR) $(ARFLAGS) $(LIBFLAME_A) - ifeq ($(OS_NAME),Darwin) -- @$(LINKER) $(SOFLAGS) -o $@ -Wl,-force_load,$(LIBFLAME_A) $(LDFLAGS) -+ @$(LINKER) $(SOFLAGS) -o $@ -Wl,-force_load,$(LIBFLAME_A),$(LAPACKE_A_PATH) $(LDFLAGS) - else -- @$(LINKER) $(SOFLAGS) -o $@ -Wl,--whole-archive,$(LIBFLAME_A),--no-whole-archive $(LDFLAGS) -+ @$(LINKER) $(SOFLAGS) -o $@ -Wl,--whole-archive,$(LIBFLAME_A),$(LAPACKE_A_PATH),--no-whole-archive $(LDFLAGS) - endif - else - # NOTE: Can't use $^ automatic variable as long as $(AR_OBJ_LIST_FILE) is in diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix index a5b657379411..2ed35d26b907 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix @@ -1,78 +1,62 @@ { lib , stdenv , fetchFromGitHub +, cmake , gfortran , python3 , amd-blis +, aocl-utils , withOpenMP ? true , blas64 ? false +, withAMDOpt ? false }: -# right now only LP64 is supported -assert !blas64; - stdenv.mkDerivation rec { pname = "amd-libflame"; - version = "3.0"; + version = "4.1"; src = fetchFromGitHub { owner = "amd"; repo = "libflame"; rev = version; - hash = "sha256-jESae5NqANw90RBbIHH2oGEq5/mudc4IONv50P/AeQ0="; + hash = "sha256-SZk11oOAnvn1vb7ucX6U9b0YtAJNxl3tQu4ExHpwwoo="; }; - patches = [ - # The LAPACKE interface is compiled as a separate static library, - # we want the main dynamic library to provide LAPACKE symbols. - # This patch adds lapacke.a to the shared library as well. - ./add-lapacke.diff - ]; - - passthru = { inherit blas64; }; - - nativeBuildInputs = [ gfortran python3 ]; + postPatch = '' + patchShebangs build - buildInputs = [ amd-blis ]; + # Enforce reproducible build compiler flags + substituteInPlace CMakeLists.txt --replace '-mtune=native' "" + ''; - configureFlags = [ - # Build a dynamic library with a LAPACK interface. - "--disable-static-build" - "--enable-dynamic-build" - "--enable-lapack2flame" + passthru = { inherit blas64; }; - # Use C BLAS interface. - "--enable-cblas-interfaces" + nativeBuildInputs = [ cmake gfortran python3 ]; - # Avoid overloading maximum number of arguments. - "--enable-max-arg-list-hack" + buildInputs = [ amd-blis aocl-utils ]; - # libflame by default leaves BLAS symbols unresolved and leaves it - # up to the application to explicitly link to a BLAS. This is - # problematic for us, since then the BLAS library becomes an - # implicit dependency. Moreover, since the point of the AMD forks - # is to optimized for recent AMD CPUs, link against AMD BLIS. - "LDFLAGS=-lcblas" + cmakeFlags = [ + "-DLIBAOCLUTILS_LIBRARY_PATH=${lib.getLib aocl-utils}/lib" + "-DLIBAOCLUTILS_INCLUDE_PATH=${lib.getDev aocl-utils}/include" + "-DENABLE_BUILTIN_LAPACK2FLAME=ON" + "-DENABLE_CBLAS_INTERFACES=ON" + "-DENABLE_EXT_LAPACK_INTERFACE=ON" ] - ++ lib.optionals withOpenMP [ "--enable-multithreading=openmp" ]; - - enableParallelBuilding = true; - - postPatch = '' - patchShebangs build - ''; + ++ lib.optional (!withOpenMP) "ENABLE_MULTITHREADING=OFF" + ++ lib.optional blas64 "ENABLE_ILP64=ON" + ++ lib.optional withAMDOpt "ENABLE_AMD_OPT=ON"; postInstall = '' - ln -s $out/lib/libflame.so.${version} $out/lib/liblapack.so.3 - ln -s $out/lib/libflame.so.${version} $out/lib/liblapacke.so.3 + 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 = with maintainers; [ ]; + 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 index a418df7050eb..744d565eddcd 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix @@ -1,8 +1,9 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake +{ lib, stdenv, fetchFromGitHub, cmake , gfortran, blas, lapack, eigen , useMpi ? false , mpi , openssh +, igraph }: # MPI version can only be built with LP64 interface. @@ -11,25 +12,15 @@ assert useMpi -> !blas.isILP64; stdenv.mkDerivation rec { pname = "arpack"; - version = "3.8.0"; + version = "3.9.1"; src = fetchFromGitHub { owner = "opencollab"; repo = "arpack-ng"; rev = version; - sha256 = "sha256-nc710iLRqy/p3EaVgbEoCRzNJ9GpKqqQp33tbn7R6lA="; + sha256 = "sha256-HCvapLba8oLqx9I5+KDAU0s/dTmdWOEilS75i4gyfC0="; }; - patches = [ - # https://github.com/opencollab/arpack-ng/pull/301 - (fetchpatch { - name = "pkg-config-paths.patch"; - url = "https://github.com/opencollab/arpack-ng/commit/47fc83cb371a9cc8a8c058097de5e0298cd548f5.patch"; - excludes = [ "CHANGES" ]; - sha256 = "1aijvrfsxkgzqmkzq2dmaj8q3jdpg2hwlqpfl8ddk9scv17gh9m8"; - }) - ]; - nativeBuildInputs = [ cmake gfortran ]; buildInputs = assert (blas.isILP64 == lapack.isILP64); [ blas @@ -56,10 +47,16 @@ stdenv.mkDerivation rec { install_name_tool -change libblas.dylib ${blas}/lib/libblas.dylib $out/lib/libarpack.dylib ''; - passthru = { inherit (blas) isILP64; }; + passthru = { + inherit (blas) isILP64; + tests = { + inherit igraph; + }; + }; meta = { homepage = "https://github.com/opencollab/arpack-ng"; + changelog = "https://github.com/opencollab/arpack-ng/blob/${src.rev}/CHANGES"; description = '' A collection of Fortran77 subroutines to solve large scale eigenvalue problems. diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix index b3753a63339a..27509ee99339 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix @@ -18,15 +18,12 @@ , gfortran , cudaCapabilities ? cudaPackages.cudaFlags.cudaCapabilities , gpuTargets ? [ ] # Non-CUDA targets, that is HIP -, hip -, hipblas -, hipsparse +, rocmPackages , lapack , lib , libpthreadstubs , magmaRelease , ninja -, openmp , rocmSupport ? false , static ? false , stdenv @@ -47,7 +44,7 @@ let # 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) hip.gpuTargets; + rocmArches = lists.map (x: strings.removePrefix "gfx" x) rocmPackages.clr.gpuTargets; supportedRocmArches = lists.intersectLists rocmArches supportedGpuTargets; unsupportedRocmArches = lists.subtractLists supportedRocmArches rocmArches; @@ -124,11 +121,13 @@ stdenv.mkDerivation { 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 [ - hip - hipblas - hipsparse - openmp + rocmPackages.clr + rocmPackages.hipblas + rocmPackages.hipsparse + rocmPackages.llvm.openmp ]; cmakeFlags = [ @@ -142,8 +141,8 @@ stdenv.mkDerivation { "-DCMAKE_CXX_COMPILER=${backendStdenv.cc}/bin/c++" "-DMAGMA_ENABLE_CUDA=ON" ] ++ lists.optionals rocmSupport [ - "-DCMAKE_C_COMPILER=${hip}/bin/hipcc" - "-DCMAKE_CXX_COMPILER=${hip}/bin/hipcc" + "-DCMAKE_C_COMPILER=${rocmPackages.clr}/bin/hipcc" + "-DCMAKE_CXX_COMPILER=${rocmPackages.clr}/bin/hipcc" "-DMAGMA_ENABLE_HIP=ON" ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix index 4422a908838f..14befd6d11fe 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { pname = "openspecfun"; - version = "0.5.5"; + version = "0.5.6"; src = fetchFromGitHub { owner = "JuliaLang"; repo = "openspecfun"; rev = "v${version}"; - sha256 = "sha256-fX2wc8LHUcF5nN/hiA60ZZ7emRTs0SznOm/0q6lD+Ko="; + sha256 = "sha256-4MPoRMtDTkdvDfhNXKk/80pZjXRNEPcysLNTb5ohxWk="; }; makeFlags = [ "prefix=$(out)" ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix index 55438c63a5e0..8f0c930eff62 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix @@ -45,6 +45,9 @@ stdenv.mkDerivation rec { 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 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/scalapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix index e2a5e76c5586..81bcec504473 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix @@ -34,6 +34,8 @@ stdenv.mkDerivation rec { sed -i '/xssep/d;/xsgsep/d;/xssyevr/d' TESTING/CMakeLists.txt ''; + outputs = [ "out" "dev" ]; + nativeBuildInputs = [ cmake ]; nativeCheckInputs = [ openssh mpiCheckPhaseHook ]; buildInputs = [ blas lapack ]; |