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Thu, 3 Feb 2022 10:05:12 GMT (envelope-from git) Date: Thu, 3 Feb 2022 10:05:12 GMT Message-Id: <202202031005.213A5CXt074454@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: c5921be58275 - main - science/dakota: Update 6.13.0 -> 6.15.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c5921be58275f99676a4ed693994aae29a2f1e24 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=c5921be58275f99676a4ed693994aae29a2f1e24 commit c5921be58275f99676a4ed693994aae29a2f1e24 Author: Yuri Victorovich AuthorDate: 2022-02-03 08:57:38 +0000 Commit: Yuri Victorovich CommitDate: 2022-02-03 10:05:09 +0000 science/dakota: Update 6.13.0 -> 6.15.0 --- science/dakota/Makefile | 85 ++++++++-------------- science/dakota/distinfo | 8 +- science/dakota/files/patch-CMakeLists.txt | 17 +++-- .../files/patch-cmake_DakotaVersionUtils.cmake | 11 --- ...nal_acro_packages_colin_src_colin_AppResponse.h | 17 ----- .../patch-packages_external_sciplot_SciPlot.c | 22 ++++++ .../patch-src_ProcessHandleApplicInterface.cpp | 14 ---- science/dakota/pkg-plist | 28 +++++-- 8 files changed, 91 insertions(+), 111 deletions(-) diff --git a/science/dakota/Makefile b/science/dakota/Makefile index d3d540180e3f..1b0b655469bd 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,8 +1,9 @@ PORTNAME= dakota -DISTVERSION= 6.13.0 -PORTREVISION= 4 +DISTVERSION= 6.15.0 CATEGORIES= science MASTER_SITES= https://dakota.sandia.gov/sites/default/files/distributions/public/ +DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Interface between analysis codes & iterative systems analysis methods @@ -10,14 +11,23 @@ COMMENT= Interface between analysis codes & iterative systems analysis methods LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= nanoflann>0:math/nanoflann LIB_DEPENDS= libblas.so:math/blas \ libboost_system.so:devel/boost-libs \ - liblapack.so:math/lapack + libgsl.so:math/gsl \ + libhdf5.so:science/hdf5 \ + liblapack.so:math/lapack \ + libnlopt.so:math/nlopt \ + libsz.so:science/szip RUN_DEPENDS= bash:shells/bash -USES= cmake compiler:c++11-lang fortran perl5 python shebangfix +USES= cmake compiler:c++11-lang fortran motif perl5 pkgconfig python shebangfix xorg +USE_XORG= ice sm x11 xau xdmcp xext xft xmu xrender xt USE_LDCONFIG= yes +USE_GITHUB= nodefault +GH_TUPLE= stan-dev:math:v2.18.0:stanmath/stanmath + SHEBANG_GLOB= *.sh *.py SHEBANG_FILES= interfaces/Python/mpitile \ scripts/pyprepro/dprepro \ @@ -25,17 +35,21 @@ SHEBANG_FILES= interfaces/Python/mpitile \ scripts/dprepro.perl \ test/dakota_test.perl -CMAKE_ON= Boost_NO_BOOST_CMAKE \ +CMAKE_ON= HAVE_X_GRAPHICS # always enable graphics because w/out it a lot of unrelated files aren't installed due to bugs in the project +CMAKE_ON+= Boost_NO_BOOST_CMAKE \ DAKOTA_GIT_checkout #CMAKE_ON+= HAVE_C3 # causes "duplicate include" error #CMAKE_ON+= DAKOTA_DL_SOLVER # fails to compile: error: declaration of anonymous class must be a definition #CMAKE_ON+= HAVE_NOWPAC # installs files into $PORTSDIR -CMAKE_ON+= HAVE_DREAM HAVE_ADAPTIVE_SAMPLING HAVE_OPTPP DAKOTA_HOPS HAVE_ACRO \ - HAVE_JEGA HAVE_NOMAD HAVE_NPSOL HAVE_NL2SOL HAVE_DOT HAVE_SURFPACK \ - HAVE_CONMIN HAVE_DDACE HAVE_FSUDACE HAVE_PSUADE HAVE_ROL HAVE_DEMO_TPL # enable some methods that aren't enabled by default, see the list @ src/DakotaIterator.cpp +CMAKE_ON+= HAVE_QUESO \ + HAVE_MUQ MUQ_USE_PYTHON \ + # enable some methods that aren't enabled by default, see the list @ src/DakotaIterator.cpp +CMAKE_ON+= DAKOTA_HAVE_GSL DAKOTA_HAVE_HDF5 CMAKE_OFF= DAKOTA_ENABLE_TESTS -CMAKE_ARGS= -DDakota_VERSION_SRC:STRING=${DISTVERSION} -DDakota_GIT_REVL:STRING=${GIT_HASH} -DDakota_RELEASE_DATE:${STRING}=20201116 +CMAKE_ARGS= -DDakota_VERSION_SRC:STRING=${DISTVERSION} -DDakota_GIT_REVL:STRING=unknown -DDakota_RELEASE_DATE:${STRING}=20211115 \ + -DPython_EXECUTABLE=${PYTHON_CMD} \ + -DMUQ_STANMATH_DIR=${WRKSRC}/stanmath FFLAGS+= -fallow-argument-mismatch LDFLAGS+= -lexecinfo @@ -43,59 +57,22 @@ LDFLAGS+= -lexecinfo CONFLICTS_BUILD= dakota # self: picks up some bundled packages from the pre-installed dakota package and then fails to install them CONFLICTS_INSTALL= openblas -USES_GIT= no -GIT_URL= https://software.sandia.gov/git/dakota -GIT_HASH= 82fd55ea1c6bb6d32e4c68e7f92d991d658ba90a - -.if ${USES_GIT} == "yes" -FETCH_DEPENDS= git:devel/git -do-fetch: - @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ - ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ - cd ${DISTDIR}/${DIST_SUBDIR} && \ - git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && \ - git checkout devel && \ - git submodule init packages/external && \ - git submodule init packages/pecos && \ - git submodule init packages/surfpack && \ - git submodule update) && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${GIT_HASH} && ${RM} -r .git) && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=bsdtar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ - ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ - fi -.else -DISTNAME= ${PORTNAME}-${DISTVERSION}-release-public.src-UI -.endif - -OPTIONS_DEFINE= GSL GUI HDF5 -OPTIONS_DEFAULT= GSL HDF5 -OPTIONS_SUB= yes - -GSL_DESC= GSL support -GSL_CMAKE_BOOL= DAKOTA_HAVE_GSL HAVE_QUESO HAVE_QUESO_GPMSA # QUESO requires GSL -GSL_LIB_DEPENDS= libgsl.so:math/gsl - -HDF5_CMAKE_BOOL= DAKOTA_HAVE_HDF5 \ - HAVE_MUQ # MUQ module requires HDF5 -HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip - -GUI_DESC= Build the Dakota/Motif Graphics package -GUI_CMAKE_BOOL= HAVE_X_GRAPHICS -GUI_BROKEN= error: non-void function 'SciPlotListReturnPtr' should return a value - post-extract: @${FIND} ${WRKSRC} -name "*.orig" -delete @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target +pre-configure: # MUQ_STANMATH_DIR is lost otherwise + @${REINPLACE_CMD} 's|find_package(PkgConfig)|set(MUQ_STANMATH_DIR ${WRKSRC}/stanmath)|' ${WRKSRC}/packages/external/muq2/cmake/finds/FindSTANMATH.cmake + post-install: # remove eigen3 that Dakota installs cd ${STAGEDIR}${PREFIX} && ${RM} -r include/eigen3 share/eigen3 + # remove cblas.h that Dakota installs + ${RM} ${STAGEDIR}${PREFIX}/include/cblas.h + # remove *.orig files + ${RM} ${STAGEDIR}${PREFIX}/include/colin/AppResponse.h.orig # install libraries that it fails to install -.for l in libmuqUtilities.so libmuqModeling.so libmuqSamplingAlgorithms.so +.for l in libmuqSamplingAlgorithms.so libmuqApproximation.so libmuqInference.so libmuqModeling.so libmuqOptimization.so libmuqUtilities.so ${INSTALL_LIB} ${BUILD_WRKSRC}/packages/external/muq2/lib/${l} ${STAGEDIR}${PREFIX}/lib .endfor diff --git a/science/dakota/distinfo b/science/dakota/distinfo index 5c0a35cf6356..49d3033add70 100644 --- a/science/dakota/distinfo +++ b/science/dakota/distinfo @@ -1,3 +1,5 @@ -TIMESTAMP = 1613774738 -SHA256 (dakota-6.13.0-release-public.src-UI.tar.gz) = 064f6e49569893cfcbe53a86b089fa3502b8b5f3c52f0122b88f93704464b9e7 -SIZE (dakota-6.13.0-release-public.src-UI.tar.gz) = 139642138 +TIMESTAMP = 1643858651 +SHA256 (dakota-6.15.0-public-src-cli.tar.gz) = b6d971b7d6fe913aa64fef29cf8fcf55d0e5339f9f55fb164e3cc38716b48f61 +SIZE (dakota-6.15.0-public-src-cli.tar.gz) = 125618819 +SHA256 (stan-dev-math-v2.18.0_GH0.tar.gz) = 53fbce2b28aea76695af7a91f51fdd356367153fc42b3573e2b91e6586eca91d +SIZE (stan-dev-math-v2.18.0_GH0.tar.gz) = 17528084 diff --git a/science/dakota/files/patch-CMakeLists.txt b/science/dakota/files/patch-CMakeLists.txt index 0638caf8d869..866abe14d720 100644 --- a/science/dakota/files/patch-CMakeLists.txt +++ b/science/dakota/files/patch-CMakeLists.txt @@ -1,17 +1,20 @@ ---- CMakeLists.txt.orig 1970-01-01 00:00:00 UTC +--- CMakeLists.txt.orig 2021-11-05 17:27:37 UTC +++ CMakeLists.txt -@@ -253,7 +253,9 @@ if(ENABLE_DAKOTA_DOCS) - add_subdirectory(docs) +@@ -258,9 +258,11 @@ if(ENABLE_DAKOTA_DOCS) endif() + # Legacy examples -add_subdirectory(examples) +if (FREEBSD_ENABLE_EXAMPLES) + add_subdirectory(examples) +endif() + # New examples library, taking care to guard against empty directory +-if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dakota-examples/CMakeLists.txt") ++if(FREEBSD_ENABLE_EXAMPLES AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dakota-examples/CMakeLists.txt") + add_subdirectory(dakota-examples) + endif() - add_subdirectory(interfaces) - -@@ -275,19 +277,23 @@ install(FILES INSTALL LICENSE COPYRIGHT README +@@ -284,19 +286,23 @@ install(FILES INSTALL LICENSE COPYRIGHT README DESTINATION ${DAKOTA_TOPFILES_INSTALL} ) @@ -33,5 +36,5 @@ ) +endif() - # Final CPack settings (depends on DAKOTA_GIT_checkout) + # Final CPack settings dakota_cpack_finalize() diff --git a/science/dakota/files/patch-cmake_DakotaVersionUtils.cmake b/science/dakota/files/patch-cmake_DakotaVersionUtils.cmake deleted file mode 100644 index 247002af29ac..000000000000 --- a/science/dakota/files/patch-cmake_DakotaVersionUtils.cmake +++ /dev/null @@ -1,11 +0,0 @@ ---- cmake/DakotaVersionUtils.cmake.orig 2021-02-10 05:46:56 UTC -+++ cmake/DakotaVersionUtils.cmake -@@ -28,7 +28,7 @@ macro(dakota_version_from_git) - - # Building in a Git repo or a source package? - set(DAKOTA_VERSION_file_path) -- set(DAKOTA_GIT_checkout FALSE) -+ set(DAKOTA_GIT_checkout TRUE) - - if(EXISTS ${Dakota_SOURCE_DIR}/.git) - diff --git a/science/dakota/files/patch-packages_external_acro_packages_colin_src_colin_AppResponse.h b/science/dakota/files/patch-packages_external_acro_packages_colin_src_colin_AppResponse.h deleted file mode 100644 index 4038b507d719..000000000000 --- a/science/dakota/files/patch-packages_external_acro_packages_colin_src_colin_AppResponse.h +++ /dev/null @@ -1,17 +0,0 @@ -- patch provided by the upstream - ---- packages/external/acro/packages/colin/src/colin/AppResponse.h.orig 2021-02-17 01:12:03 UTC -+++ packages/external/acro/packages/colin/src/colin/AppResponse.h -@@ -54,10 +54,10 @@ class AppResponse - public: // typedefs - - /// -- typedef std::pair response_pair_t; -+ typedef std::pair response_pair_t; - - /// -- typedef std::map response_map_t; -+ typedef std::map response_map_t; - - public: // construct / destruct / copy / compare methods - diff --git a/science/dakota/files/patch-packages_external_sciplot_SciPlot.c b/science/dakota/files/patch-packages_external_sciplot_SciPlot.c new file mode 100644 index 000000000000..01edfb116b20 --- /dev/null +++ b/science/dakota/files/patch-packages_external_sciplot_SciPlot.c @@ -0,0 +1,22 @@ +- reported to the ML on 2022-02-01 + +--- packages/external/sciplot/SciPlot.c.orig 2022-02-01 09:03:55 UTC ++++ packages/external/sciplot/SciPlot.c +@@ -3761,7 +3761,7 @@ realpair* SciPlotListReturnPtr (Widget wi, int idnum, + SciPlotList *p; + SciPlotWidget w; + if (!XtIsSciPlot(wi)) +- return; ++ return NULL; + w = (SciPlotWidget) wi; + + p = _ListFind(w, idnum); +@@ -3792,7 +3792,7 @@ Boolean SciPlotQuickUpdateCheck (Widget wi) + { + SciPlotWidget w; + if (!XtIsSciPlot(wi)) +- return; ++ return NULL; + w = (SciPlotWidget) wi; + + return CheckMinMax(w); diff --git a/science/dakota/files/patch-src_ProcessHandleApplicInterface.cpp b/science/dakota/files/patch-src_ProcessHandleApplicInterface.cpp deleted file mode 100644 index 770ca1196c85..000000000000 --- a/science/dakota/files/patch-src_ProcessHandleApplicInterface.cpp +++ /dev/null @@ -1,14 +0,0 @@ -- patch provided by the upstream - ---- src/ProcessHandleApplicInterface.cpp.orig 2021-02-17 01:12:32 UTC -+++ src/ProcessHandleApplicInterface.cpp -@@ -17,6 +17,9 @@ - #include "ParallelLibrary.hpp" - #include "WorkdirHelper.hpp" - #include -+#ifdef HAVE_SYS_WAIT_H -+#include // for wait process status macros (Posix only) -+#endif - - namespace Dakota { - diff --git a/science/dakota/pkg-plist b/science/dakota/pkg-plist index fb3eee8fa829..4d51517d9768 100644 --- a/science/dakota/pkg-plist +++ b/science/dakota/pkg-plist @@ -1,5 +1,6 @@ bin/coliny bin/dakota +bin/dakota-ui.sh bin/dakota.input.nspec bin/dakota.input.summary bin/dakota.sh @@ -11,6 +12,7 @@ bin/dakota_restart_util bin/dprepro bin/dprepro.perl bin/dprepro.py +bin/dprepro3 bin/fsu_cvt_standalone bin/fsu_halton_standalone bin/fsu_hammersley_standalone @@ -26,6 +28,7 @@ bin/timer include/3po/cobyla.h include/APPSEvalMgr.hpp include/APPSOptimizer.hpp +include/ActiveKey.hpp include/ActiveSubspaceModel.hpp include/AdaptedBasisModel.hpp include/AlgorithmConfig.hpp @@ -288,6 +291,8 @@ include/GeneticAlgorithmPostProcessor.hpp.inl include/GeneticAlgorithmSelector.hpp include/GeneticAlgorithmSelector.hpp.inl include/GeometricRandomVariable.hpp +include/Graph2D.hpp +include/Graphics.hpp include/GridApplicInterface.hpp include/GumbelRandomVariable.hpp include/HDF5_IO.hpp @@ -507,13 +512,16 @@ include/NegBinomialRandomVariable.hpp include/NestedModel.hpp include/NodalInterpPolyApproximation.hpp include/NomadOptimizer.hpp +include/NonDACVSampling.hpp include/NonDAdaptImpSampling.hpp include/NonDAdaptiveSampling.hpp include/NonDBayesCalibration.hpp include/NonDC3FunctionTrain.hpp include/NonDCalibration.hpp +include/NonDControlVariateSampling.hpp include/NonDCubature.hpp include/NonDDREAMBayesCalibration.hpp +include/NonDEnsembleSampling.hpp include/NonDExpansion.hpp include/NonDGPImpSampling.hpp include/NonDGPMSABayesCalibration.hpp @@ -521,6 +529,7 @@ include/NonDGlobalEvidence.hpp include/NonDGlobalInterval.hpp include/NonDGlobalReliability.hpp include/NonDGlobalSingleInterval.hpp +include/NonDHierarchSampling.hpp include/NonDIntegration.hpp include/NonDInterval.hpp include/NonDLHSEvidence.hpp @@ -532,10 +541,13 @@ include/NonDLocalInterval.hpp include/NonDLocalReliability.hpp include/NonDLocalSingleInterval.hpp include/NonDMUQBayesCalibration.hpp +include/NonDMultifidelitySampling.hpp +include/NonDMultilevControlVarSampling.hpp include/NonDMultilevelFunctionTrain.hpp include/NonDMultilevelPolynomialChaos.hpp include/NonDMultilevelSampling.hpp include/NonDMultilevelStochCollocation.hpp +include/NonDNonHierarchSampling.hpp include/NonDPOFDarts.hpp include/NonDPolynomialChaos.hpp include/NonDQUESOBayesCalibration.hpp @@ -549,6 +561,7 @@ include/NonDSurrogateExpansion.hpp include/NonDWASABIBayesCalibration.hpp include/NonDuplicatingRouletteWheelSelector.hpp include/NonDuplicatingRouletteWheelSelector.hpp.inl +include/NonHierarchSurrModel.hpp include/NonLinearConstraint.h include/NonLinearConstraintNature.hpp include/NonLinearConstraintNature.hpp.inl @@ -660,6 +673,7 @@ include/ProcessHandleApplicInterface.hpp include/ProgramOptions.hpp include/ProjectOrthogPolyApproximation.hpp include/PseudoRandomTestsOnly.h +include/Pybind11Interface.hpp include/PythonInterface.hpp include/QMEApproximation.hpp include/QUESOImpl.hpp @@ -1157,6 +1171,7 @@ include/SurrBasedMinimizer.hpp include/SurrogateData.hpp include/SurrogateModel.hpp include/SurrogatesBase.hpp +include/SurrogatesGPKernels.hpp include/SurrogatesGPObjective.hpp include/SurrogatesGaussianProcess.hpp include/SurrogatesPolynomialRegression.hpp @@ -1462,7 +1477,6 @@ include/bayes_calibration_utils.hpp include/bit_mask.hpp include/bit_mask.hpp.inl include/cb_level_log_gateway.hpp -include/cblas.h include/cdflib.h include/colin/AmplApplication.h include/colin/AmplDriver.h @@ -1471,7 +1485,6 @@ include/colin/AnalysisCodeApplication.h include/colin/AppRequest.h include/colin/AppRequest_Impl.h include/colin/AppResponse.h -include/colin/AppResponse.h.orig include/colin/AppResponseAnalysis.h include/colin/AppResponseInfo.h include/colin/AppResponseLValues.h @@ -1639,6 +1652,7 @@ include/log_gateways.hpp include/logs.hpp include/macros.hpp include/math_tools.hpp +include/menu.h include/minimal_levels.hpp include/mutex.hpp include/mutex.hpp.inl @@ -1651,6 +1665,7 @@ include/nidr.h include/null_log.hpp include/numeric_limits.hpp include/oa.h +include/optpp_blas_wrap.h include/orthogonal_matching_pursuit.hpp include/ostream_entry.hpp include/ostream_log.hpp @@ -2493,12 +2508,12 @@ lib/libcolin.so lib/libconmin.so lib/libcport.so lib/libdakota_dll_api.so +lib/libdakota_sciplot.so lib/libdakota_src.so lib/libdakota_src_fortran.so lib/libdakota_surrogates.so lib/libdakota_util.so lib/libddace.so -lib/libdemo_tpl.so lib/libdfftpack.so lib/libdream.so lib/libeutils.so @@ -2511,9 +2526,12 @@ lib/liblhs.so lib/liblhs_mod.so lib/liblhs_mods.so lib/libmoga.so -lib/libmuqUtilities.so +lib/libmuqApproximation.so +lib/libmuqInference.so lib/libmuqModeling.so +lib/libmuqOptimization.so lib/libmuqSamplingAlgorithms.so +lib/libmuqUtilities.so lib/libncsuopt.so lib/libnidr.so lib/libnomad.so @@ -2522,7 +2540,7 @@ lib/libpebbl.so lib/libpecos_src.so lib/libpecos_util.so lib/libpsuade.so -%%GSL%%lib/libqueso.so +lib/libqueso.so lib/librol.so lib/librol.so.13 lib/librol.so.13.0