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science/dakota: Update 6.13.0 -> 6.15.0

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This commit is contained in:
Yuri Victorovich 2022-02-03 00:57:38 -08:00
parent e8c81013fc
commit c5921be582
8 changed files with 91 additions and 111 deletions
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85
science/dakota/Makefile
View file

@ -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

8
science/dakota/distinfo
View file

@ -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

17
science/dakota/files/patch-CMakeLists.txt
View file

@ -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()

11
science/dakota/files/patch-cmake_DakotaVersionUtils.cmake
View file

@ -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)

17
science/dakota/files/patch-packages_external_acro_packages_colin_src_colin_AppResponse.h
View file

@ -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_info_t, const utilib::Any > response_pair_t;
+ typedef std::pair<response_info_t, utilib::Any > response_pair_t;
///
- typedef std::map<response_info_t, const utilib::Any > response_map_t;
+ typedef std::map<response_info_t, utilib::Any > response_map_t;
public: // construct / destruct / copy / compare methods

22
science/dakota/files/patch-packages_external_sciplot_SciPlot.c Normal file
View file

@ -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);

14
science/dakota/files/patch-src_ProcessHandleApplicInterface.cpp
View file

@ -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 <algorithm>
+#ifdef HAVE_SYS_WAIT_H
+#include <sys/wait.h> // for wait process status macros (Posix only)
+#endif
namespace Dakota {

28
science/dakota/pkg-plist
View file

@ -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