New port: science/dakota: Interface between analysis codes & iterative systems analysis methods

svn path=/head/; revision=566127

science/Makefile

@@ -58,6 +58,7 @@
     SUBDIR += cp2k
     SUBDIR += cp2k-data
     SUBDIR += crf++
+    SUBDIR += dakota
     SUBDIR += dalton
     SUBDIR += dcl
     SUBDIR += devisor

science/dakota/Makefile

@@ -0,0 +1,82 @@
+# $FreeBSD$
+
+PORTNAME=	dakota
+DISTVERSION=	6.13.0
+CATEGORIES=	science
+MASTER_SITES=	https://dakota.sandia.gov/sites/default/files/distributions/public/
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Interface between analysis codes & iterative systems analysis methods
+
+LICENSE=	LGPL21
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libblas.so:math/blas \
+		libboost_system.so:devel/boost-libs \
+		liblapack.so:math/lapack
+RUN_DEPENDS=	bash:shells/bash
+
+USES=		cmake compiler:c++11-lang fortran perl5 python shebangfix
+USE_LDCONFIG=	yes
+
+SHEBANG_GLOB=	*.sh *.py
+SHEBANG_FILES=	interfaces/Python/mpitile \
+		scripts/pyprepro/dprepro \
+		scripts/pyprepro/pyprepro \
+		scripts/dprepro.perl \
+		test/dakota_test.perl
+
+CMAKE_ON=	Boost_NO_BOOST_CMAKE \
+		DAKOTA_GIT_checkout
+CMAKE_OFF=	DAKOTA_ENABLE_TESTS
+CMAKE_ARGS=	-DDakota_VERSION_SRC:STRING=${DISTVERSION} -DDakota_GIT_REVL:STRING=${GIT_HASH} -DDakota_RELEASE_DATE:${STRING}=20201116
+
+FFLAGS+=	-fallow-argument-mismatch
+LDFLAGS+=	-lexecinfo
+
+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
+
+post-extract:
+	@${FIND} ${WRKSRC} -name "*.orig" -delete
+	@${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target
+
+post-install:
+	# remove eigen3 that Dakota installs
+	cd ${STAGEDIR}${PREFIX} && ${RM} -r include/eigen3 share/eigen3
+
+do-test: # from Additional Test Suites @ https://dakota.sandia.gov/content/additional-test-suites (many tests are known to fail)
+	# minimal set of fast-running tests that should NOT FAIL (may DIFF, depending on platform / compiler)
+	cd ${WRKSRC}/test && ./dakota_test.perl
+	# test suite that should PASS on any supported platform (NO DIFF or FAIL)
+	cd ${WRKSRC}/test && ./dakota_test.perl --label-regex=AcceptanceTest
+	# run all Dakota tests active in this build (should PASS or DIFF)
+	cd ${WRKSRC}/test && ./dakota_test.perl --label-regex=dakota_
+
+.include <bsd.port.mk>

science/dakota/distinfo

@@ -0,0 +1,3 @@
+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

science/dakota/files/patch-CMakeLists.txt

@@ -0,0 +1,37 @@
+--- CMakeLists.txt.orig	1970-01-01 00:00:00 UTC
++++ CMakeLists.txt
+@@ -253,7 +253,9 @@ if(ENABLE_DAKOTA_DOCS)
+   add_subdirectory(docs)
+ endif()
+ 
+-add_subdirectory(examples)
++if (FREEBSD_ENABLE_EXAMPLES)
++  add_subdirectory(examples)
++endif()
+ 
+ add_subdirectory(interfaces)
+ 
+@@ -275,19 +277,23 @@ install(FILES INSTALL LICENSE COPYRIGHT README
+   DESTINATION ${DAKOTA_TOPFILES_INSTALL}
+   )
+ 
++if (FREEBSD_ENABLE_EXAMPLES)
+ install(DIRECTORY examples DESTINATION ${DAKOTA_EXAMPLES_INSTALL}
+   USE_SOURCE_PERMISSIONS
+   PATTERN "CMakeLists.txt" EXCLUDE
+   PATTERN "*.c" EXCLUDE 
+   PATTERN "*.f" EXCLUDE 
+   )
++endif()
+ 
++if (FREEBSD_INSTALL_TESTS)
+ install(DIRECTORY test DESTINATION ${DAKOTA_TEST_INSTALL}
+   PATTERN "CMakeLists.txt" EXCLUDE
+   PATTERN "*.c" EXCLUDE 
+   PATTERN "*.cpp" EXCLUDE 
+   PATTERN "*.f" EXCLUDE 
+   )
++endif()
+ 
+ # Final CPack settings (depends on DAKOTA_GIT_checkout)
+ dakota_cpack_finalize()

science/dakota/files/patch-cmake_DakotaVersionUtils.cmake

@@ -0,0 +1,11 @@
+--- 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)
+ 

science/dakota/files/patch-packages_external_acro_packages_colin_src_colin_AppResponse.h

@@ -0,0 +1,17 @@
+- 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
+ 

science/dakota/files/patch-src_ProcessHandleApplicInterface.cpp

@@ -0,0 +1,14 @@
+- 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 {
+ 

science/dakota/pkg-descr

@@ -0,0 +1,6 @@
+The Dakota project delivers both state-of-the-art research and robust, usable
+software for optimization and UQ. Broadly, the Dakota software's advanced
+parametric analyses enable design exploration, model calibration, risk analysis,
+and quantification of margins and uncertainty with computational models.
+
+WWW: https://dakota.sandia.gov/