add science/libgeodecomp - auto-parallelizing library for computer simulations

LibGeoDecomp (Library for Geometric Decomposition codes) is an
auto-parallelizing library for computer simulations. It is specifically targeted
computational science applications in the context of supercomputers and
heterogeneous systems. The library eases development of such tightly coupled
codes by essentially taking over the parallel programming: it handles both, the
parallelization itself and parameter tuning. This enables scientists to focus on
their simulation code, rather than the technical details of the parallel
computer.

PR:		213688
Submitted by:	Kurt Kanzenbach <kurt@kmk-computers.de>
Reviewed by:	matthew
Approved by:	matthew (mentor)
Differential Revision:	https://reviews.freebsd.org/D9390

7 files changed, 279 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 9468c16b376e..2c39cbee4948 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -70,6 +70,7 @@
     SUBDIR += lamprop
     SUBDIR += libaec
     SUBDIR += libctl
+    SUBDIR += libgeodecomp
     SUBDIR += libghemical
     SUBDIR += libint
     SUBDIR += libkml
diff --git a/science/libgeodecomp/Makefile b/science/libgeodecomp/Makefile
new file mode 100644
index 000000000000..559bb8b8555e
--- /dev/null
+++ b/science/libgeodecomp/Makefile
@@ -0,0 +1,43 @@
+# Created by: Kurt Kanzenbach <kurt@kmk-computers.de>
+# $FreeBSD$
+
+PORTNAME=		libgeodecomp
+PORTVERSION=		0.4.0
+CATEGORIES=		science devel
+MASTER_SITES=		http://www.libgeodecomp.org/archive/
+
+MAINTAINER=		kurt@kmk-computers.de
+COMMENT=		LibGeoDecomp is an auto-parallelizing library for computer simulations
+
+LICENSE=		BSL
+LICENSE_FILE=		${WRKSRC}/LICENSE
+
+LIB_DEPENDS=		libboost_system.so:devel/boost-libs libboost_date_time.so:devel/boost-libs \
+			libboost_filesystem.so:devel/boost-libs
+
+USES=			cmake:outsource compiler:c++11-lib
+USE_GCC=		yes
+USE_LDCONFIG=		yes
+
+CMAKE_ARGS=		-DWITH_CUDA:BOOL=FALSE -DWITH_VISIT:BOOL=FALSE \
+			-DWITH_HPX:BOOL=FALSE -DWITH_OPENCL:BOOL=FALSE \
+			-DWITH_OPENCV:BOOL=FALSE -DWITH_TYPEMAPS=FALSE
+
+OPTIONS_DEFINE=		MPI QT4 SILO SCOTCH
+OPTIONS_DEFAULT=	MPI QT4 SILO SCOTCH
+
+MPI_LIB_DEPENDS=	libmpich.so:net/mpich2
+MPI_CMAKE_BOOL=		WITH_MPI
+
+QT4_USE=		QT4=corelib,gui,opengl,qmake_build,moc_build,rcc_build,uic_build
+QT4_CMAKE_BOOL=		WITH_QT
+
+SILO_DESC=		Enable Silo dependend output
+SILO_LIB_DEPENDS=	libsiloh5.so:science/silo
+SILO_CMAKE_BOOL=	WITH_SILO
+
+SCOTCH_DESC=		Enable graph partitioning based on Scotch/Scotch-PT
+SCOTCH_BUILD_DEPENDS=	${LOCALBASE}/lib/libscotch.a:cad/scotch
+SCOTCH_CMAKE_BOOL=	WITH_SCOTCH
+
+.include <bsd.port.mk>
diff --git a/science/libgeodecomp/distinfo b/science/libgeodecomp/distinfo
new file mode 100644
index 000000000000..525892f3eea5
--- /dev/null
+++ b/science/libgeodecomp/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1476973737
+SHA256 (libgeodecomp-0.4.0.tar.gz) = f1a4fbc0c04952a148cbe186f36fc9e2307f7b0ecaf6960b56f2135ca3b8fa4e
+SIZE (libgeodecomp-0.4.0.tar.gz) = 1022767
diff --git a/science/libgeodecomp/files/patch-lib_libflatarray_src_aligned__allocator.hpp b/science/libgeodecomp/files/patch-lib_libflatarray_src_aligned__allocator.hpp
new file mode 100644
index 000000000000..2bfd33d2287f
--- /dev/null
+++ b/science/libgeodecomp/files/patch-lib_libflatarray_src_aligned__allocator.hpp
@@ -0,0 +1,16 @@
+--- lib/libflatarray/src/aligned_allocator.hpp.orig	2014-10-28 09:12:48 UTC
++++ lib/libflatarray/src/aligned_allocator.hpp
+@@ -8,13 +8,7 @@
+ #ifndef FLAT_ARRAY_ALIGNED_ALLOCATOR_HPP
+ #define FLAT_ARRAY_ALIGNED_ALLOCATOR_HPP
+ 
+-#ifdef __APPLE__
+ #include <cstddef>
+-#include <stdlib.h>
+-#else
+-#include <malloc.h>
+-#endif
+-
+ #include <memory>
+ 
+ namespace LibFlatArray {
diff --git a/science/libgeodecomp/files/patch-src_CMakeLists.txt b/science/libgeodecomp/files/patch-src_CMakeLists.txt
new file mode 100644
index 000000000000..d6718ef83895
--- /dev/null
+++ b/science/libgeodecomp/files/patch-src_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- src/CMakeLists.txt.orig	2016-10-17 18:06:32 UTC
++++ src/CMakeLists.txt
+@@ -575,7 +575,7 @@ Version: ${PACKAGE_VERSION}
+ Libs: ${INSTALLER_LINK_FLAGS}
+ Cflags: -I${CMAKE_INSTALL_PREFIX}/include ${PKG_CONFIG_INCLUDE_FLAGS}
+ ")
+-install(FILES "${CMAKE_BINARY_DIR}/${PACKAGE_NAME}.pc" DESTINATION "${LIB_DIR}/pkgconfig")
++install(FILES "${CMAKE_BINARY_DIR}/${PACKAGE_NAME}.pc" DESTINATION "libdata/pkgconfig")
+ 
+ set(ConfigPackageLocation lib/cmake/${PACKAGE_NAME})
+ 
diff --git a/science/libgeodecomp/pkg-descr b/science/libgeodecomp/pkg-descr
new file mode 100644
index 000000000000..966abd2dabd9
--- /dev/null
+++ b/science/libgeodecomp/pkg-descr
@@ -0,0 +1,10 @@
+LibGeoDecomp (Library for Geometric Decomposition codes) is an
+auto-parallelizing library for computer simulations. It is specifically targeted
+computational science applications in the context of supercomputers and
+heterogeneous systems. The library eases development of such tightly coupled
+codes by essentially taking over the parallel programming: it handles both, the
+parallelization itself and parameter tuning. This enables scientists to focus on
+their simulation code, rather than the technical details of the parallel
+computer.
+
+WWW: http://www.libgeodecomp.org/
diff --git a/science/libgeodecomp/pkg-plist b/science/libgeodecomp/pkg-plist
new file mode 100644
index 000000000000..f1c2eedad397
--- /dev/null
+++ b/science/libgeodecomp/pkg-plist
@@ -0,0 +1,195 @@
+include/libflatarray/aggregated_member_size.hpp
+include/libflatarray/aligned_allocator.hpp
+include/libflatarray/api_traits.hpp
+include/libflatarray/coord.hpp
+include/libflatarray/cuda_allocator.hpp
+include/libflatarray/detail/dual_callback_helper.hpp
+include/libflatarray/detail/get_set_instance_functor.hpp
+include/libflatarray/detail/load_save_functor.hpp
+include/libflatarray/detail/macros.hpp
+include/libflatarray/detail/offset.hpp
+include/libflatarray/detail/set_byte_size_functor.hpp
+include/libflatarray/detail/short_vec_avx_float_8.hpp
+include/libflatarray/detail/short_vec_qpx_double_4.hpp
+include/libflatarray/detail/short_vec_sse_double_8.hpp
+include/libflatarray/detail/short_vec_sse_float_16.hpp
+include/libflatarray/detail/short_vec_sse_float_8.hpp
+include/libflatarray/detail/sqrt_reference.hpp
+include/libflatarray/flat_array.hpp
+include/libflatarray/macros.hpp
+include/libflatarray/member_ptr_to_offset.hpp
+include/libflatarray/number_of_members.hpp
+include/libflatarray/short_vec.hpp
+include/libflatarray/soa_accessor.hpp
+include/libflatarray/soa_array.hpp
+include/libflatarray/soa_grid.hpp
+include/libflatarray/testbed/benchmark.hpp
+include/libflatarray/testbed/cpu_benchmark.hpp
+include/libflatarray/testbed/evaluate.hpp
+include/libflatarray/testbed/gpu_benchmark.hpp
+include/libgeodecomp.h
+include/libgeodecomp/communication/mpilayer.h
+include/libgeodecomp/communication/patchlink.h
+include/libgeodecomp/communication/serialization.h
+include/libgeodecomp/communication/typemaps.h
+include/libgeodecomp/config.h
+include/libgeodecomp/geometry/coord.h
+include/libgeodecomp/geometry/coordbox.h
+include/libgeodecomp/geometry/cudaregion.h
+include/libgeodecomp/geometry/fixedcoord.h
+include/libgeodecomp/geometry/floatcoord.h
+include/libgeodecomp/geometry/partitionmanager.h
+include/libgeodecomp/geometry/partitions/checkerboardingpartition.h
+include/libgeodecomp/geometry/partitions/hilbertpartition.h
+include/libgeodecomp/geometry/partitions/hindexingpartition.h
+include/libgeodecomp/geometry/partitions/partition.h
+include/libgeodecomp/geometry/partitions/ptscotchpartition.h
+include/libgeodecomp/geometry/partitions/recursivebisectionpartition.h
+include/libgeodecomp/geometry/partitions/scotchpartition.h
+include/libgeodecomp/geometry/partitions/spacefillingcurve.h
+include/libgeodecomp/geometry/partitions/stripingpartition.h
+include/libgeodecomp/geometry/partitions/zcurvepartition.h
+include/libgeodecomp/geometry/region.h
+include/libgeodecomp/geometry/regionstreakiterator.h
+include/libgeodecomp/geometry/stencils.h
+include/libgeodecomp/geometry/streak.h
+include/libgeodecomp/geometry/topologies.h
+include/libgeodecomp/geometry/voronoimesher.h
+include/libgeodecomp/io/asciiwriter.h
+include/libgeodecomp/io/bovwriter.h
+include/libgeodecomp/io/collectingwriter.h
+include/libgeodecomp/io/hpxwritercollector.h
+include/libgeodecomp/io/hpxwritersink.h
+include/libgeodecomp/io/hpxwritersinkserver.h
+include/libgeodecomp/io/imagepainter.h
+include/libgeodecomp/io/initializer.h
+include/libgeodecomp/io/ioexception.h
+include/libgeodecomp/io/logger.h
+include/libgeodecomp/io/memorywriter.h
+include/libgeodecomp/io/mockinitializer.h
+include/libgeodecomp/io/mocksteerer.h
+include/libgeodecomp/io/mockwriter.h
+include/libgeodecomp/io/mpiio.h
+include/libgeodecomp/io/mpiioinitializer.h
+include/libgeodecomp/io/mpiiowriter.h
+include/libgeodecomp/io/parallelmemorywriter.h
+include/libgeodecomp/io/parallelmpiiowriter.h
+include/libgeodecomp/io/paralleltestwriter.h
+include/libgeodecomp/io/parallelwriter.h
+include/libgeodecomp/io/plotter.h
+include/libgeodecomp/io/ppmwriter.h
+include/libgeodecomp/io/qtwidgetwriter.h
+include/libgeodecomp/io/remotesteerer.h
+include/libgeodecomp/io/serialbovwriter.h
+include/libgeodecomp/io/silowriter.h
+include/libgeodecomp/io/simplecellplotter.h
+include/libgeodecomp/io/simpleinitializer.h
+include/libgeodecomp/io/steerer.h
+include/libgeodecomp/io/testinitializer.h
+include/libgeodecomp/io/teststeerer.h
+include/libgeodecomp/io/testwriter.h
+include/libgeodecomp/io/tracingwriter.h
+include/libgeodecomp/io/visitwriter.h
+include/libgeodecomp/io/writer.h
+include/libgeodecomp/loadbalancer/biasbalancer.h
+include/libgeodecomp/loadbalancer/loadbalancer.h
+include/libgeodecomp/loadbalancer/mockbalancer.h
+include/libgeodecomp/loadbalancer/noopbalancer.h
+include/libgeodecomp/loadbalancer/oozebalancer.h
+include/libgeodecomp/loadbalancer/randombalancer.h
+include/libgeodecomp/loadbalancer/tracingbalancer.h
+include/libgeodecomp/misc/apitraits.h
+include/libgeodecomp/misc/chronometer.h
+include/libgeodecomp/misc/clonable.h
+include/libgeodecomp/misc/color.h
+include/libgeodecomp/misc/cudautil.h
+include/libgeodecomp/misc/fpscounter.h
+include/libgeodecomp/misc/math.h
+include/libgeodecomp/misc/mpitest.h
+include/libgeodecomp/misc/nonpodtestcell.h
+include/libgeodecomp/misc/optimizer.h
+include/libgeodecomp/misc/palette.h
+include/libgeodecomp/misc/patternoptimizer.h
+include/libgeodecomp/misc/quickpalette.h
+include/libgeodecomp/misc/random.h
+include/libgeodecomp/misc/scopedtimer.h
+include/libgeodecomp/misc/simplexoptimizer.h
+include/libgeodecomp/misc/simulationfactory.h
+include/libgeodecomp/misc/simulationparameters.h
+include/libgeodecomp/misc/stdcontaineroverloads.h
+include/libgeodecomp/misc/stringops.h
+include/libgeodecomp/misc/stringvec.h
+include/libgeodecomp/misc/tempfile.h
+include/libgeodecomp/misc/testcell.h
+include/libgeodecomp/misc/testhelper.h
+include/libgeodecomp/parallelization/cacheblockingsimulator.h
+include/libgeodecomp/parallelization/cudasimulator.h
+include/libgeodecomp/parallelization/distributedsimulator.h
+include/libgeodecomp/parallelization/hiparsimulator.h
+include/libgeodecomp/parallelization/hiparsimulator/commonstepper.h
+include/libgeodecomp/parallelization/hiparsimulator/cudastepper.h
+include/libgeodecomp/parallelization/hiparsimulator/multicorestepper.h
+include/libgeodecomp/parallelization/hiparsimulator/offsethelper.h
+include/libgeodecomp/parallelization/hiparsimulator/openclstepper.h
+include/libgeodecomp/parallelization/hiparsimulator/parallelwriteradapter.h
+include/libgeodecomp/parallelization/hiparsimulator/steereradapter.h
+include/libgeodecomp/parallelization/hiparsimulator/stepper.h
+include/libgeodecomp/parallelization/hiparsimulator/updategroup.h
+include/libgeodecomp/parallelization/hiparsimulator/vanillastepper.h
+include/libgeodecomp/parallelization/hpxsimulator.h
+include/libgeodecomp/parallelization/hpxsimulator/createupdategroups.h
+include/libgeodecomp/parallelization/hpxsimulator/hpxstepper.h
+include/libgeodecomp/parallelization/hpxsimulator/patchlink.h
+include/libgeodecomp/parallelization/hpxsimulator/updategroup.h
+include/libgeodecomp/parallelization/hpxsimulator/updategroupserver.h
+include/libgeodecomp/parallelization/mocksimulator.h
+include/libgeodecomp/parallelization/monolithicsimulator.h
+include/libgeodecomp/parallelization/serialsimulator.h
+include/libgeodecomp/parallelization/simulator.h
+include/libgeodecomp/parallelization/stripingsimulator.h
+include/libgeodecomp/storage/boxcell.h
+include/libgeodecomp/storage/collectioninterface.h
+include/libgeodecomp/storage/containercell.h
+include/libgeodecomp/storage/coordmap.h
+include/libgeodecomp/storage/cudaarray.h
+include/libgeodecomp/storage/cudagrid.h
+include/libgeodecomp/storage/dataaccessor.h
+include/libgeodecomp/storage/defaultfilter.h
+include/libgeodecomp/storage/displacedgrid.h
+include/libgeodecomp/storage/filter.h
+include/libgeodecomp/storage/filterbase.h
+include/libgeodecomp/storage/fixedarray.h
+include/libgeodecomp/storage/fixedneighborhood.h
+include/libgeodecomp/storage/grid.h
+include/libgeodecomp/storage/gridbase.h
+include/libgeodecomp/storage/gridtypeselector.h
+include/libgeodecomp/storage/gridvecconv.h
+include/libgeodecomp/storage/image.h
+include/libgeodecomp/storage/linepointerassembly.h
+include/libgeodecomp/storage/linepointerneighborhood.h
+include/libgeodecomp/storage/linepointerupdatefunctor.h
+include/libgeodecomp/storage/meshlessadapter.h
+include/libgeodecomp/storage/mockpatchaccepter.h
+include/libgeodecomp/storage/multicontainercell.h
+include/libgeodecomp/storage/neighborhoodadapter.h
+include/libgeodecomp/storage/neighborhooditerator.h
+include/libgeodecomp/storage/patchaccepter.h
+include/libgeodecomp/storage/patchbuffer.h
+include/libgeodecomp/storage/patchbufferfixed.h
+include/libgeodecomp/storage/patchprovider.h
+include/libgeodecomp/storage/pointerneighborhood.h
+include/libgeodecomp/storage/selector.h
+include/libgeodecomp/storage/sellcsigmasparsematrixcontainer.h
+include/libgeodecomp/storage/serializationbuffer.h
+include/libgeodecomp/storage/simplefilter.h
+include/libgeodecomp/storage/soagrid.h
+include/libgeodecomp/storage/unstructuredgrid.h
+include/libgeodecomp/storage/updatefunctor.h
+include/libgeodecomp/storage/updatefunctortestbase.h
+include/libgeodecomp/storage/vanillaupdatefunctor.h
+lib/cmake/libgeodecomp/libgeodecomp-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/libgeodecomp/libgeodecomp-targets.cmake
+lib/cmake/libgeodecomp/libgeodecompConfig.cmake
+lib/cmake/libgeodecomp/libgeodecompConfigVersion.cmake
+lib/libgeodecomp.so
+libdata/pkgconfig/libgeodecomp.pc