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2016年 8月 23日 (火) 13:49:12 JST
#36532: installation on Mac el capitan failed
Open Date: 2016-08-10 13:45
Last Update: 2016-08-23 13:49
URL for this Ticket:
https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532
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Last Changes/Comment on this Ticket:
2016-08-23 13:49 Updated by: guillaumegodin
Comment:
I made those steps. I will try new clang-llvm-3.8 look like it can work too!
% all libs must used the gcc-5!
brew install gcc-5
export HOMEBREW_CC=gcc-5
export HOMEBREW_CXX=g++-5
brew reinstall openmpi --build-from-source
brew reinstall openblas --build-from-source
then install boost_1_60 using this guideline for installation: http://qiita.com/misho/items/0c0b3ca25bb8f62aa681
tar xvf boost_1_60_0.tar.bz2
cd boost_1_60_0
sublime tools/build/src/tools/darwin.jam?
=> tools/build/src/tools/darwin.jam line 582 et pas 579
--- tools/build/src/tools/darwin.jam
+++ tools/build/src/tools/darwin.jam
@@ -579,7 +579,7 @@
actions link.dll bind LIBRARIES
{
- "$(CONFIG_COMMAND)" -dynamiclib -Wl,-single_module -install_name "$(<:B)$(<:S)" -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(FRAMEWORK_PATH) -framework$(_)$(FRAMEWORK:D=:S=) $(OPTIONS) $(USER_OPTIONS)
+ "$(CONFIG_COMMAND)" -dynamiclib -Wl,-single_module -install_name "/usr/local/gcc/lib/$(<:B)$(<:S)" -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(FRAMEWORK_PATH) -framework$(_)$(FRAMEWORK:D=:S=) $(OPTIONS) $(USER_OPTIONS)
}
./bootstrap.sh --with-libraries=all --prefix=/usr/local/gcc
sublime project-config.jam
-if ! darwin in [ feature.values <toolset> ]
-{
- using darwin ;
-}
+using darwin : 5.4 : g++-5 ;
sublime ~/user_config.jam
adding a line with "using mpi ;" without quotes
./b2
./b2 install
Makefile for molds is:
"""""""""""""""
CC = mpic++
CFLAGS = -m64 -O0
override CFLAGS += -fopenmp
BOOST_TOP_DIR = /usr/local/gcc
BOOST_INC_DIR = $(BOOST_TOP_DIR)/include/
BOOST_LIB_DIR = $(BOOST_TOP_DIR)/lib/
BOOST_LIBS = -lboost_serialization -lboost_mpi -lboost_thread -lboost_system
OPENBLAS_TOP_DIR = /usr/local/opt/openblas
OPENBLAS_INC_DIR = $(OPENBLAS_TOP_DIR)/include/
OPENBLAS_LIB_DIR = $(OPENBLAS_TOP_DIR)/lib/
OPENBLAS_LIBS = -lopenblas
LIBSBASE = -lpthread -lgomp
LIBS = $(LIBSBASE) $(BOOST_LIBS) $(OPENBLAS_LIBS)
EXENAME = molds
DEPFILE = obj/objfile.dep
LDFLAGS = -Wl,-rpath,$(BOOST_LIB_DIR) -Wl,-rpath,$(OPENBLAS_LIB_DIR)
THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
ALL_CPP_FILES = ....
ALL_OBJ_FILES = ....
$(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
$(CC) -o $@ $(LDFLAGS) $(ALL_OBJ_FILES) -L$(BOOST_LIB_DIR) -L$(OPENBLAS_LIB_DIR) $(LIBS)
""""""""""""""
make clean
make -j8
./molds ../test/c2h6_am1.in
Another question related to development: can you tell me if I can add Br & I atoms for AM1 and can we also implement RM1 ?
Another question related to geometry: How you know the bonds between atoms in the geometry definition ? I would like to generate input files from/similar to mopac .in.
BR
Guillaume (https://github.com/thegodone)
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Ticket Status:
Reporter: guillaumegodin
Owner: (Aucun)
Type: Support Requests
Status: Atteints
Priority: 5 - Medium
MileStone: (Aucun)
Component: (Aucun)
Severity: 5 - Medium
Resolution: Aucun
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Ticket details:
I try to compile using g++4.9 + precompile boost 155 or boost 1.6 with mpi option. All is fine until the last ld linkage where the boost:achive failed in your MolDSException.
Here the log result same error on trunk or 0.3.1 version:
mpic++ -o molds -Wl,-rpath,/usr/local/opt/boost//lib/ obj/Enums.o obj/PrintController.o obj/MolDSException.o obj/MallocerFreer.o obj/MpiProcess.o obj/AsyncCommunicator.o obj/Blas.o obj/Lapack.o obj/Utilities.o obj/MathUtilities.o obj/EularAngle.o obj/Parameters.o obj/Atom.o obj/Hatom.o obj/Liatom.o obj/Catom.o obj/Natom.o obj/Oatom.o obj/Satom.o obj/EnvironmentalPointCharge.o obj/AtomFactory.o obj/Molecule.o obj/InputParser.o obj/GTOExpansionSTO.o obj/RealSphericalHarmonicsIndex.o obj/MOLogger.o obj/DensityLogger.o obj/HoleDensityLogger.o obj/ParticleDensityLogger.o obj/Cndo2.o obj/Indo.o obj/ZindoS.o obj/Mndo.o obj/Am1.o obj/Am1D.o obj/Pm3.o obj/Pm3D.o o
bj/Pm3Pddg.o obj/ElectronicStructureFactory.o obj/MD.o obj/MC.o obj/RPMD.o obj/NASCO.o obj/Optimizer.o obj/ConjugateGradient.o obj/SteepestDescent.o obj/BFGS.o obj/GEDIIS.o obj/OptimizerFactory.o obj/MolDS.o obj/Main.o -L/usr/local/opt/boost//lib/ -L/usr/local/opt/openblas//lib/ -lpthread -lgomp -lboost_serialization-mt -lboost_mpi-mt -lboost_thread-mt -lboost_system-mt -lopenblas
Undefined symbols for architecture x86_64:
"boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)", referenced from:
void boost::serialization::load_construct_data<boost::archive::text_iarchive>(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o
"boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::text_iarchive_impl(std::basic_istream<char, std::char_traits<char> >&, unsigned int)", referenced from:
MolDS_base::MolDSException::Deserialize(std::basic_istream<char, std::char_traits<char> >&) in MolDSException.o
"boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
boost::archive::detail::common_oarchive<boost::archive::text_oarchive>::vsave(boost::archive::class_name_type const&) in MolDSException.o
boost::archive::detail::pointer_oserializer<boost::archive::text_oarchive, MolDS_base::MolDSException>::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o
"boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::text_oarchive_impl(std::basic_ostream<char, std::char_traits<char> >&, unsigned int)", referenced from:
MolDS_base::MolDSException::Serialize(std::basic_ostream<char, std::char_traits<char> >&) in MolDSException.o
"boost::archive::basic_text_iprimitive<std::basic_istream<char, std::char_traits<char> > >::~basic_text_iprimitive()", referenced from:
MolDS_base::MolDSException::Deserialize(std::basic_istream<char, std::char_traits<char> >&) in MolDSException.o
boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::~text_iarchive_impl() in MolDSException.o
boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::~text_iarchive_impl() in MolDSException.o
boost::archive::text_iarchive::~text_iarchive() in MolDSException.o
boost::archive::text_iarchive::~text_iarchive() in MolDSException.o
boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::~text_iarchive_impl() in MolDSException.o
"boost::archive::basic_text_oprimitive<std::basic_ostream<char, std::char_traits<char> > >::~basic_text_oprimitive()", referenced from:
MolDS_base::MolDSException::Serialize(std::basic_ostream<char, std::char_traits<char> >&) in MolDSException.o
boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::~text_oarchive_impl() in MolDSException.o
boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::~text_oarchive_impl() in MolDSException.o
boost::archive::text_oarchive::~text_oarchive() in MolDSException.o
boost::archive::text_oarchive::~text_oarchive() in MolDSException.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
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Ticket information of MolDS project
MolDS Project is hosted on OSDN
Project URL: https://osdn.jp/projects/molds
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https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532
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