From noreply ＠ osdn.jp Wed Aug 10 13:45:47 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Wed, 10 Aug 2016 13:45:47 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1470804347.880208.7890.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-10 13:45 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-10 13:45 Updated by: guillaumegodin * New Ticket "installation on Mac el capitan failed" created --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Open Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Wed Aug 10 15:52:12 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Wed, 10 Aug 2016 15:52:12 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1470811932.164537.8363.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-10 15:52 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-10 15:52 Updated by: mikiya_fujii Comment: Hi guillaumegodin, Did you use the makefile included in the trunk of molds?, i.e., /trunk/src/Makefile or Makefile_GNU. The makefile is needed to be modified to suite your environment. Could you offer your makefile and also commands which you executed at the compilation? BTW, does same error occurred for the latest code in trunk? molds 0.3.1 has a bug related to boost::serialization, c.f., https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=746884 This bug is fixed for the latest code in trunk. Mikiya --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (未割り当て) Type: サポートリクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Wed Aug 10 17:30:30 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Wed, 10 Aug 2016 17:30:30 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1470817830.599274.26146.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-10 17:30 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-10 17:30 Updated by: guillaumegodin Comment: I used the Makefile with few modifications CC = mpic++ CFLAGS = -O0 override CFLAGS += -fopenmp BOOST_TOP_DIR = /usr/local/opt/boost155/ BOOST_INC_DIR = $(BOOST_TOP_DIR)/include/ BOOST_LIB_DIR = $(BOOST_TOP_DIR)/lib/ BOOST_LIBS = -lboost_serialization-mt -lboost_mpi-mt -lboost_thread-mt -lboost_system-mt #BOOST_LIBS += -lboost_atomic-mt -lboost_chrono-mt -lboost_context-mt -lboost_coroutine-mt -lboost_date_time-mt -lboost_exception-mt -lboost_filesystem-mt -lboost_graph-mt -lboost_graph_parallel-mt -lboost_iostreams-mt -lboost_locale-mt -lboost_log-mt -lboost_log_setup-mt -lboost_math_c99-mt -lboost_math_c99l-mt -lboost_math_tr1-mt -lboost_math_tr1f-mt -lboost_prg_exec_monitor-mt -lboost_program_options-mt -lboost_random-mt -lboost_regex-mt -lboost_signals-mt -lboost_test_exec_monitor-mt -lboost_thread-mt -lboost_timer-mt -lboost_unit_test_framework-mt -lboost_wave-mt 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)) .... no change there in ALL_CPP_FILES, ALL_HEAD_FILES & ALL_OBJ_FILES $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES) $(CC) -o $@ $(LDFLAGS) $(ALL_OBJ_FILES) -L$(BOOST_LIB_DIR) -L$(OPENBLAS_LIB_DIR) $(LIBS) -include $(DEPFILE) .PHONY: depend depend: -rm -f $(DEPFILE) +make -f $(THIS_MAKEFILE) $(DEPFILE) $(DEPFILE): $(THIS_MAKEFILE) $(ALL_CPP_FILES) $(ALL_HEAD_FILES) $(CC) -MM $(ALL_CPP_FILES) -I$(BOOST_INC_DIR) -I$(OPENBLAS_INC_DIR) | sed 's/^\([^ ]\)/obj\/\1/g' | sed 's/\($$*\)\.o[ :]*/\1.o : /g' > $(DEPFILE) $(ALL_OBJ_FILES): $(CC) -I$(BOOST_INC_DIR) -I$(OPENBLAS_INC_DIR) -o $@ $< $(CFLAGS) -c .PHONY: clean clean: -rm -f $(ALL_OBJ_FILES) $(EXENAME) $(DEPFILE) all: clean depend $(EXENAME) i look at the boost lib using this command and found something strange nm libboost_serialization-mt.dylib |fgrep text_iarchive |c++filt 000000000000e1d0 T boost::archive::text_iarchive_impl::text_iarchive_impl(std::__1::basic_istream >&, unsigned int) 000000000000e150 T boost::archive::text_iarchive_impl::text_iarchive_impl(std::__1::basic_istream >&, unsigned int) so the std::basic_istream is not reconized. I compile the boost155 using brew & gcc4.9 --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Open Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Mon Aug 22 20:31:01 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Mon, 22 Aug 2016 20:31:01 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1471865461.728570.28937.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-22 20:31 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-22 20:31 Updated by: guillaumegodin * Changed Ticket Close date to 2016-08-22 20:31 * ?tat was updated from Open to Atteints Comment: Using gcc5 and building openblas (brew with gcc), openmpi (brew with gcc) & boost (no brew!) it works. --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Atteints Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Tue Aug 23 00:21:09 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Tue, 23 Aug 2016 00:21:09 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1471879269.155437.28902.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-23 00:21 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-23 00:21 Updated by: mikiya_fujii Comment: Thanks for notifying me the success of the compilation. Was using gcc5 important? Or, Was using same compiler for molds, openblas, and boos important? --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (未割り当て) Type: サポートリクエスト Status: 完了 Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Tue Aug 23 13:49:12 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Tue, 23 Aug 2016 13:49:12 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1471927752.635200.24939.nullmailer@sourceforge.jp> #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 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- 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 ] -{ - 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) --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Atteints Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Wed Aug 24 01:27:49 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Wed, 24 Aug 2016 01:27:49 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1471969669.329209.8704.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-24 01:27 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-24 01:27 Updated by: mikiya_fujii Comment: Thank you for your logging to compile MolDS.[[BR]][[BR]] > Another question related to development: can you tell me if I can add Br & I atoms for AM1[[BR]] Although I have no scheduled plan to implement Br & I atoms and also RM1 now, we (developing team) are welcome to your contribution for them. [[BR]] If you have a will/interest to implement Br & I atoms, the code which have been already implemented for thickets #33721 (Add F (Fluorine)) and #33722 (Add Cl (chlorine)) may help you. [[BR]] The modification for these thickets #33721 and #33722 are summarized in r1667 and r1668, respectively. Of course, I will support you to implement Br & I atoms. [[BR]][[BR]] > and can we also implement RM1 ? [[BR]] Sure. It's very interesting try. (problem is a time to coding....)[[BR]][[BR]] > 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. Unfortunately, the current version of MolDS does not support Z-matrix (bond, angle, and dihedral) of molecular configurations and conversion between the Z-matrix and the Cartesian coordinates which are used in MolDS. Actually, in the electronic structure calculation, information about bonds are not needed. [[BR]][[BR]] As another candidate to convert the Z-matrix which are used in mopac inputs and the Cartesian coordintes (xyz format), OpenBabel is useful: http://openbabel.org/wiki/Babel[[BR]] e.g., (from mopac to MolDS) [[BR]] $ babel -imopin ethanol.in -oxyz ethanol.xyz [[BR]] Then, create an input for MolDS from the ethanol.xyz [[BR]] [[BR]] My bests, --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (未割り当て) Type: サポートリクエスト Status: 完了 Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Mon Aug 29 14:24:04 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Mon, 29 Aug 2016 14:24:04 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1472448244.867571.30056.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-29 14:24 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-29 14:24 Updated by: guillaumegodin Comment: Dear All, I implement the RM1 + adding Br & I atoms for RM1 & AM1 (caution I don't have the book to set some initial variable likke vdw etc...) For the Derivate parameters I used you little script. I tested it on CH3Br_rm1.in & CH3I_rm1.in & CH3Br_am1.in & CH3I_am1.in it works fine not sure about the results but no issues. I made a clone copy of the svn last commit in github there https://github.com/thegodone/molds-branch/commits/master I also set my makefile there. I add a question relative to geometry do you optimized it somewhere in the code, if yes how ? Best regards, Guillaume --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Atteints Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Mon Aug 29 21:16:53 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Mon, 29 Aug 2016 21:16:53 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1472473013.763846.30702.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-29 21:16 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-29 21:16 Updated by: guillaumegodin Comment: Dear, Forget my stupid question on geometry optimization. I found it! Btw, I have not or partial access to your list of the publications in your references (atom.h). So it's hard for me to grab Atom properties for Br/I/P. I've just bougth the Pople book but for the rest, I will try to use the MOPAC data when available. Can you share some publications related to whos Atoms Br/I/P or can you complete the atom defiinitions ? you can use direct contact there: guillaume.godin ＠ gmail.com BR, guillaume --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (Aucun) Type: Support Requests Status: Atteints Priority: 5 - Medium MileStone: (Aucun) Component: (Aucun) Severity: 5 - Medium Resolution: Aucun --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 From noreply ＠ osdn.jp Tue Aug 30 01:25:37 2016 From: noreply ＠ osdn.jp (OSDN Ticket System) Date: Tue, 30 Aug 2016 01:25:37 +0900 Subject: [Molds-dev] [molds] #36532: installation on Mac el capitan failed Message-ID: <1472487937.652617.22041.nullmailer@sourceforge.jp> #36532: installation on Mac el capitan failed Open Date: 2016-08-10 13:45 Last Update: 2016-08-30 01:25 URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532 --------------------------------------------------------------------- Last Changes/Comment on this Ticket: 2016-08-30 01:25 Updated by: mikiya_fujii Comment: Dear Guillaume, [[BR]] [[BR]] Thank you for your implementation ＠ github which I will see and merge to trunk. [[BR]] [[BR]] Mikiya [comment:6231:36532:1472473013 guillaumegodin] への返信 > Dear, > > Forget my stupid question on geometry optimization. I found it! > > Btw, I have not or partial access to your list of the publications in your references (atom.h). > > So it's hard for me to grab Atom properties for Br/I/P. I've just bougth the Pople book but for the rest, I will try to use the MOPAC data when available. > > Can you share some publications related to whos Atoms Br/I/P or can you complete the atom defiinitions ? > > you can use direct contact there: guillaume.godin ＠ gmail.com > > BR, > > guillaume --------------------------------------------------------------------- Ticket Status: Reporter: guillaumegodin Owner: (未割り当て) Type: サポートリクエスト Status: 完了 Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- 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::load(std::basic_string, std::allocator >&)", referenced from: void boost::serialization::load_construct_data(boost::archive::text_iarchive&, MolDS_base::MolDSException*, unsigned int) in MolDSException.o "boost::archive::text_iarchive_impl::text_iarchive_impl(std::basic_istream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o "boost::archive::text_oarchive_impl::save(std::basic_string, std::allocator > const&)", referenced from: boost::archive::detail::common_oarchive::vsave(boost::archive::class_name_type const&) in MolDSException.o boost::archive::detail::pointer_oserializer::save_object_ptr(boost::archive::detail::basic_oarchive&, void const*) const in MolDSException.o "boost::archive::text_oarchive_impl::text_oarchive_impl(std::basic_ostream >&, unsigned int)", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o "boost::archive::basic_text_iprimitive > >::~basic_text_iprimitive()", referenced from: MolDS_base::MolDSException::Deserialize(std::basic_istream >&) in MolDSException.o boost::archive::text_iarchive_impl::~text_iarchive_impl() in MolDSException.o boost::archive::text_iarchive_impl::~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::~text_iarchive_impl() in MolDSException.o "boost::archive::basic_text_oprimitive > >::~basic_text_oprimitive()", referenced from: MolDS_base::MolDSException::Serialize(std::basic_ostream >&) in MolDSException.o boost::archive::text_oarchive_impl::~text_oarchive_impl() in MolDSException.o boost::archive::text_oarchive_impl::~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 -- Ticket information of MolDS project MolDS Project is hosted on OSDN Project URL: https://osdn.jp/projects/molds OSDN: https://osdn.jp URL for this Ticket: https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532 RSS feed for this Ticket: https://osdn.jp/ticket/ticket_rss.php?group_id=6231&tid=36532