[molds] #36532: installation on Mac el capitan failed (Molds-dev) - MolDS

#36532: installation on Mac el capitan failed

  Open Date: 2016-08-10 13:45
Last Update: 2016-08-24 01:27

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    https://osdn.jp/ticket/browse.php?group_id=6231&tid=36532
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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,

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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
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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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[Molds-dev] [molds] #36532: installation on Mac el capitan failed