[CIG-SHORT] problem about installing from source

[Matthew Knepley]

On Fri, May 11, 2012 at 8:56 AM, 翁辉辉 <qfkq7850 at mail.ustc.edu.cn> wrote:

>
> dear developers：
>
>    I try to install pylith from the source ,  I have install all the
> packages pylith needs ,and they all seem installed
> well.I have some unhappy experience from the different python version. I
> have two different version python2.4 and python 2.6, I find I can install
> Numpy only using python2.6 ,but if I install FIAT using python2.6, then  I
> can't import FIAT (the error is "can't import Scientific python package"
> ).So I have to install Numpy


FIAT depends on ScientificPython. You now have to install that too.


> using python2.6 and FIAT using python2.4, then I can import they all,but
> when ./configure pylith source it only can find  module Numpy,it is
> strange.Then I change python2.4 to default python,  in the dir
> $HOME/cig/lib/python2.4/site-packages I use the command "ln -s
> $HOME/cig/lib/python2.6/site-packages/numpy" and remove the DIR
> $HOME/cig/lib/python2.6/site-packages/ from PYTHONPATH ,then it works.
>  when I configure the pylith source
> ./configure --enable-testing --prefix=/Data/DATA_wenghh/cig
> CPPFLAGS="-I/Data/DATA_wenghh/cig/include "
> LDFLAGS="-L/Data/DATA_wenghh/cig/lib" LIBS="" CC=gcc CXX=g++ GC=gfortran
> F77=gfortran CFLAGS="-g -O" CXXFLAGS="-g -O"
>
> the config.log have some error about "confdefs.h" and a warning as follows:
> configure:16803: WARNING: parallel HDF5 library not found; DO NOT attempt
> to use HDF5 in parallel OR configure HDF5 with '--enable-parallel'
>
>  and it create Makefile. when I make it,it compiles normally untill it
> have error as follows （partial make.log）:
>

You have to send the full log. Without it, we do not know what happened.

    Matt


> /bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.
> -I../.. -I../../libsrc -I/Data/DATA_wenghh/petsc-dev/include
> -I/Data/DATA_wenghh/petsc-dev/arch-linux2-cxx-debug/include
> -I/Data/DATA_wenghh/petsc-dev/include/sieve -I/usr/local/include
> -I/Data/DATA_wenghh/cig/lib/python2.4/site-packages/pythia-0.8.1.14-py2.4.egg
> -I/usr/local/include/python2.6  -DENABLE_HDF5
> -I/Data/DATA_wenghh/cig/include   -g -O -MT Formulation.lo -MD -MP -MF
> .deps/Formulation.Tpo -c -o Formulation.lo `test -f
> 'problems/Formulation.cc' || echo './'`problems/Formulation.cc
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -I../../libsrc
> -I/Data/DATA_wenghh/petsc-dev/include
> -I/Data/DATA_wenghh/petsc-dev/arch-linux2-cxx-debug/include
> -I/Data/DATA_wenghh/petsc-dev/include/sieve -I/usr/local/include
> -I/Data/DATA_wenghh/cig/lib/python2.4/site-packages/pythia-0.8.1.14-py2.4.egg
> -I/usr/local/include/python2.6 -DENABLE_HDF5
> -I/Data/DATA_wenghh/cig/include -g -O -MT Formulation.lo -MD -MP -MF
> .deps/Formulation.Tpo -c problems/Formulation.cc  -fPIC -DPIC -o
> .libs/Formulation.o
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type, field_type>::open(const
> mesh_type&, int, const char*, int)?.
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:219: error: there are no
> arguments to ?.etscViewerHDF5GetFileId?.that depend on a template
> parameter, so a declaration of ?.etscViewerHDF5GetFileId?.must be available
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:219: error: (if you use
> ?.fpermissive?. G++ will accept your code, but allowing the use of an
> undeclared name is deprecated)
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type,
> field_type>::writeVertexField(double, field_type&, const mesh_type&)?.
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:343: error: there are no
> arguments to ?.etscViewerHDF5GetFileId?.that depend on a template
> parameter, so a declaration of ?.etscViewerHDF5GetFileId?.must be available
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type,
> field_type>::writeCellField(double, field_type&, const char*, int)?.
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:434: error: there are no
> arguments to ?.etscViewerHDF5GetFileId?.that depend on a template
> parameter, so a declaration of ?.etscViewerHDF5GetFileId?.must be available
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type, field_type>::open(const
> mesh_type&, int, const char*, int) [with mesh_type =
> pylith::topology::Mesh, field_type =
> pylith::topology::Field<pylith::topology::Mesh, ALE::IGeneralSection<int,
> double, ALE::malloc_allocator<double> > >]?.
> problems/Formulation.cc:446:   instantiated from here
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:219: error:
> ?.etscViewerHDF5GetFileId?.was not declared in this scope
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type,
> field_type>::writeVertexField(double, field_type&, const mesh_type&) [with
> mesh_type = pylith::topology::Mesh, field_type =
> pylith::topology::Field<pylith::topology::Mesh, ALE::IGeneralSection<int,
> double, ALE::malloc_allocator<double> > >]?.
> problems/Formulation.cc:451:   instantiated from here
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:343: error:
> ?.etscViewerHDF5GetFileId?.was not declared in this scope
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc: In member function ?.oid
> pylith::meshio::DataWriterHDF5<mesh_type,
> field_type>::writeCellField(double, field_type&, const char*, int) [with
> mesh_type = pylith::topology::Mesh, field_type =
> pylith::topology::Field<pylith::topology::Mesh, ALE::IGeneralSection<int,
> double, ALE::malloc_allocator<double> > >]?.
> problems/Formulation.cc:471:   instantiated from here
> ../../libsrc/pylith/meshio/DataWriterHDF5.cc:434: error:
> ?.etscViewerHDF5GetFileId?.was not declared in this scope
> make[4]: *** [Formulation.lo] Error 1
> make[4]: Leaving directory `/Data/DATA_wenghh/pylith-1.6.3/libsrc/pylith'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/Data/DATA_wenghh/pylith-1.6.3/libsrc/pylith'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/Data/DATA_wenghh/pylith-1.6.3/libsrc'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/Data/DATA_wenghh/pylith-1.6.3'
> make: *** [all] Error 2
>
> it seem is something about HDF5 .I use centOS 5 ,and  I can find the
> libary in /usr/lib64 but cannot find header file,then I  install it by
> myself ,but it still can not work . any suggestion shall be appreciated.
>
> Thanks
> huihui weng
>
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>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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