[CIG-SHORT] problem about installing from source

[Brad Aagaard]

Huihui Weng,

Are you using the PyLith Installer utility? We strongly recommend that 
anyone attempting to build from source use this utility available on the 
PyLith webpage. It knows about all of the dependencies, builds them with 
the appropriate options, and builds them in the correct order.

If you make use of system installed packages, then there can be problems 
related to mismatches in compilers and options. For example, PyLith 
wants HDF5 built with --enable-parallel with the MPI compilers. Some 
system packages will use a serial version of HDF5 or may use a different 
MPI implementation. The installer utility will, by default, install most 
dependencies to eliminate these issues. Additionally, the installed 
utility can build MPI and Python, if necessary to remedy problems with 
incompatibilities with system packages.

Regards,
Brad


On 05/11/2012 07:46 AM, Matthew Knepley wrote:
> 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
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
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