[CIG-SHORT] pylith install error

[Brad Aagaard]

Birendra,

On second thought, the easiest remedy to our current incompatibility of 
PyLith 1.9 with the PETSc development version is to create a new 
installer option that allows the user to use the PyLith provided PETSc 
tarball with the spatialdata and pylith versions from the repository.

I updated the installer today and just posted a new version on the 
PyLith webpage. http://www.geodynamics.org/cig/software/pylith

PyLith v1.9.0 is incompatible with the most recent versions of SWIG. The 
installer will use SWIG v2.0.2 which is known to work. You should use 
this same version of SWIG to build your custom modules that you use with 
PyLith.

You will want to use spatialdata and PyLith from the CIG GitHub 
repositories so that you get the files SWIG needs. You also need to 
override the default behavior of using PETSc from the repositories 
(which PyLith comes from the repositories).

Therefore, I recommend using the following arguments when configuring 
the installer in addition to any you might already be using:

--enable-pcre --enable-swig \
--with-pylith-git=v1.9-stable --with-petsc-tarball --disable-git

This last option assumes you already have git installed.

Regards,
Brad


On 09/25/2013 04:18 PM, Brad Aagaard wrote:
> Birendra,
>
> SWIG creates a signature for each object that can depend on the SWIG
> version and which machine you are using.  As a result, you cannot mix
> different SWIG versions nor mix SWIG output from different machines. If
> you customize PyLith with your own modules, then you should be using the
> "development" version by checking the code out from the repository.
>
> This is easiest via the --with-svn configure options for the installer.
> For version 1.9.0 use --with-svn=stable. The repository includes the
> SWIG .i files and the --with-svn option will trigger generation of the
> *wrap.cxx and *.py via SWIG for both spatialdata and PyLith so that
> everything is compatible.
>
> Unfortunately, --with-svn also triggers use of the PETSc git repository
> which has removed Sieve (because PyLith 2.0 replaces Sieve with DMPlex).
> I will ask Matt if he can create a temporary PETSc branch that is frozen
> before Sieve was removed we can use with PyLith 1.9 until 2.0 is ready.
>
> Regards,
> Brad
>
>
> On 09/25/2013 03:29 PM, Birendra jha wrote:
>> Brad,
>>
>> I am getting following error during make. I have swig 2.0.11 in
>> /usr/local/bin. *wrap.cxx and *.py files created by the installer were
>> version 2.0.4. Since I modified a module and its module files are
>> 2.0.11, I regenerated all of them using the new version. Except
>> spatialdata-1.9.2/modulesrc/spatialdb.py and cxx files, because
>> SimpleGridAscii.i and .hh files needed by spatialdb.i are missing from
>> the installer (can I get these files?).
>>
>> /bin/bash ../../libtool --tag=CXX   --mode=compile mpicxx
>> -DHAVE_CONFIG_H -I. -I../../../pylith-1.9.0/modulesrc/topology -I../..
>> -I../../../pylith-1.9.0/libsrc -g
>> -I/home/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg
>> -I/home/bjha/pylith-1.9.0/lib/python2.7/site-packages/numpy/core/include
>> -I/usr/include/python2.7 -I/home/bjha/pylith-1.9.0/include
>> -I/home/bjha/pylith-1.9.0/include
>> -I/home/bjha/pylith-1.9.0/include/sieve
>> -I/home/bjha/pylith-1.9.0/include -I/usr/local/include  -DENABLE_HDF5
>> -DENABLE_CUBIT -I/home/bjha/pylith-1.9.0/include   -g -O2
>> -DMPICH_IGNORE_CXX_SEEK -MT topology_wrap.lo -MD -MP -MF
>> .deps/topology_wrap.Tpo -c -o topology_wrap.lo
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx
>> libtool: compile:  mpicxx -DHAVE_CONFIG_H -I.
>> -I../../../pylith-1.9.0/modulesrc/topology -I../..
>> -I../../../pylith-1.9.0/libsrc -g
>> -I/home/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg
>> -I/home/bjha/pylith-1.9.0/lib/python2.7/site-packages/numpy/core/include
>> -I/usr/include/python2.7 -I/home/bjha/pylith-1.9.0/include
>> -I/home/bjha/pylith-1.9.0/include
>> -I/home/bjha/pylith-1.9.0/include/sieve
>> -I/home/bjha/pylith-1.9.0/include -I/usr/local/include -DENABLE_HDF5
>> -DENABLE_CUBIT -I/home/bjha/pylith-1.9.0/include -g -O2
>> -DMPICH_IGNORE_CXX_SEEK -MT topology_wrap.lo -MD -MP -MF
>> .deps/topology_wrap.Tpo -c
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx  -fPIC
>> -DPIC -o .libs/topology_wrap.o
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx: In
>> function 'char* pytype_string(PyObject*)':
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3170:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3171:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3172:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3173:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3174:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3175:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3176:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3177:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3178:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3179:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3180:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3181:40:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3183:10:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx: In
>> function 'char* typecode_string(int)':
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:3197:33:
>> warning: deprecated conversion from string constant to 'char*'
>> [-Wwrite-strings]
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx: In
>> function 'PyObject* _wrap_new_SubMesh__SWIG_1(PyObject*, PyObject*)':
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:4731:72:
>> error: cannot convert
>> 'pylith::topology::Field<pylith::topology::SubMesh>::Mesh* {aka
>> pylith::topology::SubMesh*}' to 'pylith::topology::Mesh*' in assignment
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx:4737:74:
>> error: cannot convert
>> 'pylith::topology::Field<pylith::topology::SubMesh>::Mesh* {aka
>> pylith::topology::SubMesh*}' to 'pylith::topology::Mesh*' in assignment
>> ../../../pylith-1.9.0/modulesrc/topology/topology_wrap.cxx: In
>> function 'PyObject* _wrap_SubMesh_createSubMesh(PyObject*, PyObject*)':
>>
>> Is it the swig version issue? Are 2.0.4 and 2.0.11 not compatible?
>>
>> Thanks and regards
>> Birendra
>> _______________________________________________
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>>
>