[CIG-SHORT] pylith install error
Birendra jha
bjha7333 at yahoo.com
Thu Sep 26 17:30:37 PDT 2013
Brad
Thank you for this! However, I am slightly confused. To make progress, yesterday, I manually regenerated all pylith+spatialdata module files, except the following, using swig 2.0.11 installed on my machine:
1. pylith-1.9.0/modulesrc/meshio
2. pylith-1.9.0/modulesrc/topology
3. spatialdata-1.9.2/modulesrc/spatialdb
I am able to run pylith. I am analyzing some discrepancies in results but that is probably due to some change in input parameters.
I configured pylith with no extra flags, except --enable-force-install as suggested by configure after the first attempt found existing versions of system hdf.
Here is my confusion: I agree that installing pylith again, as you suggest with enable-swig, should be the straightforward way to do this. But why is it working currently with couple of old swig modules and rest new? Would you still recommend reinstallation? Should I check something to ensure that I am using right module files?
Thanks
Birendra
--------------------------------------------
On Fri, 9/27/13, Brad Aagaard <baagaard at usgs.gov> wrote:
Subject: Re: [CIG-SHORT] pylith install error
To: cig-short at geodynamics.org
Date: Friday, September 27, 2013, 4:57 AM
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
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
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