[CIG-SHORT] Pylith Install Error

Tue Aug 21 10:24:45 PDT 2012

The config.log files for the other packages are probably not relevant, 
assuming the packages installed without errors.

The config.log from nemesis shows the following error message:

merlin.UnknownExtra: pythia 0.8.1.14 has no such extra feature 'mpi'

This suggests that the pythia install did not proceed correctly. There 
is no config.log for that install because it is a pure python package. 
This may indicate a distutils problem.

Look in $PREFIX/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg. 
You should see an "mpi" directory and it should contain:

Application.py* 

CartesianCommunicator.py* 

cmpi.pxd 

CommunicatorGroup.py* 

Communicator.py* 

__init__.py* 

LauncherMPICH.py* 

Launcher.py* 

launchers/ 

_mpi.c 

_mpi.pxd 

mpi.pxd 

_mpi.pyx 

Port.py* 

pympi.h
scripts/
__vault__.odb

Do you have all of these files and directories? If you run

python
import distutils
distutils.__version__

what do you see?

On my ubuntu 11.11 machine I get

python
Python 2.7.2+ (default, Oct  4 2011, 20:06:09)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import distutils
 >>> distutils.__version__
'2.7.2'

Regards,
Brad

On 08/21/2012 09:59 AM, Niz wrote:
> here is both config.log, from the nemeis and the global one. are there
> other config files relevant?
>
> Regards
>
> 2012/8/21 Brad Aagaard <baagaard at usgs.gov>
>
>> As Matt noted, we need the config.log from the configure of nemesis to
>> know for sure what is going wrong.
>>
>> I can say that there is a build issue with merlin (one of the Python
>> packages that we use) and Python version 2.7 and later. Merlin is
>> installed during "downloading missing Python dependencies". If merlin is
>> already installed, then an infinite loop can be encountered when merlin
>> tries to get installed again. The remedy is to remove all merlin related
>> files (*merlin*) from the installation directory ($PREFIX) and then
>> continue the installation from where things go wrong.
>>
>
>
>>
>> Regards,
>> Brad
>>
>>
>> On 08/21/2012 06:15 AM, Niz wrote:
>>> 2012/8/21 Niz <niz.moussatat at gmail.com>
>>>
>>>> This is the
>>>> /home/tora/build/pylith/nemesis-build/config.log
>>>> PS: It happens when I run  make command, that the compilation stopps
>>>> earlier on a loop command [it is not systematic]. If I reran it again,
>> and
>>>> again i reach also this point.
>>>>
>>>>
>>>> 2012/8/21 Matthew Knepley <knepley at mcs.anl.gov>
>>>>
>>>>> On Tue, Aug 21, 2012 at 2:59 AM, Niz <niz.moussatat at gmail.com> wrote:
>>>>>
>>>>>> Hello Pylith People
>>>>>>
>>>>>> I never seem to get this instalation process right.
>>>>>> I did the following:
>>>>>>     mkdir -p $HOME/src/pylith
>>>>>>     cd $HOME/src/pylith
>>>>>>     mv $HOME/Downloads/pylith-installer-1.7.1-0.tgz .
>>>>>>     tar -zxf pylith-installer-1.7.1-0.tgz
>>>>>>
>>>>>>     mkdir -p $HOME/build/pylith
>>>>>>     cd $HOME/build/pylith
>>>>>>     $HOME/src/pylith/pylith-installer-1.7.1-0/configure \
>>>>>>       --with-make-threads=2 \
>>>>>>       --prefix=$HOME/pylith
>>>>>>     source setup.sh
>>>>>>     make LDFLAGS+=-ldl
>>>>>>
>>>>>> %% I added the LDFLAGS because of a previous error
>>>>>> %% and cleaned the build folder
>>>>>>
>>>>>
>>>>> Yes, this is the correct fix. The cppunit configure must be imperfect.
>>>>>
>>>>>
>>>>>> The install process advances further till it hits:
>>>>>> checking whether -lpython2.7 is a shared library... yes
>>>>>> configure: downloading missing Python dependencies
>>>>>> configure: error: in `/home/tora/build/pylith/nemesis-build':
>>>>>> configure: error: cannot download missing Python dependencies
>>>>>> See `config.log' for more details
>>>>>>
>>>>>
>>>>> This could be a connectivity issue with this machine. Can you send
>>>>> /home/tora/build/pylith/nemesis-build/config.log?
>>>>>
>>>>>     Thanks,
>>>>>
>>>>>        Matt
>>>>>
>>>>>
>>>>>>    make[3]: Entering directory `/home/tora/build/pylith/nemesis-build'
>>>>>> make[3]: *** No targets specified and no makefile found.  Stop.
>>>>>> make[3]: Leaving directory `/home/tora/build/pylith/nemesis-build'
>>>>>> make[2]: *** [nemesis] Error 2
>>>>>> make[2]: Leaving directory `/home/tora/build/pylith'
>>>>>> make[1]: *** [installed_nemesis] Error 2
>>>>>> make[1]: Leaving directory `/home/tora/build/pylith'
>>>>>> make: *** [installed_pylith] Error 2
>>>>>>
>>>>>> As said in the Config.log, I run a Ubuntu 12.04 64bit, its a clean
>>>>>> slate, meaning I am trying to make pylith work with 2 thread before
>>>>>> installing anything else.
>>>>>>
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> *******************************************************
>>>> MOUSSATAT Nizar - PhD Student
>>>> ISTerre - Maison des Geosiences - Equipe risques
>>>> Bureau 1121 (1er étage)
>>>> Université de Grenoble, 38041 Grenoble Cedex 9, France
>>>> E-mail: nizar.moussatat at obs.ujf-grenoble.fr
>>>> Tel Bureau: +33 (0)4 76 63 51 81
>>>> Mobile       +33 (0) 6 43 59 39 44
>>>> Home        +33 (0) 4 80 38 45 93
>>>> *******************************************************
>>>>
>>>>
>>>
>>>
>>>
>>>
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>>
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