[CIG-SHORT] Pylith Install Error
Niz
niz.moussatat at gmail.com
Tue Aug 21 15:22:56 PDT 2012
Seems that deleting python is not an option in Ubuntu, and I can't really
replace it by default with 3.XX anyway.
So as you suggested, I went inside build/pylith/pythia-0.8.1.14/ , and
executed the command,
so that in the folder
$HOME/build/pylith/pythia-0.8.1.14/mpi/
I have all the files you mentioned, although the install.log [file
attached] contains errors at the beginning
Should I move them manually into $PREFIX/lib/python2.7/site-packages/mpi/ ?
Regards
Niz
PS: Should I always answer to cig-short at geodynamics?
2012/8/21 Brad Aagaard <baagaard at usgs.gov>
> We have not tested PyLith with Python 3.x yet, so I don't advise doing
> using Python 3.x. You are using Python 2.7.3, so distutils is coming from
> there, which should be fine.
>
> I suggest that you try installing pythia again by running
>
> python setup.py install --prefix=$PREFIX >& install.log
>
> in the pythia source directory. If you see errors in the install.log or
> all of the files in the mpi directory are not there, send us the
> install.log file.
>
> Regards,
> Brad
>
>
>
> On 08/21/2012 01:59 PM, Niz wrote:
>
>> in $PREFIX/lib/python2.7/site-**packages/mpi/ I do not have:
>> cmpi.pxd
>> the folder launchers is not here too:
>> launchers/
>> nor are these files
>> _mpi.c
>> _mpi.pxd
>> mpi.pxd
>> _mpi.pyx
>> pympi.h
>>
>> and the folder scripts contains
>> -rw-rw-r-- 1 tora tora 340 May 25 2011 __init__.py
>> -rw-rw-r-- 1 tora tora 156 Aug 21 15:07 __init__.pyc
>> -rw-rw-r-- 1 tora tora 377 May 25 2011 mpistart.py
>> -rw-rw-r-- 1 tora tora 217 Aug 21 15:07 mpistart.pyc
>> and not this:
>> scripts/
>> __vault__.odb
>>
>> ------------------------------**--
>> As for the python version, I get this:
>> python
>> Python 2.7.3 (default, Aug 1 2012, 05:14:39)
>> [GCC 4.6.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>>> import distutils
>>>>> distutils.__version__
>>>>>
>>>> '2.7.3'
>>
>>>
>>>>>
>> I doubt I could revert to 2.7.2. So I shall test with the python 3.X.X
>> instead, or delete python and add it in the configure. maybe the later
>> would be more successful.
>>
>>
>> 2012/8/21 Brad Aagaard <baagaard at usgs.gov>
>>
>> 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<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<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
>>>>>>> *********************************************************
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ______________________________**_________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-**bin/mailman/listinfo/cig-short<http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>>>>>
>>>>>>
>>>>> ______________________________**_________________
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>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
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>>>
>>>
>>
>>
>>
>
--
*******************************************************
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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