[CIG-SHORT] Pylith Install Error
Brad Aagaard
baagaard at usgs.gov
Wed Aug 22 09:13:42 PDT 2012
Niz,
I think I have narrowed down the problem. pythia requires setuptools.
The setuptools in ubuntu 11.11 (0.6.c9) is old enough that pythia
recognizes that it needs a newer version and downloads a compatible
version (0.6.c11). In ubuntu 12.04, the version number of setuptools
provided is much newer (0.6.24 with compatibility for 0.6.c9) but it is
not compatible. If you uninstall the python-setuptools package, you
should be able to install pythia because it will install version 0.6.c11
which is known to be compatible when it can't find a system version.
There are multiple forks of setuptools, so dealing with the various
versions, etc is pretty messy.
Please let us know if this workaround is successful.
Regards,
Brad
On 08/21/2012 06:04 PM, Niz wrote:
> here is the longer install.log generated after deleting the build
> subdirectory, followed by the command.
>
> What do you mean by up to date. Its a newly installed 12.04, with selected
> third party software, and without backports, it might be late on updates
> for 48h. But the system headers are the latest. I must be doing smth wrong,
>
> Regards
> Niz
>
> 2012/8/22 Brad Aagaard <baagaard at usgs.gov>
>
>> I forgot to mention that you should remove the build directory in the
>> pythia source directory (rm -r build) and then run
>>
>>
>> python setup.py install --prefix=$PREFIX >& install.log
>>
>> We use Python 2.7.3 in building the binaries, so it is puzzling why the
>> install is failing and giving the distutils warnings. Have you checked to
>> make sure your system is up-to-date?
>>
>> Regards,
>> Brad
>>
>>
>>
>>
>>
>> On 08/21/2012 03:22 PM, Niz wrote:
>>
>>> 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>
>>>>>>>>>>>> **<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-**gren**oble.fr<http://grenoble.fr>
>>>>>>>>>> <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
>>>>>>>>>> ***********************************************************
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ______________________________****_________________
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>>>>>>>>> **<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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>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
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>>>>>> **<http://geodynamics.org/cgi-**bin/mailman/listinfo/cig-short<http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>>>>> **>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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