[CIG-SHORT] Pylith Install Error
Niz
niz.moussatat at gmail.com
Thu Aug 23 00:54:42 PDT 2012
2012/8/22 Brad Aagaard <baagaard at usgs.gov>
> 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
>
>
> Brad,
Your last suggestion worked, and pylith resumed installation [folders
contain the list of files you indicated previously].
I stumbled later:
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for pj_init_plus in -lproj... no
configure: error: Proj4 library not found; try LDFLAGS="-L<Proj4 lib
dir>"
there is in build/pylith/ 2 proj4* folders, but non of them contains a
lib/?
Regards
>
> 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>
>>>>>>>>>>>>> >
>>>>>>>>>>>>> **<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
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
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