[CIG-SHORT] Pylith Install Error
Brad Aagaard
baagaard at usgs.gov
Thu Aug 23 08:35:45 PDT 2012
Niz,
If Proj4 was installed correctly, you should see libproj.so in
$PREFIX/lib, proj_api.h in $PREFIX/include, and a proj directory in
$PREFIX/share.
If any of these are missing, then go to the proj4-build directory and
run "make clean", then "make", and "make install". If you encounter any
errors, send us the config.log from proj4-build and the complete error
message.
Regards,
Brad
On 08/23/2012 12:54 AM, Niz wrote:
> Your last suggestion worked, and pylith resumed installation [folders
> contain the list of files you indicated previously].
> I stumbled later:
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for pj_init_plus in -lproj... no
> configure: error: Proj4 library not found; try LDFLAGS="-L<Proj4 lib
> dir>"
>
> there is in build/pylith/ 2 proj4* folders, but non of them contains a
> lib/?
>
> Regards
>
>
>
>>
>> On 08/21/2012 06:04 PM, Niz wrote:
>>
>>> here is the longer install.log generated after deleting the build
>>> subdirectory, followed by the command.
>>>
>>> What do you mean by up to date. Its a newly installed 12.04, with selected
>>> third party software, and without backports, it might be late on updates
>>> for 48h. But the system headers are the latest. I must be doing smth
>>> wrong,
>>>
>>> Regards
>>> Niz
>>>
>>> 2012/8/22 Brad Aagaard <baagaard at usgs.gov>
>>>
>>> I forgot to mention that you should remove the build directory in the
>>>> pythia source directory (rm -r build) and then run
>>>>
>>>>
>>>> python setup.py install --prefix=$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
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>
More information about the CIG-SHORT
mailing list