[CIG-SHORT] merlin.UnknownExtra: pythia 0.8.1.14 has no such extra feature 'mpi'
Brad Aagaard
baagaard at usgs.gov
Tue Apr 3 11:22:51 PDT 2012
PyLith users,
Birendra's problem was resolved by installing the python-distutils
package. If you are using system python on a linux machine and using the
pylith installer, I highly recommend installing the relevant distutils
package. The error ultimately was identified by the error message:
merlin.UnknownExtra: pythia 0.8.1.14 has no such extra feature 'mpi'
and
UserWarning: Unknown distribution option: 'extras_require'
Regards,
Brad
On 4/2/12 6:10 PM, Birendra jha wrote:
> Brad
>
> It is giving me same error (merlin.UnknownExtra: pythia 0.8.1.14 has no such extra feature 'mpi') at the same point. I have attached the config.log files.
> I downloaded pylith-installer-1.6.3-2, deleted everything in $HOME/build/pylith and $HOME/pylith, ran configure:
>
> user at ubuntu:~/build/pylith$ /home/user/Documents/pylith-installer-1.6.3-2/configure --with-make-threads=1 --prefix=$HOME/pylith --enable-swig --enable-pcre
>
> user at ubuntu:~/build/pylith$ source setup.sh
> then make.
>
> Following is the pythia install output:
> user at ubuntu:~/build/pylith/pythia-0.8.1.14$ python setup.py install --prefix=$HOME/pylith
> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'entry_points'
> warnings.warn(msg)
> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'extras_require'
> warnings.warn(msg)
> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'
> warnings.warn(msg)
> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
> warnings.warn(msg)
> running install
> running build
> running build_py
> running build_scripts
> running install_lib
> running install_scripts
> copying build/scripts-2.7/ipad.py -> /home/user/pylith/bin
> copying build/scripts-2.7/idd.py -> /home/user/pylith/bin
> copying build/scripts-2.7/journald.py -> /home/user/pylith/bin
> changing mode of /home/user/pylith/bin/ipad.py to 755
> changing mode of /home/user/pylith/bin/idd.py to 755
> changing mode of /home/user/pylith/bin/journald.py to 755
> running install_egg_info
> Removing /home/user/pylith/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg-info
> Writing /home/user/pylith/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg-info
>
> As usual I tried again, deleted merlin egg pythia folders and ran make again. Same error.
>
> Please help.
> Birendra
>
> --- On Tue, 4/3/12, Brad Aagaard<baagaard at usgs.gov> wrote:
>
>> From: Brad Aagaard<baagaard at usgs.gov>
>> Subject: Re: [CIG-SHORT] Pylith install error
>> To: "Birendra jha"<bjha7333 at yahoo.com>
>> Date: Tuesday, April 3, 2012, 5:46 AM
>> Birendra,
>>
>> I updated pythia to 0.8.1-14 and the installer to 1.6.3-2.
>> The installer
>> checks for the python/MPI incompatibility and uses the newer
>> pythia
>> (which should install some files that some platforms omit).
>>
>> Brad
>>
>>
>> On 4/2/12 4:01 PM, Birendra jha wrote:
>>> Here it is.
>>>
>>> Thanks
>>> Birendra
>>> --- On Tue, 4/3/12, Brad Aagaard<baagaard at usgs.gov>
>> wrote:
>>>
>>>> From: Brad Aagaard<baagaard at usgs.gov>
>>>> Subject: Re: [CIG-SHORT] Pylith install error
>>>> To: "Birendra jha"<bjha7333 at yahoo.com>
>>>> Date: Tuesday, April 3, 2012, 4:22 AM
>>>> Birendra,
>>>>
>>>> I need the "make" log to see what happened when
>> the
>>>> installer tried to
>>>> install pythia. In other words what happens when
>> you run
>>>>
>>>> python setup.py install --prefix=$PREFIX_YOU_USED
>>>>
>>>> in the pythia directory? Please capture this in a
>> log and
>>>> send it to me.
>>>> I think this problem may already be solved in the
>> pythia
>>>> development
>>>> version, but I want to verify what is happening on
>> your
>>>> system.
>>>>
>>>> Brad
>>>>
>>>>
>>>> On 4/2/12 3:31 PM, Birendra jha wrote:
>>>>> Forgot to attach the log files
>>>>>
>>>>> --- On Tue, 4/3/12, Birendra jha<bjha7333 at yahoo.com>
>>>> wrote:
>>>>>
>>>>>> From: Birendra jha<bjha7333 at yahoo.com>
>>>>>> Subject: Re: [CIG-SHORT] Pylith install
>> error
>>>>>> To: "Brad Aagaard"<baagaard at usgs.gov>
>>>>>> Cc: cig-short at geodynamics.org
>>>>>> Date: Tuesday, April 3, 2012, 4:00 AM
>>>>>> Brad,
>>>>>>
>>>>>> Now I am back to the old error of
>>>>>> merlin.UnknownExtra: pythia 0.8.1.13 has no
>> such
>>>> extra
>>>>>> feature 'mpi'
>>>>>>
>>>>>> I have attached the
>> nemesis-build/config.log
>>>>>>
>>>>>> I already tried this: delete following
>>>>>>
>> build/pylith/nemesis-build/deps/merlin-1.7.egg
>>>>>> build/pylith/nemesis-1.0.2/merlin-1.7.egg
>>>>>> build/pylith/pythia-0.8.1.13
>>>>>>
>>>>>> and run make again. Got same error.
>>>>>>
>>>>>> What should I do to get the mpi?
>>>>>> Thanks
>>>>>> Birendra
>>>>>>
>>>>>> --- On Tue, 4/3/12, Brad Aagaard<baagaard at usgs.gov>
>>>>>> wrote:
>>>>>>
>>>>>>> From: Brad Aagaard<baagaard at usgs.gov>
>>>>>>> Subject: Re: Pylith install error
>>>>>>> To: "Birendra jha"<bjha7333 at yahoo.com>
>>>>>>> Cc: cig-short at geodynamics.org
>>>>>>> Date: Tuesday, April 3, 2012, 2:53 AM
>>>>>>> Birendra,
>>>>>>>
>>>>>>> I think I have an idea on what the
>> source of
>>>> the
>>>>>> problem is.
>>>>>>> You are
>>>>>>> requesting the system installed python
>> and the
>>>>>> installer to
>>>>>>> build
>>>>>>> OpenMPI. This is causing a conflict
>> because
>>>> the
>>>>>> installer is
>>>>>>> using the
>>>>>>> MPI compilers which add their own set
>> of
>>>> LDFLAGS and
>>>>>> python
>>>>>>> which adds
>>>>>>> its own set of LDFLAGS (-L/usr/lib). I
>> think
>>>> you need
>>>>>> to
>>>>>>> request the
>>>>>>> installed to also build Python (so that
>> it is
>>>> built
>>>>>> with the
>>>>>>> OpenMPI
>>>>>>> compilers) or use the system installed
>> mpi.
>>>>>>>
>>>>>>> Brad
>>>>>>>
>>>>>>>
>>>>>>> On 4/2/12 1:48 PM, Birendra jha wrote:
>>>>>>>> Brad,
>>>>>>>>
>>>>>>>> Yes, I did run source setup.sh
>> after
>>>> running
>>>>>> configure.
>>>>>>> Following is the output at Terminal
>> right now:
>>>>>>>>
>>>>>>>> user at ubuntu:~/build/pylith$ echo
>>>> $LD_LIBRARY_PATH
>>>>>>>>
>>>> /home/user/pylith/lib:/home/user/pylith/lib64
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Birendra
>>>>>>>>
>>>>>>>> --- On Tue, 4/3/12, Brad
>> Aagaard<baagaard at usgs.gov>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> From: Brad Aagaard<baagaard at usgs.gov>
>>>>>>>>> Subject: Re: Pylith install
>> eror
>>>>>>>>> To: "Birendra jha"<bjha7333 at yahoo.com>
>>>>>>>>> Cc: cig-short at geodynamics.org
>>>>>>>>> Date: Tuesday, April 3, 2012,
>> 2:04 AM
>>>>>>>>> Birendra,
>>>>>>>>>
>>>>>>>>> The undefined symbols are
>> coming from
>>>>>>> /usr/lib/libmpi.so.
>>>>>>>>> This should
>>>>>>>>> not be happening if the
>> configure is
>>>> detecting
>>>>>> the
>>>>>>> openmpi
>>>>>>>>> that was
>>>>>>>>> built. I don't see
>> LD_LIBRARY_PATH in
>>>> your
>>>>>>> config.log
>>>>>>>>> environment. Did
>>>>>>>>> you run "source setup.sh" after
>> running
>>>> the
>>>>>>> pylith-installer
>>>>>>>>> configure?
>>>>>>>>>
>>>>>>>>> Brad
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/2/12 1:07 PM, Birendra jha
>> wrote:
>>>>>>>>>> Hi Brad,
>>>>>>>>>>
>>>>>>>>>> My system is Ubuntu 11.04
>> 64-bit.
>>>>>>>>>> I removed all pylith files,
>> started
>>>> from
>>>>>> a
>>>>>>> clean
>>>>>>>>> $HOME/build/pylith and
>> $HOME/pylith
>>>>>> directories. I
>>>>>>> changed
>>>>>>>>> the configure command as
>> follows:
>>>>>>>>>>
>>>>>>>>>>
>> user at ubuntu:~/build/pylith$
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>> /home/user/Documents/pylith-installer-1.6.3-0/configure
>>>>>>>>> --with-make-threads=1
>>>> --enable-mpi=openmpi
>>>>>>>>> --prefix=$HOME/pylith
>> --enable-swig
>>>>>> --enable-pcre
>>>>>>>>>>
>>>>>>>>>> and I am getting error at
>> nemesis
>>>> build
>>>>>> stage.
>>>>>>> Please
>>>>>>>>> see attached
>> /build/pylith/config.log
>>>> and
>>>>>>>>>
>> /build/pylith/nemesis-build/config.log
>>>> files.
>>>>>>>>>>
>>>>>>>>>> On Terminal I see:
>>>>>>>>>>
>>>>>>>>>> checking for Python.h...
>> yes
>>>>>>>>>> checking whether
>> -lpython2.7 is a
>>>> shared
>>>>>>> library... no
>>>>>>>>>> configure: error:
>> -lpython2.7 is
>>>> not a
>>>>>> shared
>>>>>>> library
>>>>>>>>>> make[3]: Entering
>> directory
>>>>>>>>>
>>>> `/home/user/build/pylith/nemesis-build'
>>>>>>>>>> make[3]: *** No targets
>> specified
>>>> and no
>>>>>>> makefile
>>>>>>>>> found. Stop.
>>>>>>>>>> make[3]: Leaving directory
>>>>>>>>>
>>>> `/home/user/build/pylith/nemesis-build'
>>>>>>>>>> make[2]: *** [nemesis]
>> Error 2
>>>>>>>>>> make[2]: Leaving directory
>>>>>>> `/home/user/build/pylith'
>>>>>>>>>> make[1]: ***
>> [installed_nemesis]
>>>> Error 2
>>>>>>>>>> make[1]: Leaving directory
>>>>>>> `/home/user/build/pylith'
>>>>>>>>>> make: ***
>> [installed_pylith] Error
>>>> 2
>>>>>>>>>>
>>>>>>>>>> In
>>>> /build/pylith/nemesis-build/config.log
>>>>>> I
>>>>>>> see:
>>>>>>>>>>
>>>>>>>>>> /usr/lib/libmpi.so:
>> undefined
>>>> reference
>>>>>> to
>>>>>>> `MPL_trid'
>>>>>>>>>> /usr/lib/libmpi.so:
>> undefined
>>>> reference
>>>>>> to
>>>>>>>>> `MPL_trvalid'
>>>>>>>>>> /usr/lib/libmpi.so:
>> undefined
>>>> reference
>>>>>> to
>>>>>>>>> `MPL_env2int'
>>>>>>>>>> /usr/lib/libmpi.so:
>> undefined
>>>> reference
>>>>>> to
>>>>>>>>> `MPL_trrealloc'
>>>>>>>>>>
>>>>>>>>>> Looks like I am again
>> getting MPI
>>>> related
>>>>>>> errors.
>>>>>>>>>>
>>>>>>>>>> Please help.
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>> Birendra
>>>>>>>>>>
>>>>>>>>>> --- On Tue, 4/3/12, Brad
>>>> Aagaard<baagaard at usgs.gov>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> From: Brad
>> Aagaard<baagaard at usgs.gov>
>>>>>>>>>>> Subject: Re: Pylith
>> install
>>>> eror
>>>>>>>>>>> To: "Birendra
>> jha"<bjha7333 at yahoo.com>
>>>>>>>>>>> Cc: cig-short at geodynamics.org
>>>>>>>>>>> Date: Tuesday, April 3,
>> 2012,
>>>> 1:06 AM
>>>>>>>>>>> Birendra,
>>>>>>>>>>>
>>>>>>>>>>> Did you clean out any
>> old
>>>> PyLith
>>>>>> builds
>>>>>>> that may be
>>>>>>>>> in the
>>>>>>>>>>> path? There
>>>>>>>>>>> are issues with
>>>> distutils/merlin and
>>>>>> Python
>>>>>>> 2.7
>>>>>>>>> that prevent
>>>>>>>>>>> pythia from
>>>>>>>>>>> installing (infinite
>> loop in a
>>>> python
>>>>>>> function).
>>>>>>>>> The
>>>>>>>>>>> workaround is
>>>>>>>>>>> simply to remove merlin
>> and
>>>> then
>>>>>> install
>>>>>>> pythia.
>>>>>>>>>>>
>>>>>>>>>>> Brad
>>>>>>>>>>>
>>>>>>>>>>> On 4/1/12 1:58 AM,
>> Birendra
>>>> jha
>>>>>> wrote:
>>>>>>>>>>>> Dear developers,
>>>>>>>>>>>>
>>>>>>>>>>>> I am getting
>> following
>>>> error
>>>>>> while
>>>>>>> installing
>>>>>>>>> Pylith
>>>>>>>>>>> from the installer:
>>>>>>>>>>>>
>>>>>>>>>>>> checking for
>> Python.h...
>>>> yes
>>>>>>>>>>>> checking whether
>>>> -lpython2.7 is a
>>>>>>> shared
>>>>>>>>> library...
>>>>>>>>>>> yes
>>>>>>>>>>>> configure:
>> downloading
>>>> missing
>>>>>> Python
>>>>>>>>> dependencies
>>>>>>>>>>>> configure: error:
>> in
>>>>>>>>>>>
>>>>>> `/home/user/build/pylith/nemesis-build':
>>>>>>>>>>>> configure: error:
>> cannot
>>>> download
>>>>>>> missing
>>>>>>>>> Python
>>>>>>>>>>> dependencies
>>>>>>>>>>>> See `config.log'
>> for more
>>>> details
>>>>>>>>>>>> make[3]: Entering
>>>> directory
>>>>>>>>>>>
>>>>>> `/home/user/build/pylith/nemesis-build'
>>>>>>>>>>>> make[3]: *** No
>> targets
>>>> specified
>>>>>> and
>>>>>>> no
>>>>>>>>> makefile
>>>>>>>>>>> found. Stop.
>>>>>>>>>>>> make[3]: Leaving
>> directory
>>>>>>>>>>>
>>>>>> `/home/user/build/pylith/nemesis-build'
>>>>>>>>>>>> make[2]: ***
>> [nemesis]
>>>> Error 2
>>>>>>>>>>>> make[2]: Leaving
>> directory
>>>>>>>>> `/home/user/build/pylith'
>>>>>>>>>>>> make[1]: ***
>>>> [installed_nemesis]
>>>>>> Error
>>>>>>> 2
>>>>>>>>>>>> make[1]: Leaving
>> directory
>>>>>>>>> `/home/user/build/pylith'
>>>>>>>>>>>> make: ***
>>>> [installed_pylith] Error
>>>>>> 2
>>>>>>>>>>>>
>>>>>>>>>>>> I have attached
>> the
>>>>>>>>> pylith/nemesis-build/config.log
>> and
>>>>>>>>>>> pylith/config.log
>>>>>>>>>>>>
>>>>>>>>>>>> I am getting this
>> error
>>>> during
>>>>>> nemesis
>>>>>>> build. I
>>>>>>>>> had to
>>>>>>>>>>> install some missing
>> packages
>>>>>> (gfortran,
>>>>>>>>> python-dev, mpich2
>>>>>>>>>>> and its 2 dev
>> libraries,
>>>> libcr-dev)
>>>>>> along
>>>>>>> the way
>>>>>>>>> after I
>>>>>>>>>>> ran make for the first
>> time.
>>>>>>>>>>>> Do I need to do a
>> fresh
>>>> install
>>>>>> again?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>> Birendra
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>
>>>>
>>
>>
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