[CIG-SHORT] mpi missing error when trying to install nemesis

Tue Oct 5 08:32:41 PDT 2010

Birendra-

PyLith can't find spatialdata. Make sure it is built and installed.

Brad

On 10/04/2010 09:49 PM, Birendra jha wrote:
> Hi Brad,
>
> While running configure for Pylith
> ${HOME}/src/pylith-dev/configure  --config-cache  --enable-swig --enable-testing --enable-cubit --prefix=${TOOLS_DIR}  CPPFLAGS="-I${TOOLS_DIR}/include "  LDFLAGS="-L${TOOLS_DIR}/lib "  CC=mpicc CXX=mpiCC  CFLAGS="-O2 -fPIC" CXXFLAGS="-O2 -fPIC" PETSC_ARCH=linux_gcc-4.4.1_64
>
> I get following error
>
> configure: error: cannot download missing Python dependencies
>
> I have attached config.log file.
>
> Thanks
> Birendra
>
>
> --- On Tue, 10/5/10, Brad Aagaard<baagaard at usgs.gov>  wrote:
>
>> From: Brad Aagaard<baagaard at usgs.gov>
>> Subject: Re: [CIG-SHORT] mpi missing error when trying to install nemesis
>> To: cig-short at geodynamics.org
>> Date: Tuesday, October 5, 2010, 9:19 AM
>> Birendra-
>>
>> Removing the src/pythia directory did not do anything. You
>> need to
>> remove the "installed" pythia directory in
>>
>> /home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/
>>
>> Brad
>>
>>
>> On 10/4/10 8:32 PM, Birendra jha wrote:
>>> Hi Brad,
>>>
>>> I removed pythia folder from $HOME/src (trying to
>> uninstall pythia as per Leif's email), removed nemesis-dev
>> folders from src and build, checked out nemesis-dev again,
>> configured, ran make and got same errors during make
>> install.
>>> merlin.UnknownExtra: pythia 0.8.1.10 has no such extra
>> feature 'mpi'
>>>
>>> How to install nemesis "properly (with all egg
>> metadata)" as per Leif?
>>>
>>> One thing--removing pythia means I get error when
>> trying to import pyre.
>>>
>>> Thanks&   regards
>>> Birendra
>>>
>>> --- On Tue, 10/5/10, Brad Aagaard<baagaard at usgs.gov>
>> wrote:
>>>
>>>> From: Brad Aagaard<baagaard at usgs.gov>
>>>> Subject: Re: mpi missing error when trying to
>> install nemesis
>>>> To: cig-short at geodynamics.org,
>> bjha7333 at yahoo.com
>>>> Date: Tuesday, October 5, 2010, 8:35 AM
>>>> On 10/4/10 7:57 PM, Leif Strand
>>>> wrote:
>>>>> Hi Brad,
>>>>>
>>>>> I was able to reproduce this by downloading
>>>> pythia-0.8.1.10.tar.gz,
>>>>> manually installing it, adding it to my
>> PYTHONPATH,
>>>> and then installing
>>>>> 'nemesis'.
>>>>>
>>>>> I'm not sure if this is a bug or not... there
>> should
>>>> be Pythia "egg
>>>>> metadata" installed by "setuptools", but in
>> this
>>>> scenario, it is not.
>>>>>
>>>>> However, if one simply installs 'nemesis' --
>> without
>>>> manually installing
>>>>> Pythia first -- Pythia is automatically
>> downloaded
>>>> &   installed -- and
>>>>> properly (with all egg metadata).
>>>>>
>>>>> --Leif
>>>>>
>>>>>
>>>>> Brad Aagaard wrote:
>>>>>> Leif-
>>>>>>
>>>>>> A PyLith user trying to install from
>> source is
>>>> getting an odd error
>>>>>> when running "make install" for nemesis.
>> Is this
>>>> some sort of
>>>>>> PYTHONPATH issue? A merlin bug?
>>>>>>
>>>>>> Thanks,
>>>>>> Brad
>>>>>>
>>>>>>
>>>>>>
>>>>
>> bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$ make
>>>> install
>>>>>> make[1]: Entering directory
>>>>>>
>>>>
>> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
>>>>>> test -z
>> "/home/bjha/tools/gcc-4.4.1_64/bin" ||
>>>> /bin/mkdir -p
>>>>>> "/home/bjha/tools/gcc-4.4.1_64/bin"
>>>>>> /usr/bin/install -c nemesis mpinemesis
>>>>>> '/home/bjha/tools/gcc-4.4.1_64/bin'
>>>>>> make install-data-hook
>>>>>> make[2]: Entering directory
>>>>>>
>>>>
>> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
>>>>>> top_builddir=`CDPATH="${ZSH_VERSION+.}:"
>>>> &&   cd .&&
>> pwd`&&   \
>>>>>> cd
>> /home/bjha/src/nemesis-dev&&   \
>>>>>> /usr/bin/python setup.py install_deps -H
>> None -f
>>>> $top_builddir/deps
>>>>>>
>> --prefix=/home/bjha/tools/gcc-4.4.1_64&&
>>>> \
>>>>>> /usr/bin/python setup.py egg_info -e
>>>>>>
>>>>
>> /home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages
>>>>>>
>>>>
>> /home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:175:
>>>>>> DeprecationWarning: the sets module is
>> deprecated
>>>>>> from sets import ImmutableSet
>>>>>>
>>>>
>> /home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/package_index.py:7:
>>>>>> DeprecationWarning: the md5 module is
>> deprecated;
>>>> use hashlib instead
>>>>>> from md5 import md5
>>>>>> running install_deps
>>>>>> Checking .pth file support in
>>>>>>
>>>>
>> /home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages
>>>>>> /usr/bin/python -E -c pass
>>>>>> running egg_info
>>>>>> writing requirements to
>>>> nemesis.egg-info/requires.txt
>>>>>> writing nemesis.egg-info/PKG-INFO
>>>>>> writing top-level names to
>>>> nemesis.egg-info/top_level.txt
>>>>>> writing dependency_links to
>>>> nemesis.egg-info/dependency_links.txt
>>>>>> writing manifest file
>>>> 'nemesis.egg-info/SOURCES.txt'
>>>>>>
>>>>>> Installed /home/bjha/src/nemesis-dev
>>>>>> Processing dependencies for nemesis==1.0
>>>>>> Traceback (most recent call last):
>>>>>> File "setup.py", line 23,
>> in<module>
>>>>>> url = 'http://www.geodynamics.org/cig/software/packages/cs/pythia/',
>>>>>> File
>> "/usr/lib/python2.6/distutils/core.py", line
>>>> 152, in setup
>>>>>> dist.run_commands()
>>>>>> File
>> "/usr/lib/python2.6/distutils/dist.py", line
>>>> 975, in run_commands
>>>>>> self.run_command(cmd)
>>>>>> File
>> "/usr/lib/python2.6/distutils/dist.py", line
>>>> 995, in run_command
>>>>>> cmd_obj.run()
>>>>>> File
>>>>>>
>>>>
>> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/command/install_deps.py",
>>>>>> line 25, in run
>>>>>> self.install_dependencies()
>>>>>> File
>>>>>>
>>>>
>> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/command/install_deps.py",
>>>>>> line 74, in install_dependencies
>>>>>> self.process_distribution(None, self.dist,
>> not
>>>> self.no_deps)
>>>>>> File
>>>>>>
>>>>
>> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/command/easy_install.py",
>>>>>> line 526, in process_distribution
>>>>>> [requirement], self.local_index,
>>>> self.easy_install
>>>>>> File
>>>>>>
>>>>
>> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py",
>>>>>> line 650, in resolve
>>>>>>
>>>>
>> requirements.extend(dist.requires(req.extras)[::-1])
>>>>>> File
>>>>>>
>>>>
>> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py",
>>>>>> line 2219, in requires
>>>>>> "%s has no such extra feature %r" % (self,
>> ext)
>>>>>> merlin.UnknownExtra: pythia 0.8.1.10 has
>> no such
>>>> extra feature 'mpi'
>>>>>> make[2]: *** [install-data-hook] Error 1
>>>>>> make[2]: Leaving directory
>>>>>>
>>>>
>> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
>>>>>> make[1]: *** [install-data-am] Error 2
>>>>>> make[1]: Leaving directory
>>>>>>
>>>>
>> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
>>>>>> make: *** [install-am] Error 2
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
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>>> CIG-SHORT at geodynamics.org
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>>>
>>
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