[CIG-SHORT] mpi missing error when trying to install nemesis
Birendra jha
bjha7333 at yahoo.com
Mon Oct 4 21:49:12 PDT 2010
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
> >>>>
> >>>
> >>>
> >>
> >>
> >
> >
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
>
> _______________________________________________
> CIG-SHORT mailing list
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