[CIG-SHORT] mpi missing error when trying to install nemesis
Birendra jha
bjha7333 at yahoo.com
Tue Oct 5 10:31:20 PDT 2010
Brad,
I have spatialdata installed, I went through all of Step 6 successfully, including make check.
However, I did have to change
svn co http://geodynamics.org/svn/cig/cs/spatialdata-0.1/trunk spatialdata-dev
with
svn co http://geodynamics.org/svn/cig/cs/spatialdata/trunk spatialdata
Then
cd $HOME/scratch/build/$TOOLS_FORMAT/spatialdata-dev
for configure, I changed CC=icc CXX=icpc to CC=gcc CXX=g++ for my system
I went through this again, still same error during pylith configure.
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, 9:02 PM
> 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
> >>>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> _______________________________________________
> >>> CIG-SHORT mailing list
> >>> CIG-SHORT at geodynamics.org
> >>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>
> >>
> >> _______________________________________________
> >> CIG-SHORT mailing list
> >> CIG-SHORT at geodynamics.org
> >> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
More information about the CIG-SHORT
mailing list