[CIG-SHORT] Pylith install error

[Birendra jha]

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
> > >>>>
> > >>>>
> > >>
> > >>
> > >
> > 
> > 
> _______________________________________________
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>
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