[CIG-SHORT] Pylith install error

[Birendra jha]

Brad,

I am trying to follow your second advice:"use the system installed mpi".
I removed everything from /build/pylith except the downloaded tar.gz files (removed openmpi-1.4.3.tar.gz too). Ran configure without any mpi:

user at ubuntu:~/build/pylith$ /home/user/Documents/pylith-installer-1.6.3-0/configure --with-make-threads=1 --prefix=$HOME/pylith --enable-swig --enable-pcre

Ran make and again got the same error (log files attached).  

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 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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