[CIG-SHORT] Pylith install eror

[Brad Aagaard]

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
>>
>>