[CIG-SHORT] Pylith install error

[Brad Aagaard]

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
>>>>
>>>>
>>
>>
>