[CIG-SHORT] error compiling pylith 1.6.2

[Matthew Knepley]

On Mon, Nov 28, 2011 at 5:50 PM, Naveed Near-Ansari <naveed at caltech.edu>wrote:

>  Thanks.  any other thoughts?  I had that set already.  I ran a make clean
> and tried again.  LD_LIBRARY_PATH is as follows:
>
>
> /opt/pylith-1.6.2/lib:/opt/pylith-1.6.2/lib64:/opt/mpi/gcc/openmpi-1.4.3/lib64/openmpi:/opt/pylith-1.6.2/lib:/opt/pylith-1.6.2/lib64:/opt/hdf5/lib:/opt/netcdf4/lib:/opt/ncl/lib:/opt/pylith-1.6.2/lib:/opt/pylith-1.6.2/lib64:/opt/mpi/gcc/openmpi-1.4.3/lib64:/usr/lib:/usr/lib64
>

There is something clearly wrong with your OpenMPI installation. When
Python tried to open the dynamic library:

/usr/bin/python: symbol lookup error:
> /opt/mpi/gcc/openmpi-1.4.3/lib64/openmpi/mca_paffinity_linux.so:
> undefined symbol: mca_base_param_reg_int


I have no idea what library has this missing symbol. Consider using
--download-mpich for PETSc since I know
this works.

   Matt

On 11/28/2011 02:06 PM, Matthew Knepley wrote:
>
> On Mon, Nov 28, 2011 at 3:53 PM, Naveed Near-Ansari <naveed at caltech.edu>wrote:
>
>> I was attempting to build pylith on a new system and have run into an
>> error during the tests.  The message said to report it here.
>>
>
>  OpenMPI is perverse. Its shared libraries must be in your
> LD_LIBRARY_PATH.
>
>    Matt
>
>
>> Naveed
>>
>> make[6]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/libtests/utils'
>> make[5]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/libtests/utils'
>> make[5]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/libtests'
>> make[5]: Nothing to be done for `check-am'.
>> make[5]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/libtests'
>> make[4]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/libtests'
>> Making check in pytests
>> make[4]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests'
>> Making check in bc
>> make[5]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc'
>> Making check in data
>> make[6]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc/data'
>> if [ "X../../../../../pylith-1.6.2" != "X../../../.." ]; then for f in
>> tri3_disp.spatialdb tri3_vel.spatialdb tri3_tractions.spatialdb
>> tri3.mesh elasticplanestrain.spatialdb; do /bin/sh
>> /root/pylith-installer-1.6.2-0/pylith-1.6.2/aux-config/install-sh -c -m
>> 644 ../../../../../pylith-1.6.2/unittests/pytests/bc/data/$f
>> ../../../../unittests/pytests/bc/data; done; fi
>> make  check-am
>> make[7]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc/data'
>> make[7]: Nothing to be done for `check-am'.
>> make[7]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc/data'
>> make[6]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc/data'
>> make[6]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc'
>> make  testbc.py
>> make[7]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc'
>> make[7]: Nothing to be done for
>> `../../../../pylith-1.6.2/unittests/pytests/bc/testbc.py'.
>> make[7]: Leaving directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc'
>> make  check-TESTS
>> make[7]: Entering directory
>> `/root/pylith-installer-1.6.2-0/pylith-build/unittests/pytests/bc'
>>
>> /opt/pylith-1.6.2/lib/python2.4/site-packages/pythia-0.8.1.12-py2.4.egg/pyre/inventory/odb/Curator.py:200:
>> UserWarning: Module pkg_resources was already imported from
>>
>> /opt/pylith-1.6.2/lib/python2.4/site-packages/setuptools-0.6c9-py2.4.egg/pkg_resources.pyc,
>> but /opt/pylith-1.6.2/lib/python2.4/site-packages/merlin-1.7.egg is
>> being added to sys.path
>>  from pkg_resources import resource_listdir, resource_isdir,
>> resource_exists, resource_filename, Requirement
>>
>> /opt/pylith-1.6.2/lib/python2.4/site-packages/pythia-0.8.1.12-py2.4.egg/pyre/inventory/odb/Curator.py:200:
>> UserWarning: Module site was already imported from
>> /usr/lib64/python2.4/site.pyc, but
>> /opt/pylith-1.6.2/lib/python2.4/site-packages/merlin-1.7.egg is being
>> added to sys.path
>>  from pkg_resources import resource_listdir, resource_isdir,
>> resource_exists, resource_filename, Requirement
>> /usr/bin/python: symbol lookup error:
>> /opt/mpi/gcc/openmpi-1.4.3/lib64/openmpi/mca_paffinity_linux.so:
>> undefined symbol: mca_base_param_reg_int
>> FAIL: testbc.py
>> ==========================================
>> 1 of 1 test failed
>> Please report to cig-short at geodynamics.org
>>
>>
>>
>> _______________________________________________
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>> CIG-SHORT at geodynamics.org
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>>
>>
>
>
>  --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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