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Subject: Re: [OMPI users] Python Binding problem with openmpi-1.3.2
From: Rainer Keller (keller_at_[hidden])
Date: 2009-07-13 14:27:13


Hi Tom,
as discussed, the following threads may help You?

http://www.open-mpi.org/community/lists/users/2009/02/8158.php
http://www.open-mpi.org/faq/?category=running#loading-libmpi-dynamically

With best regards,
Rainer

On Monday 13 July 2009 12:53:54 pm Evans, Thomas M. wrote:
> I've been using openmpi-1.2.x for 2 years to dynamically create python
> bindings for my application code. I've just downloaded and installed
> openmpi-1.3.2, and I now get the following error when trying to run python
> with one of my bindings:
>
> /data/python/current/bin/python: symbol lookup error:
> /data/mpi/gcc-4.3.2/openmpi-1.3.2/lib/openmpi/mca_paffinity_linux.so:
> undefined symbol: mca_base_param_reg_int
>
> All of my regular executables work fine.
>
> To build one of my bindings I use the following configure line:
>
> mpic++ -pthread -shared -Xlinker
> -R/data/vendors/gcc/silo/lib/:/data/vendors/gsl-1.9/lib/:/data/mpi/gcc-4.3.
>2
> /openmpi-1.3.2/lib:/data/gcc/current/lib:/home/9te/work/Sn/build/debug/deno
>v
> o/src/pykba:/home/9te/work/Sn/build/debug/denovo/src/pykba/..:/home/9te/wor
>k /Sn/build/debug/lib -o _hybrid.so hybrid_wrap.o SC.pt.o Database.o
> denovo.o Mavric_Parser.o Source.o Mat.o Objects.o Map.o Viz.o Angles.o
> MC_Manager.o WW.o Problem_Output.o -L/home/9te/work/Sn/build/debug/lib
> -ldenovo_kba_utils -ldenovo_kba -ldenovo_source -ldenovo_material
> -ldenovo_angle
> -ldenovo_database -ldenovo_meshing -ldenovo_utils -ldenovo_comm
> -ldenovo_harness -ldenovo_release -L/data/vendors/gcc/trilinos/ompicxx/lib/
> -lamesos -laztecoo -lepetraext -lepetra -lteuchos -ltriutils
> -L/data/vendors/gsl-1.9/lib/ -lgsl -lgslcblas
> -L/data/vendors/gcc/atlas/lib/ -llapack -lf77blas -lcblas -latlas
> -L/data/vendors/gcc/silo/lib/ -lsiloh5 -L/data/vendors/gcc/hdf5/lib/ -lhdf5
> -lz
> -L/home/data/gcc/gcc-4.3.2/bin/../lib/gcc/i686-pc-linux-gnu/4.3.2
> -L/home/data/gcc/gcc-4.3.2/bin/../lib/gcc
> -L/home/data/gcc/gcc-4.3.2/bin/../lib/gcc/i686-pc-linux-gnu/4.3.2/../../..
> -lgfortranbegin -lgfortran -lm -lgcc_s -lm
>
> I noticed on the mail archive a post related to this issue back in 2005 (
> From: Jeff Squyres (jsquyres_at_[hidden]) Date: 2005-09-15 15:32:21);
> however, I am assuming that this issue has been resolved since then. Is
> there something I need to do extra? I know the symbol in question is
> defined in libopen-pal.so, so it does exist, and mpic++ does include it on
> the link-line. As mentioned in the older post, LD_LIBRARY_PATH tinkering
> will not fix the problem. Any help is greatly appreciated.
>
> Tom

-- 
------------------------------------------------------------------------
Rainer Keller, PhD                  Tel: +1 (865) 241-6293
Oak Ridge National Lab          Fax: +1 (865) 241-4811
PO Box 2008 MS 6164           Email: keller_at_[hidden]
Oak Ridge, TN 37831-2008    AIM/Skype: rusraink