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Subject: [OMPI users] Python Binding problem with openmpi-1.3.2
From: Evans, Thomas M. (evanstm_at_[hidden])
Date: 2009-07-13 12:53:54


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/denov
o/src/pykba:/home/9te/work/Sn/build/debug/denovo/src/pykba/..:/home/9te/work
/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

-- 
Tom Evans
Radiation Transport and Shielding
Nuclear Science and Technology Division
------------------------------------------------
(865) 576-3535     Oak Ridge National Laboratory
(865) 574-9619 fax PO Box 2008 MS6172
evanstm_at_[hidden]   Oak Ridge, TN 37831-6170
www.ornl.gov/sci/radiation_transport_criticality
------------------------------------------------