undefined symbol at run time

Asked by high end compute

I've downloaded v2.3.3 and compiled on Red Hat Enterprise Linux Server 6.5 with Boost 1.59.0 & Python 2.7.8. However when I attempt to run the esysparticle examples I get a run time error:

$ mpirun -np 2 `which esysparticle` bingle_output.py
CSubLatticeControler::initMPI()
Traceback (most recent call last):
  File "bingle_output.py", line 15, in <module>
    from esys.lsm import *
  File "/gpfs/stfc/local/HCPhi020/mxb01/mxb52-mxb01/ESys-Particle/test_rob/DIST/lib/python2.7/site-packages/esys/lsm/__init__.py", line 15, in <module>
    from .util import InstallInfo
  File "/gpfs/stfc/local/HCPhi020/mxb01/mxb52-mxb01/ESys-Particle/test_rob/DIST/lib/python2.7/site-packages/esys/lsm/util/__init__.py", line 13, in <module>
    from esys.lsm.util.FoundationPy import *
ImportError: /gpfs/stfc/local/HCPhi020/mxb01/mxb52-mxb01/ESys-Particle/test_rob/DIST/lib/python2.7/site-packages/esys/lsm/util/libFoundationPy.so.0: undefined symbol: _ZN5boost6python6detail12gcc_demangleEPKc

UPDATE: by adding "-Wl,-z,defs" to compile/link flags I find the initial undef is actually:

Making all in pis
make[2]: Entering directory `/gpfs/stfc/local/HCPhi020/mxb01/mxb52-mxb01/ESys-Particle/test_rob/ESyS-Particle-2.3.3/pis'
/bin/sh ../libtool --tag=CXX --mode=link mpicxx -z defs -release 2.3.2 -L/gpfs/stfc/local/apps/intel/boost/1.59.0/lib -Wl,-R,/gpfs/stfc/local/apps/intel/boost/1.59.0/lib -Wl,-z,defs -L/gpfs/stfc/local/apps/gcc/utilities/lib -L/gpfs/stfc/local/apps/gcc/python/2.7.8/lib -o libpis.la -rpath /gpfs/stfc/local/HCPhi020/mxb01/mxb52-mxb01/ESys-Particle/test_rob/DIST/lib pi_storage.lo -lpython2.7 -lmpi
libtool: link: mpicxx -fPIC -DPIC -shared -nostdlib /usr/lib/../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o .libs/pi_storage.o -L/gpfs/stfc/local/apps/intel/boost/1.59.0/lib -L/gpfs/stfc/local/apps/gcc/utilities/lib -L/gpfs/stfc/local/apps/gcc/python/2.7.8/lib -lpython2.7 -L/gpfs/stfc/local/apps/intel/intel_mpi/5.0.3.048/intel64/lib/release_mt -L/gpfs/stfc/local/apps/intel/intel_mpi/5.0.3.048/intel64/lib -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/local/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lmpicxx -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/../lib64/crtn.o -Wl,-R -Wl,/gpfs/stfc/local/apps/intel/boost/1.59.0/lib -Wl,-z -Wl,defs -Wl,-soname -Wl,libpis-2.3.2.so -o .libs/libpis-2.3.2.so
.libs/pi_storage.o: In function `AParallelInteractionStorage::~AParallelInteractionStorage()':
pi_storage.cpp:(.text._ZN27AParallelInteractionStorageD2Ev[_ZN27AParallelInteractionStorageD5Ev]+0x26): undefined reference to `esys::lsm::CheckPointable::~CheckPointable()'
.libs/pi_storage.o:(.data.rel.ro._ZTI27AParallelInteractionStorage[typeinfo for AParallelInteractionStorage]+0x10): undefined reference to `typeinfo for esys::lsm::CheckPointable'
collect2: ld returned 1 exit status
make[2]: *** [libpis.la] Error 1

I'm not an expert in C++/Python hybridisation so help welcome. Yours, M
http://highendcompute.co.uk

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re-opened since this has not yet been addressed. Thanks, M
Revision history for this message
high end compute (enq) said :
#1

anybody able to help me resolve this?

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Launchpad Janitor (janitor) said :
#2

This question was expired because it remained in the 'Open' state without activity for the last 15 days.

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high end compute (enq) said :
#3

still unanswered...

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Launchpad Janitor (janitor) said :
#4

This question was expired because it remained in the 'Open' state without activity for the last 15 days.