problem of installation ESyS-Particle-2.1 in ubuntu 11.10

Hi Tao,

on Ubuntu-systems you can install pre-packaged version of
Esys-Particle [1] (stable 2.1 or development bzr-version). In this
case you skip the compilation step.

[1] https://answers.launchpad.net/esys-particle/+faq/1792

Anton

Hi Anton,
Thanks for your suggestion. I have tried the pre-packaged version of ESyS. I got one error when I tried to run some scripts:

CSubLatticeControler::initMPI()
Traceback (most recent call last):
  File "test_1dupsp.py", line 10, in <module>
    from esys.lsm import *
  File "/usr/lib/python2.7/dist-packages/esys/lsm/__init__.py", line 15, in <module>
    from util import InstallInfo
  File "/usr/lib/python2.7/dist-packages/esys/lsm/util/__init__.py", line 13, in <module>
    from FoundationPy import *
ImportError: /usr/lib/python2.7/dist-packages/esys/lsm/util/libFoundationPy.so.0: undefined symbol: _ZTIN5boost6python15instance_holderE

I do not how to solve this problem. As for my original problem of compiling ESyS in ubuntu 11.10, I am sure there is something wrong with some boost library. Could anyone give me any suggestion?

Thanks.

Tao

Hi all,
I think I have found a possible solution for my problem that I installed the old version of libboost. I think the latest version of libboost (version 1.46) is not compatible with ESyS-Particle-2.1, thus, I installed libboost 1.42. This change seems to be a good solution except one other error. Could anyone help me with this?

mv -f .deps/Worker.Tpo .deps/Worker.Po
/bin/bash ../libtool --tag=CXX --mode=link mpic++ -g -O2 -release 2.1 -L/usr/lib -o ESySParticleBEWorker Worker.o ../Parallel/libParallel.la ../ntable/src/libntable.la ../tml/message/libTmlMessage.la ../tml/type/libTmlType.la ../ppa/src/libppa.la ../Fields/libFields.la ../Geometry/libGgGeometry.la -lboost_filesystem-mt -lpython2.7
libtool: link: warning: `-release' is ignored for programs
libtool: link: mpic++ -g -O2 -o .libs/ESySParticleBEWorker Worker.o -L/usr/lib ../Parallel/.libs/libParallel.so ../ntable/src/.libs/libntable.so ../tml/message/.libs/libTmlMessage.so ../tml/type/.libs/libTmlType.so ../ppa/src/.libs/libppa.so ../Fields/.libs/libFields.so ../Geometry/.libs/libGgGeometry.so -lboost_filesystem-mt -lpython2.7
/usr/bin/ld: Worker.o: undefined reference to symbol 'console'
/usr/bin/ld: note: 'console' is defined in DSO /home/tao/ESyS-Particle-2.1/Foundation/.libs/libFoundation-2.1.so so try adding it to the linker command line
/home/tao/ESyS-Particle-2.1/Foundation/.libs/libFoundation-2.1.so: could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[2]: *** [ESySParticleBEWorker] Error 1
make[2]: Leaving directory `/home/tao/ESyS-Particle-2.1/MainBE'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/tao/ESyS-Particle-2.1'
make: *** [all] Error 2

Thanks.

Tao

Hello Tao.

Your problem may well still be with Boost. If you installed one version of the Boost libraries alongside another (for example, 1.42 with 1.46), there will be conflicts. Remove the ESyS-Particle package and all traces of all Boost versions. I suggest that you check manually that all Boost files are in fact gone: search for locations that contain "include/boost" in the path; search also for libraries starting with "libboost_" (cf. https://answers.launchpad.net/esys-particle/+faq/1235); and remove any remaining. Then try installing the ESyS-Particle package again with apt-get or aptitude.

Also, ensure that you do not have any other versions of ESyS-Particle installed anywhere on your system.

Regards,

Vince

Hi Vince,
Thank you for your suggestion, but I still have the same problem even if I have reinstalled the Ubuntu 11.10 system. The error message is as below:

tao@engs-19052:~/esys-particle/example/test$ mpirun -np 3 esysparticle bingle.py
CSubLatticeControler::initMPI()
CSubLatticeControler::initMPI()
Traceback (most recent call last):
  File "bingle.py", line 3, in <module>
    from esys.lsm import *
  File "/usr/local/lib/python2.7/dist-packages/esys/lsm/__init__.py", line 15, in <module>
    from util import InstallInfo
  File "/usr/local/lib/python2.7/dist-packages/esys/lsm/util/__init__.py", line 13, in <module>
    from FoundationPy import *
ImportError: /usr/local/lib/python2.7/dist-packages/esys/lsm/util/libFoundationPy.so.0: undefined symbol: _ZTIN5boost6python15instance_holderE

I also think there is something wrong with the boost library in the system. but I do now know how to fix it. Please can anyone help me with this problem?

Thanks.

Tao

Hi all,
what's more, I also used the command to see the links as:

tao@engs-19052:/usr/local/lib/python2.7/dist-packages/esys/lsm/util$ ldd libFoundationPy.so
 linux-vdso.so.1 => (0x00007fff5b979000)
 libFoundation-2.2.so => /usr/local/lib/libFoundation-2.2.so (0x00007ff62ce53000)
 libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00007ff62c93e000)
 libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007ff62c636000)
 libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff62c3b2000)
 libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff62c195000)
 libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff62bdf5000)
 libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ff62bbdf000)
 libboost_filesystem.so.1.46.1 => /usr/lib/libboost_filesystem.so.1.46.1 (0x00007ff62b9c1000)
 libboost_system.so.1.46.1 => /usr/lib/libboost_system.so.1.46.1 (0x00007ff62b7bc000)
 libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00007ff62b5a2000)
 libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007ff62b2f1000)
 libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007ff62b09f000)
 libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007ff62acf0000)
 libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007ff62aad8000)
 libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff62a8d3000)
 libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007ff62a6d0000)
 /lib64/ld-linux-x86-64.so.2 (0x00007ff62d2d7000)
 libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007ff62a481000)
 libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007ff62a22a000)

The problem is clear now: why the libFoundationPy.so cannot link to the libBoostPython.so ? I do not know how to fix this. Does anyone know how to fix this?

Best regards.

Tao

Hi Tao and others,

I've confirmed this problem on a clean install of lubuntu-11.10 (32bit). It is definitely a linking problem but no amount of coercion seems to get the ESyS-Particle build system to play nicely. I'm about to create a bug report linked to this thread.

Things I have tried:
1) Anton's pre-built packages with boost-1.46 and python2.7
           result: undefined symbol: _ZTIN5boost6python15instance_holderE
2) Latest source trunk with boost-1.46 and python2.7:
           result: undefined symbol: _ZTIN5boost6python15instance_holderE
3) Latest source trunk with boost-1.42 and python2.7:
           result: undefined symbol: _ZTIN5boost6python15instance_holderE
4) For any of the above three cases, running python using the following commandline switches to a different error:
           command: LD_PRELOAD=/usr/lib/libboost_python.so python
           result: ImportError: /usr/local/lib/libFields-2.2.so: undefined symbol: _ZN8SGetTypeclIiEEP15ompi_datatype_tRKT_

Similar errors (as first three above) from other OSS projects suggest it may be related to ensuring shared libraries that link to libboost_python also link to libpython2.X as well. The last attempt suggests there is a major linking issue causing the error to affect multiple ESyS-Particle shared libraries.

I'll start twisting arms to have someone look deeply into this tomorrow.

Cheers,

Dion

A bug report on this issue has been created. Please direct further related comments to:
https://bugs.launchpad.net/esys-particle/+bug/916724

Cheers,

Dion.

This bug has been fixed. See Bazaar rev. 1046.

Vince