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[Bug 630516] Re: Python module does not link to correct DOLFIN lib

To: dolfin@xxxxxxxxxxxxxxxxxxx
From: Garth Wells <630516@xxxxxxxxxxxxxxxxxx>
Date: Wed, 23 Feb 2011 23:42:00 -0000
Reply-to: Bug 630516 <630516@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
** Changed in: dolfin
       Status: Fix Committed => Fix Released

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https://bugs.launchpad.net/bugs/630516

Title:
  Python module does not link to correct DOLFIN lib

Status in DOLFIN:
  Fix Released

Bug description:
  I'm having problems getting dorsal to make a working dolfin on Ubuntu 10.4
  There seems to be some kind of linking problem.

  dorsal.cfg looks like this:

  # Meta-project to build
  PROJECT=FEniCS
  # Where do you want the downloaded source files to go?
  DOWNLOAD_PATH=/opt/fenics/src
  # Where do you want the compiled software installed?
  INSTALL_PATH=/opt/fenics
  # How many processes would you like to build using?
  PROCS=1
  # Would you like to build stable versions of FEniCS projects?
  STABLE_BUILD=false

  After building, and running "source /opt/fenics/share/dolfin/dolfin.conf"
   python will not import dolfin, with errors like:

  ImportError: /opt/fenics/lib/python2.6/site-packages/dolfin/_cpp.so:
  undefined symbol:
  _ZNK6dolfin10Expression21compute_vertex_valuesERNS_5ArrayIdEERKNS_4MeshE

  Below is the output from: ldd /opt/fenics/lib/python2.6/site-
  packages/dolfin/_cpp.so

  As you can see, it has linked against the system installed dolfin in /usr/lib
  instead of the new dolfin in /opt/fenics.
  I do have a large number of system installed packages, which may conflict with dolfin 
  packages (e.g. petsc,cgal). Surely the dorsal build should use the packages it has downloaded
  by preference? 

  Any ideas? As far as I know, I have a completely standard install of Ubuntu Lucid, and dorsal is
  downloading into a clean directory structure.

          linux-vdso.so.1 =>  (0x00007fff657ff000)
          libdolfin.so.0 => /usr/lib/libdolfin.so.0 (0x00007f988750e000)
          libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0x00007f988705c000)
          libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f9886d0c000)
          libarmadillo.so.0 => /usr/lib/libarmadillo.so.0 (0x00007f9886b0a000)
          libboost_filesystem.so.1.40.0 => /usr/lib/libboost_filesystem.so.1.40.0 (0x00007f98868f4000)
          libboost_program_options.so.1.40.0 => /usr/lib/libboost_program_options.so.1.40.0 (0x00007f98866a6000)
          libboost_system.so.1.40.0 => /usr/lib/libboost_system.so.1.40.0 (0x00007f98864a2000)
          libpetsc.so => /opt/fenics/src/petsc-3.1-p4/linux-gnu-cxx-opt/lib/libpetsc.so (0x00007f988586e000)
          libX11.so.6 => /usr/lib/libX11.so.6 (0x00007f9885538000)
          libparmetis.so.3.1 => /usr/lib/libparmetis.so.3.1 (0x00007f98852f8000)
          libmetis.so.3.1 => /usr/lib/libmetis.so.3.1 (0x00007f98850ac000)
          liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00007f98844cb000)
          libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f9884230000)
          libdl.so.2 => /lib/libdl.so.2 (0x00007f9884010000)
          libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00007f9883d60000)
          libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00007f9883b14000)
          libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00007f988389f000)
          libnsl.so.1 => /lib/libnsl.so.1 (0x00007f9883685000)
          libutil.so.1 => /lib/libutil.so.1 (0x00007f9883482000)
          libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f988326a000)
          libpthread.so.0 => /lib/libpthread.so.0 (0x00007f988304d000)
          libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x00007f9882e49000)
          libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00007f9882c10000)
          libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f9882923000)
          libm.so.6 => /lib/libm.so.6 (0x00007f98826a0000)
          libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00007f9882485000)
          libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f9882171000)
          libatlas.so.3gf => /usr/lib/libatlas.so.3gf (0x00007f988180d000)
          libcholmod.so.1.7.1 => /usr/lib/libcholmod.so.1.7.1 (0x00007f988150e000)
          libcamd.so.2.2.0 => /usr/lib/libcamd.so.2.2.0 (0x00007f9881303000)
          libcolamd.so.2.7.1 => /usr/lib/libcolamd.so.2.7.1 (0x00007f98810fb000)
          libccolamd.so.2.7.1 => /usr/lib/libccolamd.so.2.7.1 (0x00007f9880eee000)
          libCGAL.so.4 => /usr/lib/libCGAL.so.4 (0x00007f9880cbf000)
          libgmpxx.so.4 => /usr/lib/libgmpxx.so.4 (0x00007f9880aba000)
          libmpfr.so.1 => /usr/lib/libmpfr.so.1 (0x00007f988086a000)
          libgmp.so.3 => /usr/lib/libgmp.so.3 (0x00007f988060a000)
          libboost_thread.so.1.40.0 => /usr/lib/libboost_thread.so.1.40.0 (0x00007f98803f4000)
          libz.so.1 => /lib/libz.so.1 (0x00007f98801dc000)
          libcppunit-1.12.so.1 => /usr/lib/libcppunit-1.12.so.1 (0x00007f987ff97000)
          libc.so.6 => /lib/libc.so.6 (0x00007f987fc14000)
          libumfpack.so.5.4.0 => /usr/lib/libumfpack.so.5.4.0 (0x00007f987f953000)
          libamd.so.2.2.0 => /usr/lib/libamd.so.2.2.0 (0x00007f987f749000)
          libslepc.so.3.0.0 => /usr/lib/libslepc.so.3.0.0 (0x00007f987f4db000)
          libparpack.so.2 => /usr/lib/libparpack.so.2 (0x00007f987f28d000)
          libarpack.so.2 => /usr/lib/libarpack.so.2 (0x00007f987f039000)
          libpetscts.so.3.0.0 => /usr/lib/libpetscts.so.3.0.0 (0x00007f987ee20000)
          libpetscsnes.so.3.0.0 => /usr/lib/libpetscsnes.so.3.0.0 (0x00007f987ebe4000)
          libpetscksp.so.3.0.0 => /usr/lib/libpetscksp.so.3.0.0 (0x00007f987e807000)
          libpetscdm.so.3.0.0 => /usr/lib/libpetscdm.so.3.0.0 (0x00007f987e592000)
          libpetscmat.so.3.0.0 => /usr/lib/libpetscmat.so.3.0.0 (0x00007f987e15d000)
          libpetscvec.so.3.0.0 => /usr/lib/libpetscvec.so.3.0.0 (0x00007f987dedc000)
          libpetsc.so.3.0.0 => /usr/lib/libpetsc.so.3.0.0 (0x00007f987dc1d000)
          libssl.so.0.9.8 => /usr/lib/libssl.so.0.9.8 (0x00007f987d9cc000)
          libcrypto.so.0.9.8 => /usr/lib/libcrypto.so.0.9.8 (0x00007f987d63c000)
          librt.so.1 => /lib/librt.so.1 (0x00007f987d433000)
          libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f987d217000)
          /lib64/ld-linux-x86-64.so.2 (0x00007f9887e1a000)
          libboost_thread-mt.so.1.38.0 => /usr/lib/libboost_thread-mt.so.1.38.0 (0x00007f987cfff000)
          libspooles.so.2.2 => /usr/lib/libspooles.so.2.2 (0x00007f987cc9a000)
          libHYPRE-2.4.0.so => /usr/lib/libHYPRE-2.4.0.so (0x00007f987ca98000)
          libsuperlu.so.3 => /usr/lib/libsuperlu.so.3 (0x00007f987c848000)
          libscotch-5.1.so => /usr/lib/libscotch-5.1.so (0x00007f987c5e6000)
          libXau.so.6 => /usr/lib/libXau.so.6 (0x00007f987c3e1000)
          libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007f987c1db000)
          libHYPRE_utilities-2.4.0.so => /usr/lib/libHYPRE_utilities-2.4.0.so (0x00007f987bfd0000)
          libHYPRE_multivector-2.4.0.so => /usr/lib/libHYPRE_multivector-2.4.0.so (0x00007f987bdca000)
          libHYPRE_krylov-2.4.0.so => /usr/lib/libHYPRE_krylov-2.4.0.so (0x00007f987bbb4000)
          libHYPRE_struct_mv-2.4.0.so => /usr/lib/libHYPRE_struct_mv-2.4.0.so (0x00007f987b987000)
          libHYPRE_struct_ls-2.4.0.so => /usr/lib/libHYPRE_struct_ls-2.4.0.so (0x00007f987b706000)
          libHYPRE_sstruct_mv-2.4.0.so => /usr/lib/libHYPRE_sstruct_mv-2.4.0.so (0x00007f987b4eb000)
          libHYPRE_sstruct_ls-2.4.0.so => /usr/lib/libHYPRE_sstruct_ls-2.4.0.so (0x00007f987b285000)
          libHYPRE_seq_mv-2.4.0.so => /usr/lib/libHYPRE_seq_mv-2.4.0.so (0x00007f987b07d000)
          libHYPRE_parcsr_mv-2.4.0.so => /usr/lib/libHYPRE_parcsr_mv-2.4.0.so (0x00007f987ae5c000)
          libHYPRE_parcsr_block_mv-2.4.0.so => /usr/lib/libHYPRE_parcsr_block_mv-2.4.0.so (0x00007f987ac3f000)
          libHYPRE_DistributedMatrix-2.4.0.so => /usr/lib/libHYPRE_DistributedMatrix-2.4.0.so (0x00007f987aa3b000)
          libHYPRE_MatrixMatrix-2.4.0.so => /usr/lib/libHYPRE_MatrixMatrix-2.4.0.so (0x00007f987a839000)
          libHYPRE_IJ_mv-2.4.0.so => /usr/lib/libHYPRE_IJ_mv-2.4.0.so (0x00007f987a628000)
          libHYPRE_Euclid-2.4.0.so => /usr/lib/libHYPRE_Euclid-2.4.0.so (0x00007f987a3e5000)
          libHYPRE_ParaSails-2.4.0.so => /usr/lib/libHYPRE_ParaSails-2.4.0.so (0x00007f987a1d4000)
          libHYPRE_DistributedMatrixPilutSolver-2.4.0.so => /usr/lib/libHYPRE_DistributedMatrixPilutSolver-2.4.0.so (0x00007f9879fc3000)
          libHYPRE_parcsr_ls-2.4.0.so => /usr/lib/libHYPRE_parcsr_ls-2.4.0.so (0x00007f9879d23000)
          libHYPRE_FEI_fgmres-2.4.0.so => /usr/lib/libHYPRE_FEI_fgmres-2.4.0.so (0x00007f9879b1f000)
          libHYPRE_mli-2.4.0.so => /usr/lib/libHYPRE_mli-2.4.0.so (0x00007f987988e000)
          libHYPRE_FEI-2.4.0.so => /usr/lib/libHYPRE_FEI-2.4.0.so (0x00007f98795c2000)
          libscotcherr-5.1.so => /usr/lib/libscotcherr-5.1.so (0x00007f98793bf000)
References

[Bug 630516] [NEW] Python module does not link to correct DOLFIN lib
From: Garth Wells, 2010-09-04