dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On Wed, Oct 31, 2012 at 4:57 PM, Anders Logg <logg@xxxxxxxxx> wrote:
> On Wed, Oct 31, 2012 at 09:34:06AM +0000, Garth N. Wells wrote:
>
>> Not using Dorsal, I don't know. I do not add the paths of my
>> home-baked libraries to LD_LIBRARY_PATH, but rely on CMake to 'bake
>> in' the library paths (rpath). I like this because I can be sure which
>> libs are being linked in, rather than random bits and pieces that lie
>> in the system paths.
>>
>> What error do you get from Dorsal?
>
> I don't get the errors from Dorsal. The error is when I build
> everything except DOLFIN with Dorsal, then build DOLFIN against that
> build with cmake.local.
>
> What happens then is Python applications (not C++ which are working
> fine) fail with this error:
>

Try building DOLFIN with the MPI compiler wrappers.

It looks like the MPI libs that you built cannot find each other. I've
found that I do have to add the path of some shared libs to get the
Python module to link correctly.  Maybe it works with RPATH=OFF
because it picks up system installed MPI libs (which are usually
installed if you have other packages installed, e.g. ParaView).

Garth

> logg@host:~/scratch/src/dolfin/trunk-logg/demo/pde/poisson/python$
>> python demo_poisson.py
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_paffinity_hwloc:
>> /home/logg/scratch/fenics/lib/openmpi/mca_paffinity_hwloc.so:
>> undefined symbol: opal_hwloc_topology (ignored)
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_carto_auto_detect:
>> /home/logg/scratch/fenics/lib/openmpi/mca_carto_auto_detect.so:
>> undefined symbol: opal_carto_base_graph_get_host_graph_fn (ignored)
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_carto_file:
>> /home/logg/scratch/fenics/lib/openmpi/mca_carto_file.so: undefined
>> symbol: opal_carto_base_graph_get_host_graph_fn (ignored)
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_mmap:
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_mmap.so: undefined
>> symbol: opal_show_help (ignored)
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_posix:
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_posix.so: undefined
>> symbol: opal_shmem_base_output (ignored)
>> [host:25692] mca: base: component_find: unable to open
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_sysv:
>> /home/logg/scratch/fenics/lib/openmpi/mca_shmem_sysv.so: undefined
>> symbol: opal_show_help (ignored)
>
> This goes away if I rebuild DOLFIN with the RPATH=OFF option, or if I
> build everything including DOLFIN with Dorsal (since Dorsal adds the
> RPATH=OFF option).
>
> --
> Anders