dolfin team mailing list archive

[johannr@xxxxxxxxx]

On Thu, Mar 13, 2008 Anders Logg wrote:
> On Wed, Mar 12, 2008 at 08:48:52PM +0100, Åsmund Ødegård wrote:
>> On Wed, Mar 12, 2008 at 8:35 PM, Anders Logg <logg@xxxxxxxxx> wrote:
>> >
>> > On Wed, Mar 12, 2008 at 08:29:39PM +0100, Johan Hake wrote:
>> >  > On Wednesday 12 March 2008 18:56:08 Anders Logg wrote:
>> >  > > On Wed, Mar 12, 2008 at 11:48:19AM +0100, Johan Hake wrote:
>> >  > > > On Tuesday 11 March 2008 17:47:09 Matthew Knepley wrote:
>> >  > > > > On Tue, Mar 11, 2008 at 11:40 AM, Anders Logg
>> <logg@xxxxxxxxx> wrote:
>> >  > > > > > Compiling and running C++ applications against DOLFIN now
>> works fine
>> >  > > > > >
>> >  > > > > >  for me, but it breaks in Python:
>> >  > > > > >  >>> from dolfin import *
>> >  > > > > >
>> >  > > > > >  Traceback (most recent call last):
>> >  > > > > >   File "<stdin>", line 1, in <module>
>> >  > > > > >   File
>> >  > > > > >   "/home/logg/local/lib/python2.5/site-packages/dolfin/__init__.py",
>> >  > > > > >   line 4, in <module>
>> >  > > > > >     from assemble import *
>> >  > > > > >   File
>> >  > > > > >   "/home/logg/local/lib/python2.5/site-packages/dolfin/assemble.py",
>> >  > > > > >   line 17, in <module>
>> >  > > > > >     from dolfin import *
>> >  > > > > >   File
>> >  > > > > >   "/home/logg/local/lib/python2.5/site-packages/dolfin/dolfin.py",
>> >  > > > > >   line 7, in <module>
>> >  > > > > >     import _dolfin
>> >  > > > > >  ImportError: libpetscsnes.so: cannot open shared object
>> file: No
>> >  > > > > > such file or directory
>> >  > > > > >
>> >  > > > > >  # pkg-config --libs dolfin
>> >  > > > > >  -Wl,-rpath,/usr/local/lib/petsc/lib/linux-gnu-cxx-debug
>> -pthread
>> >  > > > > >  -Wl,--export-dynamic -L/home/logg/local/lib
>> -L/usr/lib/atlas
>> >  > > > > >  -L/usr/local/lib/petsc/lib/linux-gnu-cxx-debug -ldolfin
>> -lblas
>> >  > > > > >  -llapack -lumfpack -lamd -lpetscsnes -lpetscmat -lpetscvec
>> -lpetscts
>> >  > > > > >  -lpetsc -lpetscdm -lpetscksp -lgts -lxml2 -lgthread-2.0
>> -lrt
>> >  > > > > >  -lgmodule-2.0 -ldl -lglib-2.0
>> >  > > > > >
>> >  > > > > >  Any ideas?
>> >  > > > > >
>> >  > > > > >  I guess the path to PETSc libraries was built into
>> libdolfin.so in
>> >  > > > > >  some way before, but not anymore?
>> >  > > > >
>> >  > > > > Either you put -Wl,-rpath options in along with the -L
>> options, or
>> >  > > > > you do some incantation with ldconfig (not my preferred
>> option).
>> >  > > >
>> >  > > > This is possible whith scons, but Åsmund actively descided to
>> not use it
>> >  > > > for simula-scons. He has experienced some problems with darwin.
>> Maybe
>> >  > > > Åsmund can elaborate?
>> >  > > >
>> >  > > > Johan
>> >  > >
>> >  > > But how does it help to put in the -Wl,-rpath options to
>> pkg-config
>> >  > > --libs when importing the DOLFIN Python module into Python? As
>> far as
>> >  > > I know, Python does not call pkg-config, or should these options
>> be
>> >  > > present when compiling the SWIG-generated wrapper?
>> >  >
>> >  > I understand the -Wl,-rpath options as "hardcoding" the path to
>> external
>> >  > shared library at compile/linking time, so you do not have to
>> provide it
>> >  > during runtime with e.g. the LD_LIBRARY_PATH. As far as I know the
>> old dolfin
>> >  > build system included this information when the wrapper code was
>> generated.
>> >  >
>> >  > It wont help putting this path into the pkg-config file as any such
>> >  > information will be ignored when parsed by simula-scons, and wont
>> be used.
>> >  > Åsmund can probably elaborate on the why's here.
>> >  >
>> >  > > Does PyDOLFIN work for anyone else with the new build system?
>> >  >
>> >  > Here it works fine. I have compiled with petsc, and I have its path
>> in the
>> >  > LD_LIBRARY_PATH.
>> >
>> >  It works for me also if I add the location of PETSc to my
>> LD_LIBRARY_PATH.
>> >  Is this how it's supposed to work?
>> >
>> >  It seems strange that you both need to set a PETSC_DIR and then also
>> >  have PETSC_DIR/lib/$arch/ in the LD_LIBRARY_PATH.
>> >
>> >  Either there's a PETSC_DIR *or* PETSc is installed somewhere (in
>> which
>> >  case it needs to be in a standard place like /usr/lib or in the
>> >  LD_LIBRARY_PATH)?
>>
>> That's obvious, isn't it? Either you have to link statically, in that
>> case PETSC_DIR could be used during compile. Or you link dynamically,
>> and the linker have to know where to look during run. Either by using
>> LD_LIBRARY_PATH or ldconfig.
>
> Yes! I agree, but it seems that this is not the case.
>
> My PETSc installation is in some location only known by
> PETSC_DIR. This means I must set PETSC_DIR when building DOLFIN.
>
> I then expect to be able to build applications against the compiled
> DOLFIN by just using what pkg-config --cflags --libs dolfin gives me.
>
> But that doesn't seem to work. I also need to put the place where I
> have installed PETSc in my LD_LIBRARY_PATH, which I don't want...

It is because of the 'Requires' line in dolfin.pc:

Requires: numpy-1 slepc scotch ufc-1 umfpack python-2 petsc gts boost
libxml-2.0

You also need the generated pkg-config for petsc, scotch, etc. to be
present in PKG_CONFIG_PATH.

Johannes

> --
> Anders
>
>
>> I don't like to have rpath in the system, as it is not a
>> crossplattform solution. Meaning we have to add complexity by
>> branching the different archs.
>>
>>
>> >
>> >
>> >
>> > _______________________________________________
>> >  DOLFIN-dev mailing list
>> >  DOLFIN-dev@xxxxxxxxxx
>> >  http://www.fenics.org/mailman/listinfo/dolfin-dev
>> >
>>
>> Åsmund
>> _______________________________________________
>> DOLFIN-dev mailing list
>> DOLFIN-dev@xxxxxxxxxx
>> http://www.fenics.org/mailman/listinfo/dolfin-dev
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/mailman/listinfo/dolfin-dev
>