dolfin team mailing list archive

[johannr@xxxxxxxxx]

On Thu, Mar 13, 2008 Anders Logg wrote:
> On Thu, Mar 13, 2008 at 12:24:31PM +0100, johannr@xxxxxxxxx wrote:
>> 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
>
> So do you mean I also need to call pkg-config --libs petsc when
> compiling an application?

No. I just thought that you perhaps didn't have petsc.pc in your
PKG_CONFIG_DIR variable. But that would probably lead to an error so I
might have been to fast this time :)

Johannes