dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Mon, Nov 29, 2010 at 07:08:16PM -0000, Garth Wells wrote:
>
> On 29/11/10 18:50, Johan Hake wrote:
> > On Monday November 29 2010 10:23:43 Mikael Mortensen wrote:
> >> On 29 November 2010 17:06, Johan Hake<681415@xxxxxxxxxxxxxxxxxx>  wrote:
> >>> On Monday November 29 2010 00:35:27 Mikael Mortensen wrote:
> >>>> Please don't.
> >>>>
> >>>> The subspace functionality is used for example to compute the
> >>>> streamfunction, where the subspace of the velocity VectorFunctionSpace
> >>>> is used. I also use the subspace functionality to assemble into parts
> >>>> of the Navier-Stokes coefficient matrix componentwise. For example
> >>>>
> >>>> uc = TrialFunction(V.sub(0))
> >>>> vc = TestFunction(V.sub(0))
> >>>> a = assemble(inner(grad(uc), grad(vc))*dx)
> >>>>
> >>>> and then I can copy this 'small' matrix to the three diagonal slots of
> >>>> the 3*3 Laplacian matrix that makes up for the whole velocity
> >>>> vectorfield. I understand this is not the regular way of assembling,
> >>>> but it is much faster than switching V.sub(0) above to V and
> >>>> assembling the whole thing by itself.
> >>>
> >>> What hinders you to do:
> >>>   Vs = FunctionSpace(mesh, "CG", 1)
> >>>   V  = MixedFunctionSpace([Vs]*3)
> >>>   ...
> >>>   uc = TrialFunction(Vs)
> >>>   vc = TestFunction(Vs)
> >>>
> >>>    a = assemble(inner(grad(uc), grad(vc))*dx)
> >>
> >> Nothing really. I used to do that. However, I want to be able to grab the
> >> velocity subpace when I'm computing the streamfunction as I want to use the
> >> same functionspace for the streamfunction as a velocity-component to avoid
> >> any interpolation. I understand that it's not strictly necessary, it's just
> >> a nice functionality the way I see it and I can use the same
> >> streamfunction-code for all velocity-functionspaces.
> >
> > Ok.
> >
> > What if we keep the original subspaces (without offset) in a protected
> > list.
> >
> >    _spaces = [Vs0, Vs1, Vs2]
> >
> > Then we add a kwarg: 'with_offset=True' to the 'sub' method. If 'with_offset'
> > is False we just return the "original" subspace without offset. You then need
> > to change your code to:
> >
> >    uc = TrialFunction(V.sub(0, False))
> >    vc = TestFunction(V.sub(0, False))
> >    a = assemble(inner(grad(uc), grad(vc))*dx)
> >
> > Then we make it impossible to instantiate a Function, TrialFunction,
> > TestFunction with a FunctionSpace including an offset.
> >
> > How do I read out from a FunctionSpace that it includes a ufc offset?
> >
>
> I've tried to eliminate 'ufc offsets' in the code - it's a recipe for
> disaster with renumbering.
>
> What we want to to know whether we have stand-alone function space or a
> view into another space. This can't be checked at the moment. We should
> be able to add a member function to FunctionaSpace to do this, but I
> need to think about whether or not it will be robust. We could check if
> a space is stand-alone or a view in the constructor of a Function.
>
> It would be nice to mirror the design that we have for Function, where
> we have deep and shallow copies. The idea would then be that only deep
> copies could be used to create Functions.
>
> Garth

We had a discussion a while back about adding a member function that
could be used to compare the size (as in the number of dofs) of the
subspace (sub dofmap) with the size of the bigger space. Maybe that
could be a solution.

--
Anders

>
> > This will diverge the C++ and Python implementation more...
> >
> > Johan
> >
> >> Mikael
> >>
> >>> Johan
> >>>
> >>>
> >>> Status in DOLFIN: Confirmed
> >>>
> >>> Bug description:
> >>> Hi,
> >>>
> >>> I have trouble using MixedFunctionSpace. Basically I want to project a
> >>>
> >>> function to a subspace of a MixedFunctionSpace:
> >>>    from dolfin import *
> >>>    mesh=UnitInterval(10)
> >>>    U = FunctionSpace(mesh, "CG", 1)
> >>>    V = FunctionSpace(mesh, "CG", 1)
> >>>    W=U*V
> >>>    f1=Function(W.sub(0))
> >>>    f1.vector()[:]=1.0
> >>>    #f2=project(f1, V)   # This works!
> >>>    f2=project(f1, W.sub(1))  # This doesn't!
> >>>
> >>> The output of that script is attached to the end of this question. Now,
> >>> the confusing thing is that the projection works fine if one projects to
> >>> V instead of W.sub(1), although they are mathematically the same spaces.
> >>>
> >>> I hope I haven't missed a similar question already reported.
> >>>
> >>> Best wishes,
> >>>
> >>> Simon
> >>>
> >>>
> >>> [0]PETSC ERROR:
> >>> ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> >>> probably memory access out of range
> >>> [0]PETSC ERROR: Try option -start_in_debugger or
> >>> -on_error_attach_debugger [0]PETSC ERROR: or see
> >>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#
> >>> Signal[0]PETSCERROR: or try http://valgrind.org on GNU/linux and Apple
> >>> Mac OS X to find memory corruption errors
> >>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> >>> and run
> >>> [0]PETSC ERROR: to get more information on the crash.
> >>> [0]PETSC ERROR: --------------------- Error Message
> >>> ------------------------------------
> >>> [0]PETSC ERROR: Signal received!
> >>> [0]PETSC ERROR:
> >>> ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4 15:34:52
> >>> CDT 2010
> >>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> >>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >>> [0]PETSC ERROR: See docs/index.html for manual pages.
> >>> [0]PETSC ERROR:
> >>> ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: Unknown Name on a linux-gnu named doodson by sf1409 Thu
> >>> Nov 25 13:17:44 2010
> >>> [0]PETSC ERROR: Libraries linked from
> >>> /build/buildd/petsc-3.1.dfsg/linux-gnu-c-opt/lib
> >>> [0]PETSC ERROR: Configure run at Fri Sep 10 04:57:14 2010
> >>> [0]PETSC ERROR: Configure options --with-shared --with-debugging=0
> >>> --useThreads 0 --with-clanguage=C++ --with-c-support
> >>> --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi
> >>> --with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack
> >>> --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse
> >>> --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]"
> >>> --with-spooles=1 --with-spooles-include=/usr/include/spooles
> >>> --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1
> >>> --with-hypre-dir=/usr --with-scotch=1
> >>> --with-scotch-include=/usr/include/scotch
> >>> --with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1
> >>> --with-hdf5-dir=/usr [0]PETSC ERROR:
> >>> ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> >>> unknown file
> >>> -------------------------------------------------------------------------
> >>> - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >>> with errorcode 59.
> >>>
> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >>> You may or may not see output from other processes, depending on
> >>> exactly when Open MPI kills them.
> >>> -------------------------------------------------------------------------
> >>> -
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Mailing list:
> >>> https://launchpad.net/~dolfin<https://launchpad.net/%7Edolfin>  Post to
> >>>    : dolfin@xxxxxxxxxxxxxxxxxxx
> >>> Unsubscribe :
> >>> https://launchpad.net/~dolfin<https://launchpad.net/%7Edolfin>  More help
> >>>    : https://help.launchpad.net/ListHelp
> >
>

-- 
Problem using sub-spaces
https://bugs.launchpad.net/bugs/681415
You received this bug notification because you are a member of DOLFIN
Team, which is subscribed to DOLFIN.

Status in DOLFIN: Confirmed

Bug description:
Hi,

I have trouble using MixedFunctionSpace. Basically I want to project a function to a subspace of a MixedFunctionSpace:

   from dolfin import *
   mesh=UnitInterval(10)
   U = FunctionSpace(mesh, "CG", 1)
   V = FunctionSpace(mesh, "CG", 1)
   W=U*V
   f1=Function(W.sub(0))
   f1.vector()[:]=1.0
   #f2=project(f1, V)   # This works!
   f2=project(f1, W.sub(1))  # This doesn't!


The output of that script is attached to the end of this question. Now, the confusing thing is that the projection works fine if one projects to V instead of W.sub(1), although they are mathematically the same spaces. 

I hope I haven't missed a similar question already reported. 

Best wishes,

Simon


[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4 15:34:52 CDT 2010
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a linux-gnu named doodson by sf1409 Thu Nov 25 13:17:44 2010
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.1.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Fri Sep 10 04:57:14 2010
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-clanguage=C++ --with-c-support --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]" --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1 --with-hdf5-dir=/usr
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------