dolfin team mailing list archive

[Johan Hake <681415@xxxxxxxxxxxxxxxxxx>]

On Monday November 29 2010 11:08:16 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.

Ok.

> 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.

Agree. If such method is exposed to DOLFIN we can then add a check for Test 
and Trial-Functions in the PyDOLFIN layer.

> 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.

Agree.

Johan

> Garth
> 
> > This will diverge the C++ and Python implementation more...
> > 
> > Johan
> > 
> >> Mikael
> >> 
> >>> Johan
> >>> 
> >>> --
> >>> 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.htm
> >>> l# 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.
--------------------------------------------------------------------------