A collapsed function space lacks the python layer

[Martin Sandve Alnæs]

When trying to convert a VariationalProblem based solve
to using solve(), I created a Function for the solution,
and got the message that I should collapse the function
space (which was a subspace). So I call V.collapse(),
but the new function space is not wrapped in the python
layer. Details:

In [23]: V = VectorFunctionSpace(mesh, "CG", 1)

In [24]: U = V.sub(0)

In [25]: W = U.collapse()

In [26]: f = Function(V)

In [27]: g = Function(U)
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)

/home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()

/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/function.pyc in __init__(self, *args)
    139 if len(args) == 1:
    140 # Instantiate cpp base classes

--> 141 cpp.Function.__init__(self, V)
    142 elif len(args) == 2:
    143 # If passing FunctionSpace together with cpp.Function

/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/cpp.pyc in __init__(self, *args)
  16161
  16162 """
> 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
  16164 __swig_destroy__ = _cpp.delete_Function
  16165 def assign(self, *args):

RuntimeError: *** Error: Cannot create Functions using subspaces. Consider collapsing the FunctionSpace.

In [28]: h = Function(W)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)

/home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()

/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/function.pyc in __init__(self, *args)
    104
    105 if not isinstance(args[0], (FunctionSpaceBase, Function)):
--> 106 raise TypeError, "expected a FunctionSpace or a Function as argument 1"
    107
    108 # If using the copy constuctor

TypeError: expected a FunctionSpace or a Function as argument 1

In [29]: type(V)
Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>

In [30]: type(U)
Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>

In [31]: type(W)
Out[31]: <class 'dolfin.cpp.FunctionSpace'>

[Garth Wells (garth-wells)]

Would it help if 'collapse' returned a shared_ptr rather than a plain pointer, as it does now?

[Johan Hake (johan-hake)]

On Wednesday September 21 2011 12:08:51 Garth Wells wrote:
> Would it help if 'collapse' returned a shared_ptr rather than a plain
> pointer, as it does now?

AFAIK it already returns a shared_ptr version.

We have these kindof problems when we have built a Python class around the cpp
class. We just need to manually rewrap the returned object to the Python
class. For FunctionSpace we have a particular class to handle this situation
FunctionSpaceFromCpp.

I will soon commit a fix.

Johan

> > 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>
> 16164 __swig_destroy__ = _cpp.delete_Function
> 16165 def assign(self, *args):
>
> RuntimeError: *** Error: Cannot create Functions using subspaces.
> Consider collapsing the FunctionSpace.
>
> In [28]: h = Function(W)
>
> --------------------------------------------------------------------------
> - TypeError Traceback (most recent call
> last)
>
> /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
>
>
> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/f
> unction.pyc in __init__(self, *args) 104
> 105 if not isinstance(args[0], (FunctionSpaceBase,
> Function)): --> 106 raise TypeError, "expected a FunctionSpace
> or a Function as argument 1" 107
> 108 # If using the copy constuctor
>
>
> TypeError: expected a FunctionSpace or a Function as argument 1
>
> In [29]: type(V)
> Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>
>
> In [30]: type(U)
> Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>
>
> In [31]: type(W)
> Out[31]: <class 'dolfin.cpp.FunctionSpace'>
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions

[Garth Wells (garth-wells)]

On 21 September 2011 20:34, Johan Hake <email address hidden> wrote:
> On Wednesday September 21 2011 12:08:51 Garth Wells wrote:
>> Would it help if 'collapse' returned a shared_ptr rather than a plain
>> pointer, as it does now?
>
> AFAIK it already returns a shared_ptr version.
>

It's a raw pointer. I guess we could run into some memory issues.

Garth

> We have these kindof problems when we have built a Python class around the cpp
> class. We just need to manually rewrap the returned object to the Python
> class. For FunctionSpace we have a particular class to handle this situation
> FunctionSpaceFromCpp.
>
> I will soon commit a fix.
>
> Johan
>
>
>>   > 16163         _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>>
>>     16164     __swig_destroy__ = _cpp.delete_Function
>>     16165     def assign(self, *args):
>>
>>   RuntimeError: *** Error: Cannot create Functions using subspaces.
>>   Consider collapsing the FunctionSpace.
>>
>>   In [28]: h = Function(W)
>>
>> --------------------------------------------------------------------------
>> - TypeError                                 Traceback (most recent call
>> last)
>>
>>   /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
>>
>>
>> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/f
>> unction.pyc in __init__(self, *args) 104
>>       105         if not isinstance(args[0], (FunctionSpaceBase,
>> Function)): --> 106             raise TypeError, "expected a FunctionSpace
>> or a Function as argument 1" 107
>>       108         # If using the copy constuctor
>>
>>
>>   TypeError: expected a FunctionSpace or a Function as argument 1
>>
>>   In [29]: type(V)
>>   Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>
>>
>>   In [30]: type(U)
>>   Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>
>>
>>   In [31]: type(W)
>>   Out[31]: <class 'dolfin.cpp.FunctionSpace'>
>>
>> To manage notifications about this bug go to:
>> https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions
>
>
> ** Changed in: dolfin
>       Status: In Progress => Fix Committed
>
> --
> You received this bug notification because you are a member of DOLFIN
> Core Team, which is subscribed to DOLFIN.
> https://bugs.launchpad.net/bugs/855362
>
> Title:
>  A collapsed function space lacks the python layer
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions
>

--
Garth N. Wells
Department of Engineering, University of Cambridge
http://www.eng.cam.ac.uk/~gnw20

[Johan Hake (johan-hake)]

On Wednesday September 21 2011 12:48:59 Garth Wells wrote:
> On 21 September 2011 20:34, Johan Hake <email address hidden> wrote:
> > On Wednesday September 21 2011 12:08:51 Garth Wells wrote:
> >> Would it help if 'collapse' returned a shared_ptr rather than a plain
> >> pointer, as it does now?
> >
> > AFAIK it already returns a shared_ptr version.
>
> It's a raw pointer. I guess we could run into some memory issues.

We are not talking about the same collapse :)

I guess you are talking about DofMap::collapse, and this bug is about
FunctionSpace::collapse.

Using a shared_ptr version of the DofMap::collapse would make sense. However,
we do not provide a typemap for boost::unordered_set so it is not usable from
Python anyhow. But that can be fixed :)

Johan

> Garth
>
> > We have these kindof problems when we have built a Python class around
> > the cpp class. We just need to manually rewrap the returned object to
> > the Python class. For FunctionSpace we have a particular class to handle
> > this situation FunctionSpaceFromCpp.
> >
> > I will soon commit a fix.
> >
> > Johan
> >
> >> > 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
> >>
> >> 16164 __swig_destroy__ = _cpp.delete_Function
> >> 16165 def assign(self, *args):
> >>
> >> RuntimeError: *** Error: Cannot create Functions using subspaces.
> >> Consider collapsing the FunctionSpace.
> >>
> >> In [28]: h = Function(W)
> >>
> >> ------------------------------------------------------------------------
> >> -- - TypeError Traceback (most recent
> >> call last)
> >>
> >> /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
> >>
> >>
> >> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions
> >> /f unction.pyc in __init__(self, *args) 104
> >> 105 if not isinstance(args[0], (FunctionSpaceBase,
> >> Function)): --> 106 raise TypeError, "expected a
> >> FunctionSpace or a Function as argument 1" 107
> >> 108 # If using the copy constuctor
> >>
> >>
> >> TypeError: expected a FunctionSpace or a Function as argument 1
> >>
> >> In [29]: type(V)
> >> Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>
> >>
> >> In [30]: type(U)
> >> Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>
> >>
> >> In [31]: type(W)
> >> Out[31]: <class 'dolfin.cpp.FunctionSpace'>
> >>
> >> To manage notifications about this bug go to:
> >> https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions
> >
> > ** Changed in: dolfin
> > Status: In Progress => Fix Committed
> >
> > --
> > You received this bug notification because you are a member of DOLFIN
> > Core Team, which is subscribed to DOLFIN.
> > https://bugs.launchpad.net/bugs/855362
> >
> > Title:
> > A collapsed function space lacks the python layer
> >
> > To manage notifications about this bug go to:
> > https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions
> >
> > 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>
> 16164 __swig_destroy__ = _cpp.delete_Function
> 16165 ...

[Martin Sandve Alnæs (martinal)]

Now Function doesn't see that a function space is collapsed, and I'm back to the original problem, not being able to create a Function from a subspace:

    V = u.function_space().sub(0)
    ...
    V2 = V.collapse()
    psi = Function(V2)

Traceback (most recent call last):
  File "./ns", line 141, in <module>
    sys.exit(main(sys.argv[1:]))
  File "./ns", line 124, in main
    u, p = solver.solve(problem)
  File "/home/martinal/dev/cbc/nsbench/work/solvers/ipcs.py", line 108, in solve
    self.update(problem, t, u1, p1)
  File "/home/martinal/dev/cbc/nsbench/work/solvers/solverbase.py", line 75, in update
    M = problem.functional(t, u, p)
  File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line 61, in functional
    psi = StreamFunction(u)
  File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line 103, in StreamFunction
    psi = Function(V2)
  File "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/function.py", line 141, in __init__
    cpp.Function.__init__(self, V)
  File "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/cpp.py", line 16532, in __init__
    _cpp.Function_swiginit(self,_cpp.new_Function(*args))
RuntimeError: *** Error: Cannot create Functions using subspaces. Consider collapsing the FunctionSpace.

The code is from
  lp:~martinal/nsbench/cleanup
I run it with
  ./ns drivencavity ipcs

[Johan Hake (johan-hake)]

Then I think the bug has changed to:

  Cannont create Function from subspaces.

Johan

On Thursday September 22 2011 01:25:09 Martin Sandve Alnæs wrote:
> Now Function doesn't see that a function space is collapsed, and I'm
> back to the original problem, not being able to create a Function from a
> subspace:
>
> V = u.function_space().sub(0)
> ...
> V2 = V.collapse()
> psi = Function(V2)
>
> Traceback (most recent call last):
> File "./ns", line 141, in <module>
> sys.exit(main(sys.argv[1:]))
> File "./ns", line 124, in main
> u, p = solver.solve(problem)
> File "/home/martinal/dev/cbc/nsbench/work/solvers/ipcs.py", line 108, in
> solve self.update(problem, t, u1, p1)
> File "/home/martinal/dev/cbc/nsbench/work/solvers/solverbase.py", line
> 75, in update M = problem.functional(t, u, p)
> File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line
> 61, in functional psi = StreamFunction(u)
> File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line
> 103, in StreamFunction psi = Function(V2)
> File
> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/
> function.py", line 141, in __init__ cpp.Function.__init__(self, V)
> File
> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/cpp.py",
> line 16532, in __init__
> _cpp.Function_swiginit(self,_cpp.new_Function(*args))
> RuntimeError: *** Error: Cannot create Functions using subspaces. Consider
> collapsing the FunctionSpace.
>
>
> The code is from
> lp:~martinal/nsbench/cleanup
> I run it with
> ./ns drivencavity ipcs
>
> > 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>
> 16164 __swig_destroy__ = _cpp.delete_Function
> 16165 def assign(self, *args):
>
> RuntimeError: *** Error: Cannot create Functions using subspaces.
> Consider collapsing the FunctionSpace.
>
> In [28]: h = Function(W)
>
> --------------------------------------------------------------------------
> - TypeError Traceback (most recent call
> last)
>
> /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
>
>
> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/f
> unction.pyc in __init__(self, *args) 104
> 105 if not isinstance(args[0], (FunctionSpaceBase,
> Function)): --> 106 raise TypeError, "expected a FunctionSpace
> or a Function as argument 1" 107
> 108 # If using the copy constuctor
>
>
> TypeError: expected a FunctionSpace or a Function as argument 1
>
> In [29]: type(V)
> Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>
>
> In [30]: type(U)
> Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>
>
> In [31]: type(W)
> Out[31]: <class 'dolfin.cpp.FunctionSpace'>
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/dolfin/+bug/855362/+subscriptions

[Martin Sandve Alnæs (martinal)]

On 22 September 2011 17:02, Johan Hake <email address hidden> wrote:
> Then I think the bug has changed to:
>
>  Cannont create Function from subspaces.
>
> Johan

No, not really. The way I understand the message, is that collapse is
supposed to return something that is _not_ a subspace. So your new
python layer fix for collapse doesn't quite work.

Martin

> On Thursday September 22 2011 01:25:09 Martin Sandve Alnæs wrote:
>> Now Function doesn't see that a function space is collapsed, and I'm
>> back to the original problem, not being able to create a Function from a
>> subspace:
>>
>>     V   = u.function_space().sub(0)
>>     ...
>>     V2 = V.collapse()
>>     psi = Function(V2)
>>
>> Traceback (most recent call last):
>>   File "./ns", line 141, in <module>
>>     sys.exit(main(sys.argv[1:]))
>>   File "./ns", line 124, in main
>>     u, p = solver.solve(problem)
>>   File "/home/martinal/dev/cbc/nsbench/work/solvers/ipcs.py", line 108, in
>> solve self.update(problem, t, u1, p1)
>>   File "/home/martinal/dev/cbc/nsbench/work/solvers/solverbase.py", line
>> 75, in update M = problem.functional(t, u, p)
>>   File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line
>> 61, in functional psi = StreamFunction(u)
>>   File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py", line
>> 103, in StreamFunction psi = Function(V2)
>>   File
>> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/
>> function.py", line 141, in __init__ cpp.Function.__init__(self, V)
>>   File
>> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/cpp.py",
>> line 16532, in __init__
>> _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>> RuntimeError: *** Error: Cannot create Functions using subspaces. Consider
>> collapsing the FunctionSpace.
>>
>>
>> The code is from
>>   lp:~martinal/nsbench/cleanup
>> I run it with
>>   ./ns drivencavity ipcs
>>
>>   > 16163         _cpp.Function_swiginit(self,_cpp.new_Function(*args))
>>
>>     16164     __swig_destroy__ = _cpp.delete_Function
>>     16165     def assign(self, *args):
>>
>>   RuntimeError: *** Error: Cannot create Functions using subspaces.
>>   Consider collapsing the FunctionSpace.
>>
>>   In [28]: h = Function(W)
>>
>> --------------------------------------------------------------------------
>> - TypeError                                 Traceback (most recent call
>> last)
>>
>>   /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
>>
>>
>> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions/f
>> unction.pyc in __init__(self, *args) 104
>>       105         if not isinstance(args[0], (FunctionSpaceBase,
>> Function)): --> 106             raise TypeError, "expected a FunctionSpace
>> or a Function as argument 1" 107
>>       108         # If using the copy constuctor
>>
>>
>>   TypeError: expected a FunctionSpace or a Function as argument 1
>>
>>   In [29]: type(V)
>>   Out[29]: <class 'dolfin.functions.functionspace.VectorFunctionSpace'>
>>
>>   In [30]: type(U)
>>   Out[30]: <class 'dolfin.functions.functionspace.FunctionSpaceFromCpp'>
>>
>>   In [31]: type(W)
>>   Out[31]: <class 'dolfin.cpp.Function...

[Johan Hake (johan-hake)]

On Thursday September 22 2011 13:54:59 Martin Sandve Alnæs wrote:
> On 22 September 2011 17:02, Johan Hake <email address hidden> wrote:
> > Then I think the bug has changed to:
> >
> > Cannont create Function from subspaces.
> >
> > Johan
>
> No, not really. The way I understand the message, is that collapse is
> supposed to return something that is _not_ a subspace. So your new
> python layer fix for collapse doesn't quite work.

Well, _now_ it should be fixed... A small bug was introduced and hidden by an
erronious unit test :P

Johan

> Martin
>
> > On Thursday September 22 2011 01:25:09 Martin Sandve Alnæs wrote:
> >> Now Function doesn't see that a function space is collapsed, and I'm
> >> back to the original problem, not being able to create a Function from a
> >> subspace:
> >>
> >> V = u.function_space().sub(0)
> >> ...
> >> V2 = V.collapse()
> >> psi = Function(V2)
> >>
> >> Traceback (most recent call last):
> >> File "./ns", line 141, in <module>
> >> sys.exit(main(sys.argv[1:]))
> >> File "./ns", line 124, in main
> >> u, p = solver.solve(problem)
> >> File "/home/martinal/dev/cbc/nsbench/work/solvers/ipcs.py", line 108,
> >> in solve self.update(problem, t, u1, p1)
> >> File "/home/martinal/dev/cbc/nsbench/work/solvers/solverbase.py", line
> >> 75, in update M = problem.functional(t, u, p)
> >> File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py",
> >> line 61, in functional psi = StreamFunction(u)
> >> File "/home/martinal/dev/cbc/nsbench/work/problems/drivencavity.py",
> >> line 103, in StreamFunction psi = Function(V2)
> >> File
> >> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/function
> >> s/ function.py", line 141, in __init__ cpp.Function.__init__(self, V)
> >> File
> >> "/opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/cpp.py",
> >> line 16532, in __init__
> >> _cpp.Function_swiginit(self,_cpp.new_Function(*args))
> >> RuntimeError: *** Error: Cannot create Functions using subspaces.
> >> Consider collapsing the FunctionSpace.
> >>
> >>
> >> The code is from
> >> lp:~martinal/nsbench/cleanup
> >> I run it with
> >> ./ns drivencavity ipcs
> >>
> >> > 16163 _cpp.Function_swiginit(self,_cpp.new_Function(*args))
> >>
> >> 16164 __swig_destroy__ = _cpp.delete_Function
> >> 16165 def assign(self, *args):
> >>
> >> RuntimeError: *** Error: Cannot create Functions using subspaces.
> >> Consider collapsing the FunctionSpace.
> >>
> >> In [28]: h = Function(W)
> >>
> >> ------------------------------------------------------------------------
> >> -- - TypeError Traceback (most recent
> >> call last)
> >>
> >> /home/martinal/dev/cbc/nsbench/work/<ipython console> in <module>()
> >>
> >>
> >> /opt/fenics/dorsal-unstable/lib/python2.7/site-packages/dolfin/functions
> >> /f unction.pyc in __init__(self, *args) 104
> >> 105 if not isinstance(args[0], (FunctionSpaceBase,
> >> Function)): --> 106 raise TypeError, "expected a
> >> FunctionSpace or a Function as argument 1" 107
> >> 108 # If using the copy constuctor
> >>...