New subject: Mixed system

15 Sep 2016

      I suspect Andrew is correct. However the deeper issue is that you edited
the installed file, which is never a safe thing to do. One must always edit
the file in the source directory and then (if necessary) re-install.

Anyway, I have committed Andrew's patch to the repository, so hopefully the
problem will go away if you do a git update.

Regards,

David

On Wed, 14 Sep 2016 at 18:39 Andrew McRae <A.T.T.McRae@bath.ac.uk> wrote:
...
Probably related to installing Firedrake in development mode or not.
I can't help any further here; I don't know if someone else can.
On 14 September 2016 at 16:13, Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
...
Ok, so I replace line 3366 in file “
/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py” with
the suggested patch, but I now get the error below.
Note that the error I get comes from file
firedrake/lib/python2.7/site-packages/pyop2/base.py
while in the reported issue the error comes from
firedrake/src/PyOP2/pyop2/base.py
so the two might not be related after all.
Thanks,
Anna.
...
Traceback (most recent call last):
  File "buoy-swe.py", line 89, in <module>
    F_solver = solver_F(phi0_5, eta1, mu0_5, I, w, phi0, eta0, Z0, W0,
step_b, etaR, phi_t, eta_t, mu_t, I_t, v1, v2, v3, v4, dt, Hb, H0, L,
dR_dt, g, rho, Mass, solvers_print);
  File "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Mixed
system/solvers.py", line 41, in solver_F
    F_solver = LinearVariationalSolver(F_problem,
solver_parameters=solvers_print)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 264, in __init__
    super(LinearVariationalSolver, self).__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 127, in __init__
    ctx = solving_utils._SNESContext(problem)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in __init__
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in <genexpr>
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 67, in assemble
    inverse=inverse, nest=nest)
  File "<decorator-gen-294>", line 2, in _assemble
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/utils.py",
line 62, in wrapper
    return f(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 179, in _assemble
    nest=nest)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/backends.py",
line 118, in __call__
    return t(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
122, in __new__
    args, kwargs = cls._process_args(*args, **kwargs)
  File "<decorator-gen-258>", line 2, in _process_args
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line
130, in wrapper
    return f(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3592, in _process_args
    if not (pair[0].toset == dsets[0].set and
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line
64, in __get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3373, in toset
    m.toset for m in self._maps))
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
156, in __new__
    obj = make_obj()
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
137, in make_obj
    obj.__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
977, in __init__
    "All components of a MixedSet must have the same number of layers."
AssertionError: All components of a MixedSet must have the same number of
layers.
...
**********************************************************
...
Dr Anna Kalogirou
Research Fellow
Department of Applied Mathematics
...
University of Leeds
Web: http://www1.maths.leeds.ac.uk/~matak/
Youtube: https://www.youtube.com/channel/UCUZAYHtVoiMqepQflisp66g
...
**********************************************************
Leverhulme Trust Early Career Fellow 2017-2019
**********************************************************
On 14 Sep 2016, at 16:00, Andrew McRae <A.T.T.McRae@bath.ac.uk> wrote:
Not as a branch, but you can change PyOP2 locally using the code at the
bottom of that post, "Suggested patch"
On 14 September 2016 at 15:54, Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
Hi Andrew,
...
Yes indeed, the two might be related. Was there a fix for the issue
reported on github?
Best, Anna.
**********************************************************
...
Dr Anna Kalogirou
Research Fellow
Department of Applied Mathematics
...
University of Leeds
Web: http://www1.maths.leeds.ac.uk/~matak/
Youtube: https://www.youtube.com/channel/UCUZAYHtVoiMqepQflisp66g
...
**********************************************************
Leverhulme Trust Early Career Fellow 2017-2019
**********************************************************
On 13 Sep 2016, at 16:34, Andrew McRae <A.T.T.McRae@bath.ac.uk> wrote:
Probably related to
https://github.com/firedrakeproject/firedrake/issues/862 (third post,
not first).  You might be able to adapt the fix; I haven't looked in detail.
On 12 September 2016 at 16:34, Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
Dear all,
...
Regarding the problem described in my email sent of Friday, I fixed a
minor typo and now get the error below. Any ideas what might be causing it?
Thanks!
Best, Anna.
Traceback (most recent call last):
  File "buoy-swe.py", line 89, in <module>
    F_solver = solver_F(phi0_5, eta1, mu0_5, I, w, phi0, eta0, Z0, W0,
step_b, etaR, phi_t, eta_t, mu_t, I_t, v1, v2, v3, v4, dt, Hb, H0, L,
dR_dt, g, rho, Mass, solvers_print);
  File "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Mixed
system/solvers.py", line 41, in solver_F
    F_solver = LinearVariationalSolver(F_problem,
solver_parameters=solvers_print)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 264, in __init__
    super(LinearVariationalSolver, self).__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 127, in __init__
    ctx = solving_utils._SNESContext(problem)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in __init__
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in <genexpr>
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 67, in assemble
    inverse=inverse, nest=nest)
  File "<decorator-gen-294>", line 2, in _assemble
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/utils.py",
line 62, in wrapper
    return f(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 163, in _assemble
    map_pairs.append((op2.DecoratedMap(test.cell_node_map(),
cell_domains),
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/functionspaceimpl.py",
line 646, in cell_node_map
    for i, s in enumerate(self._spaces))
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/backends.py",
line 118, in __call__
    return t(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
156, in __new__
    obj = make_obj()
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
137, in make_obj
    obj.__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3342, in __init__
    if not all(m is None or m.iterset == self.iterset for m in
self._maps):
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3342, in <genexpr>
    if not all(m is None or m.iterset == self.iterset for m in
self._maps):
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line
64, in __get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3366, in iterset
    return reduce(lambda a, b: a if a is None else a.iterset or b if b
is None else b.iterset, self._maps)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
3366, in <lambda>
    return reduce(lambda a, b: a if a is None else a.iterset or b if b
is None else b.iterset, self._maps)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/base.py", line
799, in __getattr__
    return getattr(self._parent, name)
AttributeError: 'Set' object has no attribute ‘iterset'
**********************************************************
...
Dr Anna Kalogirou
Research Fellow
Department of Applied Mathematics
...
University of Leeds
Web: http://www1.maths.leeds.ac.uk/~matak/
Youtube: https://www.youtube.com/channel/UCUZAYHtVoiMqepQflisp66g
...
**********************************************************
Leverhulme Trust Early Career Fellow 2017-2019
**********************************************************
On 9 Sep 2016, at 17:37, Anna Kalogirou <a.kalogirou@leeds.ac.uk>
wrote:
Hi David,
I have tried to implement my problem (attached) using the real function
spaces but I get the error below. The code can be found here
<https://bitbucket.org/annakalog/buoy2d/src/d6a805b6a8d0/Mixed%20system/?at=master>
.
I define the real space by V_R = FunctionSpace(mesh, "R", 0). Is that
correct?
Also, is it a problem that the linear part of the variational form does
not depend on one of the test functions from the mixed function space (only
depends on v1, v2, v3 and not v4)?
Best,
Anna.
Traceback (most recent call last):
  File "buoy-swe.py", line 89, in <module>
    F_solver = solver_F(phi0_5, eta1, mu0_5, I, w, phi0, eta0, Z0, W0,
step_b, etaR, phi_t, eta_t, mu_t, I_t, v1, v2, v3, v4, dt, Hb, H0, L,
dR_dt, g, rho, Mass, solvers_print);
  File "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Mixed
system/solvers.py", line 41, in solver_F
    F_solver = LinearVariationalSolver(F_problem,
solver_parameters=solvers_print)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 264, in __init__
    super(LinearVariationalSolver, self).__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py",
line 127, in __init__
    ctx = solving_utils._SNESContext(problem)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in __init__
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py",
line 107, in <genexpr>
    for problem in problems)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 67, in assemble
    inverse=inverse, nest=nest)
  File "<decorator-gen-294>", line 2, in _assemble
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/utils.py",
line 62, in wrapper
    return f(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/assemble.py",
line 101, in _assemble
    inverse=inverse)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py",
line 307, in compile_form
    number_map).kernels
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
198, in __new__
    obj = make_obj()
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line
188, in make_obj
    obj.__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py",
line 212, in __init__
    tree = tsfc_compile_form(form, prefix=name, parameters=parameters)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/tsfc/driver.py", line
47, in compile_form
    do_estimate_degrees=True)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/algorithms/compute_form_data.py",
line 386, in compute_form_data
    check_form_arity(preprocessed_form,
self.original_form.arguments())  # Currently testing how fast this is
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
line 152, in check_form_arity
    check_integrand_arity(itg.integrand(), arguments)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
line 145, in check_integrand_arity
    args = map_expr_dag(rules, expr, compress=False)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/corealg/map_dag.py",
line 37, in map_expr_dag
    result, = map_expr_dags(function, [expression], compress=compress)
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/corealg/map_dag.py",
line 86, in map_expr_dags
    r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in
v.ufl_operands])
  File
"/Users/matak/firedrake/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
line 42, in sum
    raise ArityMismatch("Adding expressions with non-matching form
arguments {0} vs {1}.".format(a, b))
ufl.algorithms.check_arities.ArityMismatch: Adding expressions with
non-matching form arguments () vs
(Argument(WithGeometry(IndexedProxyFunctionSpace(<firedrake.mesh.ExtrudedMeshTopology
object at 0x113e6b890>, TensorProductElement(FiniteElement('Lagrange',
interval, 1), FiniteElement('Lagrange', interval, 1),
cell=TensorProductCell(interval, interval)), name=None, index=0,
component=None),
Mesh(VectorElement(TensorProductElement(FiniteElement('Lagrange', interval,
1), FiniteElement('Lagrange', interval, 1),
cell=TensorProductCell(interval, interval)), dim=2), 4)), 1, None),).
<coupled_system.pdf>
On 18 Aug 2016, at 16:03, David Ham <david.ham@imperial.ac.uk> wrote:
Hi Anna,
Real function spaces now pass some simple tests, at least on my
machine. You need the real-function-space branch of firedrake, and the
globals_matrices branch of PyOP2. It's not going to get merged before I
disappear for a week - not least because I need to update documentation.
However you should be able to test it out on the branches.
Regards,
David
On Wed, 10 Aug 2016 at 16:58 David Ham <David.Ham@imperial.ac.uk>
wrote:
...
Unfortunately, It isn't as simple as saying "no mpi". MPI pervades
Firedrake. Unless real function spaces play nicely with communicators,
Firedrake will simply crash. I'm sorry that this feature is not available
right now, but it actually does require significant work.
On Wed, 10 Aug 2016 at 16:51 Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
...
Yes indeed, but I believe David would want to make it work for all
cases. The merge is necessary in order to proceed with my simulations, so
an update as soon as possible would be greatly appreciated.
Best, Anna.
On 10 Aug 2016, at 16:29, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
We would already be helped for the case without MPI, I think that is
correct, Anna?
*From:* firedrake-bounces@imperial.ac.uk <
firedrake-bounces@imperial.ac.uk> on behalf of David Ham <
David.Ham@imperial.ac.uk>
*Sent:* Wednesday, August 10, 2016 10:01 AM
*To:* firedrake
*Subject:* Re: [firedrake] Mixed system
The short version is it depends on when I find some time to work on
it. It is not simply the case that we have new features lying around
waiting to be merged. The current proximate issue is to make the real
spaces work properly with MPI communicators. I can't guarantee that will be
the last issue.
On Tue, 9 Aug 2016 at 17:37 Onno Bokhove <O.Bokhove@leeds.ac.uk>
wrote:
> It is possible to merge the branch for the mixed system
> relatively soon?
> Anna's results are relevant for the grant application Colin and I
> aim to submit in Sept. on further wave-ship modelling.
> Sorry for asking!
> ------------------------------
> *From:* firedrake-bounces@imperial.ac.uk <
> firedrake-bounces@imperial.ac.uk> on behalf of David Ham <
> David.Ham@imperial.ac.uk>
> *Sent:* Friday, August 5, 2016 11:37:23 AM
> *To:* firedrake
> *Subject:* Re: [firedrake] Mixed system
>
>
>
> On Fri, 5 Aug 2016 at 11:31 Anna Kalogirou <a.kalogirou@leeds.ac.uk>
> wrote:
>
>> Hi Kramer,
>>
>> Thank you for the reply.
>>
>> The only problem I see with the solution you suggest, is that both
>> I and
>> lambda will be trial functions, so both terms should be on the
>> bilinear
>> part of the variational form.
>>
>
> Not quite. I and lambda together form a Function in a mixed finite
> element space. You solve for both of them together, just like pressure and
> velocity in a fluid simulation.
>
>
>>
>> I could, of course, define a residual and solve everything using
>> nonlinear solvers, but I don't know how efficient that would be.
>>
>
> I think you are confused. None of the relevant issues change in the
> nonlinear case. After all, the nonlinear solver will differentiate the
> residual to create a bilinear form anyway.
>
> Incidentally, there is no particular reason to believe that writing
> the problem in nonlinear form would be inefficient.
>
> Regards,
>
> David
>
>
>>
>> Best,
>>
>> Anna.
>>
>>   Dr Anna Kalogirou
>>   Research Fellow
>>   School of Mathematics
>>   University of Leeds
>>
>>   http://www1.maths.leeds.ac.uk/~matak/
>>
>> On 04/08/16 17:29, Stephan Kramer wrote:
>> > On 27/07/16 11:01, Anna Kalogirou wrote:
>> >> Dear all,
>> >>
>> >> I am trying to solve the system found in the attached pdf as a
>> mixed
>> >> system. I want to solve the same
>> >> problem as the one found here
>> >> <
>> https://bitbucket.org/annakalog/buoy2d/src/14334d3c20b9f10ed7c1246cde9e3cb60...
>> >,
>> >>
>> >> but with the use of Schur complements and not linear algebra.
>> >>
>> >> In a previous discussion about this problem, Lawrence mentioned
>> that the
>> >> test function for integral(lambda*Theta(x-Lp)dx) needs to be
>> considered
>> >> as coming from the real space of constant functions. Could you
>> please
>> >> elaborate on this?
>> >
>> > My guess at what Lawrence means is (it's how I would probably
>> approach
>> > it), is that you add an additional equation that says
>> >
>> >  (1)  I = integral(lambda*Theta(x-Lp)dx)
>> >
>> > and then substitute I in your third equation. Equation (1) can
>> > be turned into a finite element weak formulation by considering
>> the
>> > function space of functions that are constant over the entire
>> domain
>> > This function space is just 1-dimensional and therefore
>> equivalent to
>> > the space of reals R and hence we denote this function space of
>> > constants simply as R. Then we can consider I to be a trial
>> function
>> > in R, and with a test function v4 in R, we can write:
>> >
>> >   v4*lambda*Theta(x-Lp)*dx == v4*I*dx/area(domain)
>> >
>> > This is a proper finite element equation that you could solve in
>> > conjuction with the other equations. I believe however that this
>> > function space R is not currently implemented in Firedrake. It is
>> > available in fenics, and is on the wishlist.
>> >
>> > Cheers
>> > Stephan
>> >
>> > _______________________________________________
>> > firedrake mailing list
>> > firedrake@imperial.ac.uk
>> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake@imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
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Re: [firedrake] Mixed system

David Ham

David Ham

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