New subject: Mixed system

16 Sep 2016

      Hi Anna,

Are you certain that the test you are running is the one you pointed to on
the web. Line 89 from your error message does not appear in the version on
bitbucket, and the last commit was 4 days ago.

Regards,

David

On Fri, 16 Sep 2016 at 17:03 Anna Kalogirou <A.Kalogirou@leeds.ac.uk> wrote:
...
When I run
firedrake-zenodo -m "Versions I am using now”
I get
Failed to retrieve git hash for optional component 'SLOPE', continuing
without it
The file firedrake.json contains the following (up to ufl it’s the same
as yours):
{"fiat": "1bc440ca34d4b127897cf5a36d63bf8a41a3d55c", "COFFEE":
"8e03328d659fd8d8871bf5b7bc3f08b769f0ab9d", "ufl":
"2fc6d00f7e4b5e0639c6d01f27f9b2bbc0d4696e", "firedrake":
"71cf933f05508427287dc6464e15d2d7adf1b179", "tsfc":
"f867938c58f475f1cd332421e2bf14cffa2f5aef", "petsc4py":
"0b590afa9d3c42e0b4f863061b6e082d6f0227f6", "petsc":
"21143a8c817f512a23f8e18da648891eb40f5217", "PyOP2":
"d9ea13e1e17fcb1e05adcf1db31bd8190974520d", "message": "Versions I am using
now"}
On 16 Sep 2016, at 16:49, David Ham <David.Ham@imperial.ac.uk> wrote:
OK. Let's do some sanity checking.
1. Please confirm that the current firedrake checkout is in developer mode
and has always been in developer mode (I can see that it is in developer
mode from the error message but I want to make sure there cannot be stale
files around from a non-developer mode past).
2. Run firedrake-clean and check that the error still occurs.
2. Please run the following command:
firedrake-zenodo -m "Versions I am using now"
This will create a file firedrake.json . Please check that its contents
exactly match what is below:
{"fiat": "1bc440ca34d4b127897cf5a36d63bf8a41a3d55c", "COFFEE":
"8e03328d659fd8d8871bf5b7bc3f08b769f0ab9d", "ufl":
"2fc6d00f7e4b5e0639c6d01f27f9b2bbc0d4696e", "firedrake":
"71cf933f05508427287dc6464e15d2d7adf1b179", "tsfc":
"f867938c58f475f1cd332421e2bf14cffa2f5aef", "petsc4py":
"0b590afa9d3c42e0b4f863061b6e082d6f0227f6", "petsc":
"21143a8c817f512a23f8e18da648891eb40f5217", "PyOP2":
"d9ea13e1e17fcb1e05adcf1db31bd8190974520d", "message": "Versions I am using
now"}
On Fri, 16 Sep 2016 at 16:28 Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
...
That is the same version I have.
On 16 Sep 2016, at 16:23, David Ham <David.Ham@imperial.ac.uk> wrote:
Hi Anna,
Please confirm the git revision of your PyOP2. You can retrieve this by
typing the following command in the PyOP2 directory:
git rev-parse HEAD
You should have:
d9ea13e1e17fcb1e05adcf1db31bd8190974520d
Regards,
David
On Fri, 16 Sep 2016 at 15:59 Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
...
Hi David,
Thank you for the reply. Indeed, the problem was with the virtualenv; I
had to deactivate and activate it again. Unfortunately I still get errors,
which are probably due to the firedrake I have installed (since you said
that it works on your computer):
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/src/firedrake/firedrake/variational_solver.py",
line 264, in __init__
    super(LinearVariationalSolver, self).__init__(*args, **kwargs)
  File
"/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py",
line 127, in __init__
    ctx = solving_utils._SNESContext(problem)
  File
"/Users/matak/firedrake/src/firedrake/firedrake/solving_utils.py", line
107, in __init__
    for problem in problems)
  File
"/Users/matak/firedrake/src/firedrake/firedrake/solving_utils.py", line
107, in <genexpr>
    for problem in problems)
  File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py",
line 67, in assemble
    inverse=inverse, nest=nest)
  File "<decorator-gen-294>", line 2, in _assemble
  File "/Users/matak/firedrake/src/firedrake/firedrake/utils.py", line
62, in wrapper
    return f(*args, **kwargs)
  File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py",
line 179, in _assemble
    nest=nest)
  File "/Users/matak/firedrake/src/PyOP2/pyop2/backends.py", line 118,
in __call__
    return t(*args, **kwargs)
  File "/Users/matak/firedrake/src/PyOP2/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/src/PyOP2/pyop2/utils.py", line 130, in
wrapper
    return f(*args, **kwargs)
  File "/Users/matak/firedrake/src/PyOP2/pyop2/base.py", line 3591, in
_process_args
    if not (pair[0].toset == dsets[0].set and
  File "/Users/matak/firedrake/src/PyOP2/pyop2/utils.py", line 64, in
__get__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  File "/Users/matak/firedrake/src/PyOP2/pyop2/base.py", line 3372, in
toset
    m.toset for m in self._maps))
  File "/Users/matak/firedrake/src/PyOP2/pyop2/caching.py", line 156, in
__new__
    obj = make_obj()
  File "/Users/matak/firedrake/src/PyOP2/pyop2/caching.py", line 137, in
make_obj
    obj.__init__(*args, **kwargs)
  File "/Users/matak/firedrake/src/PyOP2/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.
On 16 Sep 2016, at 15:47, David Ham <David.Ham@imperial.ac.uk> wrote:
Hi Anna,
Your code works for me (in the sense that it appears to run without
error. I have no idea whether the answer is right ;)
Please also note that Miklos is correct: your error is definitely from a
global firedrake install. You can tell because the paths start /usr/local.
Your previous error messages are from a local install. You can tell that
because the paths start /Users/matak . Are you sure your virtualenv is
active?
Regards,
David
On Fri, 16 Sep 2016 at 15:16 Anna Kalogirou <A.Kalogirou@leeds.ac.uk>
wrote:
...
During the past few days I have been working on my laptop (not the
desktop at Leeds) and I don’t believe there are multiple installations of
firedrake on this machine.
Can someone please try to run my code
<https://bitbucket.org/annakalog/buoy2d/src/673fef3466b06c98ac11f5a120ff42117679d41e/Mixed%20system/?at=master> so
that we know for sure if the problem is in my code or related with the
installation? Thanks.
On 16 Sep 2016, at 14:54, Colin Cotter <colin.cotter@imperial.ac.uk>
wrote:
Ah yes, that tallies with Daniel Ruprecht's reports that Firedrake is
part of the standard installation at Leeds!
On 16 September 2016 at 14:53, Homolya, Miklós <
m.homolya14@imperial.ac.uk> wrote:
It seems that the Firedrake you're importing is a system wide
...
installation. No wonder that updating your own installation doesn't fix it.
Get Outlook for Android <https://aka.ms/ghei36>
...
On Thu, Sep 15, 2016 at 8:33 PM +0100, "Anna Kalogirou" <
A.Kalogirou@leeds.ac.uk> wrote:
Ok thanks, I get the error below:
Traceback (most recent call last):
File "buoy-swe.py", line 6, in <module>
...
from firedrake import *
  File "/usr/local/lib/python2.7/site-packages/firedrake/__init__.py",
line 30, in <module>
    from assemble import *
  File "/usr/local/lib/python2.7/site-packages/firedrake/assemble.py",
line 8, in <module>
    import assembly_cache
  File
"/usr/local/lib/python2.7/site-packages/firedrake/assembly_cache.py", line
40, in <module>
    import function
  File "/usr/local/lib/python2.7/site-packages/firedrake/function.py",
line 9, in <module>
    import assemble_expressions
  File
"/usr/local/lib/python2.7/site-packages/firedrake/assemble_expressions.py",
line 15, in <module>
    import functionspace
  File
"/usr/local/lib/python2.7/site-packages/firedrake/functionspace.py", line
10, in <module>
    import dmplex
ImportError:
dlopen(/usr/local/lib/python2.7/site-packages/firedrake/dmplex.so, 2):
Library not loaded:
/usr/local/lib/python2.7/site-packages/petsc/lib/libpetsc.3.05.2.dylib
  Referenced from:
/usr/local/lib/python2.7/site-packages/firedrake/dmplex.so
  Reason: image not found
On 15 Sep 2016, at 18:21, Andrew McRae <A.T.T.McRae@bath.ac.uk> wrote:
...
To give credit where it's due,
s/Andrew's patch/Miklós's patch/
On 15 September 2016 at 18:16, David Ham <David.Ham@imperial.ac.uk>
wrote:
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
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>> _______________________________________________
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Re: [firedrake] Mixed system

David Ham

Anna Kalogirou

Onno Bokhove

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participants (3)