September 2016 - firedrake

Re: [firedrake] Mixed system
by David Ham 05 Oct '16

05 Oct '16

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(a)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(a)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(a)leeds.ac.uk> > wrote: > >> That is the same version I have. >> >> >> On 16 Sep 2016, at 16:23, David Ham <David.Ham(a)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(a)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(a)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(a)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/673fef3466b06c98ac11f5a120ff4211…> 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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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=…> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>>> 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(a)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(a)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(a)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(a)leeds.ac.uk> >>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> We would already be helped for the case without MPI, I think >>>>>>>>>>>> that is correct, Anna? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> *From:* firedrake-bounces(a)imperial.ac.uk < >>>>>>>>>>>> firedrake-bounces(a)imperial.ac.uk> on behalf of David Ham < >>>>>>>>>>>> David.Ham(a)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(a)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(a)imperial.ac.uk < >>>>>>>>>>>>> firedrake-bounces(a)imperial.ac.uk> on behalf of David Ham < >>>>>>>>>>>>> David.Ham(a)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(a)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/14334d3c20b9f10ed7c1246cde9e3cb6… >>>>>>>>>>>>>> >, >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> 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(a)imperial.ac.uk >>>>>>>>>>>>>> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> firedrake mailing list >>>>>>>>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> firedrake mailing list >>>>>>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>> firedrake mailing list >>>>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> firedrake mailing list >>>>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> firedrake mailing list >>>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> firedrake mailing list >>>>>>>> firedrake(a)imperial.ac.uk >>>>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>>>>> >>>>>>>> _______________________________________________ >>>>> firedrake mailing list >>>>> firedrake(a)imperial.ac.uk >>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>>> >>>>> -- >>>> http://www.imperial.ac.uk/people/colin.cotter >>>> >>>> www.cambridge.org/9781107663916 >>>> >>>> >>>> _______________________________________________ >>>> firedrake mailing list >>>> firedrake(a)imperial.ac.uk >>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>> >>>> _______________________________________________ >>> firedrake mailing list >>> firedrake(a)imperial.ac.uk >>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>> >>> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> >> _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

3 2

Re: [firedrake] DG for advection-diffusion
by David Ham 05 Oct '16

05 Oct '16

On Thu, 29 Sep 2016 at 10:34 Justin Chang <jychang48(a)gmail.com> wrote: > Hi all, > > I have written here the Discontinuous Galerkin method for 1D > advection-diffusion equations using backward euler time discretization: > > mesh = UnitIntervalMesh(100) > V = FunctionSpace(mesh, 'DG', 1) > u = TrialFunction(V) > v = TestFunction(V) > > u0 = Function(V, name="initial") > sol = Function(V, name="solution") > > # Diffusivity > D = Constant(0.005) > > # Velocity > vel = as_vector((Constant(1.0),)) > > # Forcing function > f = interpolate(Expression(....),V) > > # Penalty > k = 1 > d = 1 > gamma = Constant((k+1)*(k+d)/d)*FacetArea(mesh)/avg(CellVolume(mesh)) # > based on the formula in > http://webpages.sdsmt.edu/~kshahbaz/shahbazi_05.pdf > > # Other parameters > n = FacetNormal(mesh) > h = CellSize(mesh) > vn = 0.5*(dot(vel,n) + abs(dot(vel,n))) > > # Weak form > a = v*u/dt*dx - dot(grad(v),vel*u)*dx + > dot(jump(v),vn('+')*u('+')-vn('-')*u('-'))*dS + dot(v, vn*u)*ds \ > + dot(grad(v),D*grad(u))*dx - dot(jump(v,n),avg(D*grad(u)))*dS - > dot(avg(D*grad(v)),jump(u,n))*dS \ > + gamma*dot(jump(v,n),jump(u,n))*dS > L = v*f*dx + v*u0/dt*dx > > > ... > > I have a couple questions: > > 1) If say I am solving for the transport of 4 chemical species, Normally I > would create a mixed function space like V_mixed = V*V*V*V, split u into > u1, u2, u3, and u4, write bilinear and linear forms for each of these > individual components and add them up. That is, a = a1 + a2 + a3 + a4, L = > L1 + L2 + L3 + L4. This can become quite a lot of code if I end up having > to solve ~20 chemical species eventually. The catch is that the velocity > and diffusivity will be the same for all species but the forcing function > and boundary conditions are going to be different. Is there a more > efficient of writing the bilinear and linear form instead of having to copy > and paste the a = ... and L = ... multiple times and changing the > trial/test functions? > a) If you are independently advecting lots of species (ie no reaction) then you probably want to just solve the equations separately, rather than making a massive mixed function space. b) You can avoid lots of retyping by just using normal Python functions to construct forms. You could, for example, write a function which takes a test and trial function, and maybe some BC information, and returns the appropriate forms. > > 2) I see that in FEniCS's undocumented dg-advection-diffusion example, > they enforce the DirichletBC's strongly. Is it possible to enforce them > weakly like the SIPG or DG upwinding techniques for the pure diffusion or > advection equations? > Yes, just substitute boundary conditions for surface integrals in the usual way. > > Thanks, > Justin > > >

2 1

FSI coupling disagreement
by Tomasz Salwa [RPG] 29 Sep '16

29 Sep '16

Dear all (especially David and Lawrence), I work with a coupled fluid-structure interaction problem. I have a plain python code for verification. For a simple test setup (see attached file init_cond_py.pdf), I expect the same result from Firedrake as from my code. The result is very close, but slightly different. Grey plots show results from my code, coloured from Firedrake. The energy looks basically the same. However, in the inspection of convergence of energy with dt (expected second order convergence), Firedrake code results in a slight energy drift, which is unexpected. The uncoupled subsystems behave properly, so I suspect that the source of this discrepancy lies in the coupling terms. The relevant part is ... # given the definitions: V_f = FunctionSpace(mesh, "CG", 1) V_s = VectorFunctionSpace(mesh, "CG", 1) mixed_V = V_f * V_s trial_f, trial_s = TrialFunctions(mixed_V) v_f, v_s = TestFunctions(mixed_V) phi = Function(V_f) U = Function(V_s) n_normal = FacetNormal(mesh) # n - normal vector at the interface #I_s, I_f - indicator functions, 1(0) in solid, 0(1) in fluid, respectively n = (I_s("+") * I_f("-") - I_s("-") * I_f("+")) * n_normal("-") .... # the coupling terms are: ... + dot( avg(v_s), n ) * avg(trial_f) * dS ... + dot( avg(v_s), n ) * avg(phi) * dS ... - dot( n, avg(trial_s) ) * avg(v_f) * dS ... - dt * dot( n, avg(U) ) * avg(v_f) * dS Can it be that the energy drift is caused by the averages above or by a method Firedrake assembles those terms? I would welcome any suggestions, as I have run out of ideas what I may be doing wrong. The full code is here: https://bitbucket.org/mmtjs/lin_coupled_fd_2d with relevant part in lib/coupled_system.py Thank you, Tomasz

2 4

DG for advection-diffusion
by Justin Chang 29 Sep '16

29 Sep '16

Hi all, I have written here the Discontinuous Galerkin method for 1D advection-diffusion equations using backward euler time discretization: mesh = UnitIntervalMesh(100) V = FunctionSpace(mesh, 'DG', 1) u = TrialFunction(V) v = TestFunction(V) u0 = Function(V, name="initial") sol = Function(V, name="solution") # Diffusivity D = Constant(0.005) # Velocity vel = as_vector((Constant(1.0),)) # Forcing function f = interpolate(Expression(....),V) # Penalty k = 1 d = 1 gamma = Constant((k+1)*(k+d)/d)*FacetArea(mesh)/avg(CellVolume(mesh)) # based on the formula in http://webpages.sdsmt.edu/~kshahbaz/shahbazi_05.pdf # Other parameters n = FacetNormal(mesh) h = CellSize(mesh) vn = 0.5*(dot(vel,n) + abs(dot(vel,n))) # Weak form a = v*u/dt*dx - dot(grad(v),vel*u)*dx + dot(jump(v),vn('+')*u('+')-vn('-')*u('-'))*dS + dot(v, vn*u)*ds \ + dot(grad(v),D*grad(u))*dx - dot(jump(v,n),avg(D*grad(u)))*dS - dot(avg(D*grad(v)),jump(u,n))*dS \ + gamma*dot(jump(v,n),jump(u,n))*dS L = v*f*dx + v*u0/dt*dx ... I have a couple questions: 1) If say I am solving for the transport of 4 chemical species, Normally I would create a mixed function space like V_mixed = V*V*V*V, split u into u1, u2, u3, and u4, write bilinear and linear forms for each of these individual components and add them up. That is, a = a1 + a2 + a3 + a4, L = L1 + L2 + L3 + L4. This can become quite a lot of code if I end up having to solve ~20 chemical species eventually. The catch is that the velocity and diffusivity will be the same for all species but the forcing function and boundary conditions are going to be different. Is there a more efficient of writing the bilinear and linear form instead of having to copy and paste the a = ... and L = ... multiple times and changing the trial/test functions? 2) I see that in FEniCS's undocumented dg-advection-diffusion example, they enforce the DirichletBC's strongly. Is it possible to enforce them weakly like the SIPG or DG upwinding techniques for the pure diffusion or advection equations? Thanks, Justin

1 0

kernel of operator
by Colin Cotter 27 Sep '16

27 Sep '16

Dear Firedrakers, I have a (non-symmetric) system that I would like to extract a kernel from, probably using QR factorisation or similar. What is the best way to do this at scale? all the best --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

1 0

Re: [firedrake] Strange MPI error/warning after upgrading homebrew
by David Ham 22 Sep '16

22 Sep '16

Hmm. FWIW I can't reproduce this. I've updated everything from homebrew and in particular have open-mpi 2.0.1 and mpi4py 2.0.0 installed as above. If I run: python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank" then I just get the expected output of "0" Regards, David On Wed, 21 Sep 2016 at 04:37 Justin Chang <jychang48(a)gmail.com> wrote: > It has come back. I tried the steps Lawrence suggested but the messages > won't go away: > > (firedrake)*➜ **~* python -c "from firedrake import *" > > [Justins-MacBook-Pro-2.local:00492] [[25811,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00492] [[25811,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > (firedrake)*➜ **~* python -c "from mpi4py import MPI; print > MPI.COMM_WORLD.rank" > > [Justins-MacBook-Pro-2.local:00563] [[26380,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00563] [[26380,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > 0 > > (firedrake)*➜ **~* pip uninstall mpi4py > > > Uninstalling mpi4py-2.0.0: > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py-2.0.0-py2.7.egg-info > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.so > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.py > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.pyc > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.py > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.pyc > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/dl.so > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pyx > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/libmpi.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi.pxi > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.i > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libmpe.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-hyb.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-mpi.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/libmpi.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/mpi.cfg > > Proceed (y/n)? y > > Successfully uninstalled mpi4py-2.0.0 > > (firedrake)*➜ **~* pip install --no-binary :all: mpi4py > > > Collecting mpi4py > > Using cached mpi4py-2.0.0.tar.gz > > Skipping bdist_wheel for mpi4py, due to binaries being disabled for it. > > Installing collected packages: mpi4py > > Running setup.py install for mpi4py ... done > > Successfully installed mpi4py-2.0.0 > > (firedrake)*➜ **~* python -c "from mpi4py import MPI; print > MPI.COMM_WORLD.rank" > > [Justins-MacBook-Pro-2.local:00849] [[26222,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00849] [[26222,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > 0 > > Any ideas here? > > Thanks, > Justin > > On Tue, Sep 20, 2016 at 4:47 AM, Justin Chang <jychang48(a)gmail.com> wrote: > >> Wait, sorry, my MPI error/warning messages disappeared without a trace. I >> am not sure how I "fixed" it. >> >> I'll holler again if I see something else. >> >> On Tue, Sep 20, 2016 at 4:39 AM, Lawrence Mitchell < >> lawrence.mitchell(a)imperial.ac.uk> wrote: >> >>> >>> >>> On 20/09/16 09:30, Justin Chang wrote: >>> > Hi all, >>> > >>> > I upgraded homebrew on my macbook and had to remove firedrake because >>> > the compiled libraries were pointing to old/nonexistent brew packages. >>> > So when I tried to install a fresh copy of firedrake, i get this >>> message: >>> > >>> > $ python firedrake-install --developer --disable_ssh --log >>> > >>> > Installing command line tools... >>> > >>> > Installing required packages via homebrew. You can safely ignore >>> > warnings that packages are already installed >>> > >>> > Creating firedrake virtualenv in 'firedrake'. >>> > >>> > /Users/justin/Software/firedrake/bin/pip install -vvv -U pip >>> > >>> > >>> > Traceback (most recent call last): >>> > >>> > File "firedrake-install", line 1016, in <module> >>> > >>> > framework = fix_osx_virtualenv_python() >>> > >>> > File "firedrake-install", line 973, in fix_osx_virtualenv_python >>> > >>> > shutil.copytree(appsrc, appdest) >>> > >>> > File >>> > >>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", >>> > line 208, in copytree >>> > >>> > raise Error, errors >>> > >>> > shutil.Error: >>> > >>> [('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS', "[Errno >>> > 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Resources', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Resources'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/version.plist', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/version.plist'"), >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', >>> > '/Users/justin/Software/firedrake/Python.app/Contents', "[Errno 1] >>> > Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', >>> > '/Users/justin/Software/firedrake/Python.app', "[Errno 1] Operation >>> > not permitted: '/Users/justin/Software/firedrake/Python.app'")] >>> > >>> > >>> > And when I run the script again, it installs correctly. I guess this >>> > meant the virtualenv was "successfully" installed the first time. >>> > >>> > However, I get this strange MPI warning/error that I have never before >>> > seen: >>> > >>> > $ python -c "from firedrake import *" >>> > >>> > [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] bind() failed on >>> > error Address already in use (48) >>> > >>> > [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] ORTE_ERROR_LOG: >>> > Error in file oob_usock_component.c at line 228 >>> > >>> > >>> > My firedrake programs appear to run without any error, but these >>> > messages still seem very suspicious. Any ideas what this could be? My >>> > homebrew upgrade/update has now given me Open MPI 2.0.1, and I am >>> > wondering if anyone else is having this issue. >>> >>> Can you run an mpi4py program? >>> >>> In the virtualenv: >>> >>> $ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank" >>> >>> If that fails, try uninstalling mpi4py >>> >>> $ pip uninstall mpi4py >>> >>> And then reinstalling, but crucially without using the pip cache: >>> >>> $ pip install --no-binary :all: mpi4py >>> >>> >>> Cheers, >>> >>> Lawrence >>> >>> >>> _______________________________________________ >>> firedrake mailing list >>> firedrake(a)imperial.ac.uk >>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>> >> >

2 2

Re: [firedrake] (no subject)
by Colin Cotter 22 Sep '16

22 Sep '16

On the other hand, extra memory is very cheap... On 22 September 2016 at 17:09, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > Hi Floriane, > > I'm afraid that you're not going to be able to run very large problems on > a machine with only 6G of RAM. You could attempt to shut down running > processes to free more memory, but in reality you're really just asking too > much of your hardware. Similarly, tweaking preconditioners to reduce memory > usage might help a bit, but you're still going to be very close to the line. > > Regards, > > David > > On Thu, 22 Sep 2016 at 16:55 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> Indeed, I have less than 5G memory available: >> >> MemTotal: 5941348 kB >> MemFree: 1429500 kB >> MemAvailable: 2994648 kB >> >> Is there a way for me to free some memory? >> >> Thank you, >> Floriane >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* jeudi 22 septembre 2016 16:30:14 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Dear Floriane, >> >> I've run your code and it runs without error on current master for me. >> Looking at your last error message, it appears that you have run out of >> memory. How much memory does your machine have? For me, that problem peaks >> at a bit over 5G of memory. >> >> If that is the problem, there may be solver options we can set which >> might use less memory, or perhaps you need a larger machine. >> >> As an aside, running that problem in parallel is effective. On 8 >> processors I get about a 3x speedup. >> >> Regards, >> >> David >> >> >> >> On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear David, >>> >>> >>> Sorry about that. You should be able to access my code on that link: >>> https://bitbucket.org/Floriane_Gidel/test_bl . >>> >>> >>> Thank you, >>> Floriane >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>> ac.uk> de la part de David Ham <David.Ham(a)imperial.ac.uk> >>> *Envoyé :* jeudi 22 septembre 2016 10:32:07 >>> >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> Hi Floriane, >>> >>> Sorry for taking a couple of days to get on to this. Unfortunately those >>> files are not attached, they are on a University of Leeds sharepoint which >>> my Imperial microsoft account cannot access. Could you please provide the >>> files via an open route. >>> >>> Thanks, >>> >>> David >>> >>> On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> wrote: >>> >>>> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >>>> vous. Pour les afficher, cliquez sur les liens ci-dessous. >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> horizontal.msh >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> BL.py >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> Dear David, >>>> >>>> >>>> Attached is the "short" piece of code (BL.py), together with the mesh >>>> file (horizontal.msh). When running it, I get the error below. However, if >>>> I remove the weak formulations for eta(n+1) and phi(n+1) and solve >>>> only phi_solver_half and q_solver_half, then the error is for the line >>>> q_solver_half.solve(). If I also remove the solver for q_half and keeps >>>> only phi_solver_half, then it works. >>>> >>>> Thank you, >>>> >>>> Floriane >>>> >>>> >>>> Traceback (most recent call last): >>>> File "BL.py", line 69, in <module> >>>> phi_solver_half.solve() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/ >>>> firedrake/variational_solver.py", line 198, in solve >>>> >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:170168) >>>> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >>>> (src/petsc4py.PETSc.c:33847) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 261, in form_jacobian >>>> ctx._jacs[lvl].force_evaluation() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>>> line 248, in force_evaluation >>>> self.assemble() >>>> File "<decorator-gen-283>", line 2, in assemble >>>> >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>>> line 191, in assemble >>>> self._assembly_callback(self.bcs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>> line 357, in inner >>>> r = thunk(bcs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 279, in thunk >>>> zero_tensor() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 219, in <lambda> >>>> zero_tensor = lambda: tensor.zero() >>>> File "<decorator-gen-300>", line 2, in zero >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 126, in zeroes >>>> _force_copies(self) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 104, in _force_copies >>>> c._cow_actual_copy(obj) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >>>> line 687, in _cow_actual_copy >>>> self.handle = src.handle.duplicate(copy=True) >>>> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >>>> (src/petsc4py.PETSc.c:119330) >>>> petsc4py.PETSc.Error: error code 1 >>>> [0] SNESSolve() line 4060 in /tmp/pip-xbPEGV-build/src/ >>>> snes/interface/snes.c >>>> [0] SNESSolve_NEWTONLS() line 228 in /tmp/pip-xbPEGV-build/src/ >>>> snes/impls/ls/ls.c >>>> [0] SNESComputeJacobian() line 2365 in /tmp/pip-xbPEGV-build/src/ >>>> snes/interface/snes.c >>>> [0] MatDuplicate() line 4389 in /tmp/pip-xbPEGV-build/src/mat/ >>>> interface/matrix.c >>>> [0] MatDuplicate_SeqAIJ() line 4126 in /tmp/pip-xbPEGV-build/src/mat/ >>>> impls/aij/seq/aij.c >>>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>>> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >>>> [0] Memory requested 422967946 >>>> >>>> >>>> ------------------------------ >>>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>>> ac.uk> de la part de David Ham <David.Ham(a)imperial.ac.uk> >>>> *Envoyé :* mardi 20 septembre 2016 10:13:20 >>>> >>>> *À :* firedrake >>>> *Objet :* Re: [firedrake] (no subject) >>>> Dear Floriane, >>>> >>>> Please provide a minimal failing example so we can see what is going >>>> on. By a minimal failing example, we mean that you remove everything from >>>> the example that is not related to the failure. Often this requires some >>>> trial and error. The objective is to produce a very short piece of code >>>> which illustrates the problem so that we can (a) check if we can reproduce >>>> it and if so (b) find the problem easily. >>>> >>>> Regards, >>>> >>>> David >>>> >>>> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>>> wrote: >>>> >>>>> Dear all, >>>>> >>>>> >>>>> Some of my codes do not work either since I updated firedrake. I have >>>>> run firedrake-clean but still have the same error when calling the >>>>> nonlinear solvers. The error is pasted below. >>>>> >>>>> Any idea of what I could do ? >>>>> >>>>> Thanks, >>>>> >>>>> Floriane >>>>> >>>>> >>>>> >>>>> Traceback (most recent call last): >>>>> File "3D_NL.py", line 232, in <module> >>>>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/ >>>>> firedrake/variational_solver.py", line 137, in __init__ >>>>> appctx=appctx) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 138, in __init__ >>>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 138, in <genexpr> >>>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 81, in assemble >>>>> >>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>>> line 62, in wrapper >>>>> return f(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 120, in _assemble >>>>> inverse=inverse) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>>> line 189, in compile_form >>>>> number_map).kernels >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 198, in __new__ >>>>> obj = make_obj() >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 188, in make_obj >>>>> obj.__init__(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>>> line 119, in __init__ >>>>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>>> line 118, in __call__ >>>>> return t(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 198, in __new__ >>>>> obj = make_obj() >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 188, in make_obj >>>>> obj.__init__(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 3778, in __init__ >>>>> self._code = self._ast_to_c(self._ast, opts) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", >>>>> line 60, in _ast_to_c >>>>> ast_handler.plan_cpu(self._opts) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", >>>>> line 119, in plan_cpu >>>>> loop_opt.rewrite(rewrite) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>>>> line 142, in rewrite >>>>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>>> line 181, in merge >>>>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>>> line 74, in _merge_loops >>>>> while isinstance(loop_b.children[0], (Block, For)): >>>>> IndexError: list index out of range >>>>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>>>> attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ >>>>> of <firedrake.variational_solver.NonlinearVariationalSolver object at >>>>> 0x595a250>> ignored >>>>> >>>>> ------------------------------ >>>>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>>>> ac.uk> de la part de Fabio Luporini <f.luporini12(a)imperial.ac.uk> >>>>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>>>> *À :* firedrake >>>>> *Objet :* Re: [firedrake] (no subject) >>>>> >>>>> Hi Will, >>>>> >>>>> Could you just try a firedrake-clean and run it again ? it should then >>>>> work >>>>> >>>>> Thanks >>>>> >>>>> -- Fabio >>>>> >>>>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>>>> >>>>>> Hi firedrakers, >>>>>> >>>>>> I had this script working on an older version of firedrake (24th >>>>>> Aug), but when I updated today I now get the following error when I try to >>>>>> run it: >>>>>> >>>>>> Traceback (most recent call last): >>>>>> File "compressible_stratified.py", line 77, in <module> >>>>>> solve ( a_u_project == L_u_project , dHdu0 , >>>>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving.py", line 119, in solve >>>>>> _solve_varproblem(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving.py", line 147, in >>>>>> _solve_varproblem >>>>>> solver.solve() >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/variational_solver.py", line 198, >>>>>> in solve >>>>>> self.snes.solve(None, v) >>>>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>>>> (src/petsc4py.PETSc.c:170168) >>>>>> File "PETSc/petscsnes.pxi", line 261, in >>>>>> petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33322) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving_utils.py", line 216, in >>>>>> form_function >>>>>> form_compiler_parameters=problem.form_compiler_parameters) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 81, in assemble >>>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/utils.py", line 62, in wrapper >>>>>> return f(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 444, in >>>>>> _assemble >>>>>> return thunk(bcs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assembly_cache.py", line 357, in >>>>>> inner >>>>>> r = thunk(bcs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 394, in thunk >>>>>> op2.par_loop(*args, **kwargs) >>>>>> File "<decorator-gen-269>", line 2, in par_loop >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/versioning.py", line 154, in >>>>>> modifies_arguments >>>>>> retval = func(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/op2.py", line 269, in par_loop >>>>>> return backends._BackendSelector._backend.par_loop(kernel, >>>>>> iterset, *args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/base.py", line 4369, in par_loop >>>>>> return _make_object('ParLoop', kernel, it_space, *args, >>>>>> **kwargs).enqueue() >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/backends.py", line 72, in _make_object >>>>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>>>> File "<decorator-gen-262>", line 2, in __init__ >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/utils.py", line 130, in wrapper >>>>>> return f(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/base.py", line 3999, in __init__ >>>>>> fundecl = kernel._attached_info['fundecl'] >>>>>> TypeError: 'bool' object has no attribute '__getitem__' >>>>>> >>>>>> >>>>>> What needs to be changed to get it to compile again? >>>>>> >>>>>> Thanks >>>>>> Will >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

2 1

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Hi Floriane, I'm afraid that you're not going to be able to run very large problems on a machine with only 6G of RAM. You could attempt to shut down running processes to free more memory, but in reality you're really just asking too much of your hardware. Similarly, tweaking preconditioners to reduce memory usage might help a bit, but you're still going to be very close to the line. Regards, David On Thu, 22 Sep 2016 at 16:55 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > Indeed, I have less than 5G memory available: > > MemTotal: 5941348 kB > MemFree: 1429500 kB > MemAvailable: 2994648 kB > > Is there a way for me to free some memory? > > Thank you, > Floriane > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* jeudi 22 septembre 2016 16:30:14 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Dear Floriane, > > I've run your code and it runs without error on current master for me. > Looking at your last error message, it appears that you have run out of > memory. How much memory does your machine have? For me, that problem peaks > at a bit over 5G of memory. > > If that is the problem, there may be solver options we can set which might > use less memory, or perhaps you need a larger machine. > > As an aside, running that problem in parallel is effective. On 8 > processors I get about a 3x speedup. > > Regards, > > David > > > > On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> Sorry about that. You should be able to access my code on that link: >> https://bitbucket.org/Floriane_Gidel/test_bl . >> >> >> Thank you, >> Floriane >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* jeudi 22 septembre 2016 10:32:07 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Hi Floriane, >> >> Sorry for taking a couple of days to get on to this. Unfortunately those >> files are not attached, they are on a University of Leeds sharepoint which >> my Imperial microsoft account cannot access. Could you please provide the >> files via an open route. >> >> Thanks, >> >> David >> >> On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >>> vous. Pour les afficher, cliquez sur les liens ci-dessous. >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> horizontal.msh >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> BL.py >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> Dear David, >>> >>> >>> Attached is the "short" piece of code (BL.py), together with the mesh >>> file (horizontal.msh). When running it, I get the error below. However, if >>> I remove the weak formulations for eta(n+1) and phi(n+1) and solve only >>> phi_solver_half and q_solver_half, then the error is for the line >>> q_solver_half.solve(). If I also remove the solver for q_half and keeps >>> only phi_solver_half, then it works. >>> >>> Thank you, >>> >>> Floriane >>> >>> >>> Traceback (most recent call last): >>> File "BL.py", line 69, in <module> >>> phi_solver_half.solve() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 198, in solve >>> >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:170168) >>> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >>> (src/petsc4py.PETSc.c:33847) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 261, in form_jacobian >>> ctx._jacs[lvl].force_evaluation() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>> line 248, in force_evaluation >>> self.assemble() >>> File "<decorator-gen-283>", line 2, in assemble >>> >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>> line 191, in assemble >>> self._assembly_callback(self.bcs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>> line 357, in inner >>> r = thunk(bcs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 279, in thunk >>> zero_tensor() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 219, in <lambda> >>> zero_tensor = lambda: tensor.zero() >>> File "<decorator-gen-300>", line 2, in zero >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 126, in zeroes >>> _force_copies(self) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 104, in _force_copies >>> c._cow_actual_copy(obj) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >>> line 687, in _cow_actual_copy >>> self.handle = src.handle.duplicate(copy=True) >>> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >>> (src/petsc4py.PETSc.c:119330) >>> petsc4py.PETSc.Error: error code 1 >>> [0] SNESSolve() line 4060 in >>> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >>> [0] SNESSolve_NEWTONLS() line 228 in >>> /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c >>> [0] SNESComputeJacobian() line 2365 in >>> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >>> [0] MatDuplicate() line 4389 in >>> /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c >>> [0] MatDuplicate_SeqAIJ() line 4126 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >>> [0] Memory requested 422967946 >>> >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> de la part de David Ham < >>> David.Ham(a)imperial.ac.uk> >>> *Envoyé :* mardi 20 septembre 2016 10:13:20 >>> >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> Dear Floriane, >>> >>> Please provide a minimal failing example so we can see what is going on. >>> By a minimal failing example, we mean that you remove everything from the >>> example that is not related to the failure. Often this requires some trial >>> and error. The objective is to produce a very short piece of code which >>> illustrates the problem so that we can (a) check if we can reproduce it and >>> if so (b) find the problem easily. >>> >>> Regards, >>> >>> David >>> >>> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> wrote: >>> >>>> Dear all, >>>> >>>> >>>> Some of my codes do not work either since I updated firedrake. I have >>>> run firedrake-clean but still have the same error when calling the >>>> nonlinear solvers. The error is pasted below. >>>> >>>> Any idea of what I could do ? >>>> >>>> Thanks, >>>> >>>> Floriane >>>> >>>> >>>> >>>> Traceback (most recent call last): >>>> File "3D_NL.py", line 232, in <module> >>>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 137, in __init__ >>>> appctx=appctx) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 138, in __init__ >>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 138, in <genexpr> >>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 81, in assemble >>>> >>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>> File "<decorator-gen-295>", line 2, in _assemble >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 120, in _assemble >>>> inverse=inverse) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>> line 189, in compile_form >>>> number_map).kernels >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 198, in __new__ >>>> obj = make_obj() >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 188, in make_obj >>>> obj.__init__(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>> line 119, in __init__ >>>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>> line 118, in __call__ >>>> return t(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 198, in __new__ >>>> obj = make_obj() >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 188, in make_obj >>>> obj.__init__(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >>>> 3778, in __init__ >>>> self._code = self._ast_to_c(self._ast, opts) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >>>> 60, in _ast_to_c >>>> ast_handler.plan_cpu(self._opts) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >>>> 119, in plan_cpu >>>> loop_opt.rewrite(rewrite) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>>> line 142, in rewrite >>>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>> line 181, in merge >>>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>> line 74, in _merge_loops >>>> while isinstance(loop_b.children[0], (Block, For)): >>>> IndexError: list index out of range >>>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>>> attribute '_parameters'" in <bound method >>>> NonlinearVariationalSolver.__del__ of >>>> <firedrake.variational_solver.NonlinearVariationalSolver object at >>>> 0x595a250>> ignored >>>> >>>> ------------------------------ >>>> *De :* firedrake-bounces(a)imperial.ac.uk < >>>> firedrake-bounces(a)imperial.ac.uk> de la part de Fabio Luporini < >>>> f.luporini12(a)imperial.ac.uk> >>>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>>> *À :* firedrake >>>> *Objet :* Re: [firedrake] (no subject) >>>> >>>> Hi Will, >>>> >>>> Could you just try a firedrake-clean and run it again ? it should then >>>> work >>>> >>>> Thanks >>>> >>>> -- Fabio >>>> >>>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>>> >>>>> Hi firedrakers, >>>>> >>>>> I had this script working on an older version of firedrake (24th Aug), >>>>> but when I updated today I now get the following error when I try to run it: >>>>> >>>>> Traceback (most recent call last): >>>>> File "compressible_stratified.py", line 77, in <module> >>>>> solve ( a_u_project == L_u_project , dHdu0 , >>>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>>> line 119, in solve >>>>> _solve_varproblem(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>>> line 147, in _solve_varproblem >>>>> solver.solve() >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>>> line 198, in solve >>>>> self.snes.solve(None, v) >>>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>>> (src/petsc4py.PETSc.c:170168) >>>>> File "PETSc/petscsnes.pxi", line 261, in >>>>> petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33322) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 216, in form_function >>>>> form_compiler_parameters=problem.form_compiler_parameters) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 81, in assemble >>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>>> line 62, in wrapper >>>>> return f(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 444, in _assemble >>>>> return thunk(bcs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>>> line 357, in inner >>>>> r = thunk(bcs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 394, in thunk >>>>> op2.par_loop(*args, **kwargs) >>>>> File "<decorator-gen-269>", line 2, in par_loop >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>>> line 154, in modifies_arguments >>>>> retval = func(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>>>> line 269, in par_loop >>>>> return backends._BackendSelector._backend.par_loop(kernel, >>>>> iterset, *args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 4369, in par_loop >>>>> return _make_object('ParLoop', kernel, it_space, *args, >>>>> **kwargs).enqueue() >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>>> line 72, in _make_object >>>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>>> File "<decorator-gen-262>", line 2, in __init__ >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>>>> line 130, in wrapper >>>>> return f(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 3999, in __init__ >>>>> fundecl = kernel._attached_info['fundecl'] >>>>> TypeError: 'bool' object has no attribute '__getitem__' >>>>> >>>>> >>>>> What needs to be changed to get it to compile again? >>>>> >>>>> Thanks >>>>> Will >>>>> >>>>> >>>>> >>>>> >>>>> >>>>

1 0

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Dear Floriane, I've run your code and it runs without error on current master for me. Looking at your last error message, it appears that you have run out of memory. How much memory does your machine have? For me, that problem peaks at a bit over 5G of memory. If that is the problem, there may be solver options we can set which might use less memory, or perhaps you need a larger machine. As an aside, running that problem in parallel is effective. On 8 processors I get about a 3x speedup. Regards, David On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > Sorry about that. You should be able to access my code on that link: > https://bitbucket.org/Floriane_Gidel/test_bl . > > > Thank you, > Floriane > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* jeudi 22 septembre 2016 10:32:07 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Hi Floriane, > > Sorry for taking a couple of days to get on to this. Unfortunately those > files are not attached, they are on a University of Leeds sharepoint which > my Imperial microsoft account cannot access. Could you please provide the > files via an open route. > > Thanks, > > David > > On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >> vous. Pour les afficher, cliquez sur les liens ci-dessous. >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> horizontal.msh >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> BL.py >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> Dear David, >> >> >> Attached is the "short" piece of code (BL.py), together with the mesh >> file (horizontal.msh). When running it, I get the error below. However, if >> I remove the weak formulations for eta(n+1) and phi(n+1) and solve only >> phi_solver_half and q_solver_half, then the error is for the line >> q_solver_half.solve(). If I also remove the solver for q_half and keeps >> only phi_solver_half, then it works. >> >> Thank you, >> >> Floriane >> >> >> Traceback (most recent call last): >> File "BL.py", line 69, in <module> >> phi_solver_half.solve() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >> line 198, in solve >> >> self.snes.solve(None, v) >> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >> (src/petsc4py.PETSc.c:170168) >> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >> (src/petsc4py.PETSc.c:33847) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 261, in form_jacobian >> ctx._jacs[lvl].force_evaluation() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >> line 248, in force_evaluation >> self.assemble() >> File "<decorator-gen-283>", line 2, in assemble >> >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >> line 62, in wrapper >> return f(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >> line 191, in assemble >> self._assembly_callback(self.bcs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >> line 357, in inner >> r = thunk(bcs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 279, in thunk >> zero_tensor() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 219, in <lambda> >> zero_tensor = lambda: tensor.zero() >> File "<decorator-gen-300>", line 2, in zero >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >> line 126, in zeroes >> _force_copies(self) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >> line 104, in _force_copies >> c._cow_actual_copy(obj) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >> line 687, in _cow_actual_copy >> self.handle = src.handle.duplicate(copy=True) >> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >> (src/petsc4py.PETSc.c:119330) >> petsc4py.PETSc.Error: error code 1 >> [0] SNESSolve() line 4060 in >> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >> [0] SNESSolve_NEWTONLS() line 228 in >> /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c >> [0] SNESComputeJacobian() line 2365 in >> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >> [0] MatDuplicate() line 4389 in >> /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c >> [0] MatDuplicate_SeqAIJ() line 4126 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >> [0] Memory requested 422967946 >> >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* mardi 20 septembre 2016 10:13:20 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Dear Floriane, >> >> Please provide a minimal failing example so we can see what is going on. >> By a minimal failing example, we mean that you remove everything from the >> example that is not related to the failure. Often this requires some trial >> and error. The objective is to produce a very short piece of code which >> illustrates the problem so that we can (a) check if we can reproduce it and >> if so (b) find the problem easily. >> >> Regards, >> >> David >> >> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear all, >>> >>> >>> Some of my codes do not work either since I updated firedrake. I have >>> run firedrake-clean but still have the same error when calling the >>> nonlinear solvers. The error is pasted below. >>> >>> Any idea of what I could do ? >>> >>> Thanks, >>> >>> Floriane >>> >>> >>> >>> Traceback (most recent call last): >>> File "3D_NL.py", line 232, in <module> >>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 137, in __init__ >>> appctx=appctx) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 138, in __init__ >>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 138, in <genexpr> >>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 81, in assemble >>> >>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>> File "<decorator-gen-295>", line 2, in _assemble >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 120, in _assemble >>> inverse=inverse) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>> line 189, in compile_form >>> number_map).kernels >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 198, in __new__ >>> obj = make_obj() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 188, in make_obj >>> obj.__init__(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>> line 119, in __init__ >>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>> line 118, in __call__ >>> return t(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 198, in __new__ >>> obj = make_obj() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 188, in make_obj >>> obj.__init__(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >>> 3778, in __init__ >>> self._code = self._ast_to_c(self._ast, opts) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >>> 60, in _ast_to_c >>> ast_handler.plan_cpu(self._opts) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >>> 119, in plan_cpu >>> loop_opt.rewrite(rewrite) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>> line 142, in rewrite >>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>> line 181, in merge >>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>> line 74, in _merge_loops >>> while isinstance(loop_b.children[0], (Block, For)): >>> IndexError: list index out of range >>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>> attribute '_parameters'" in <bound method >>> NonlinearVariationalSolver.__del__ of >>> <firedrake.variational_solver.NonlinearVariationalSolver object at >>> 0x595a250>> ignored >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> de la part de Fabio Luporini < >>> f.luporini12(a)imperial.ac.uk> >>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> >>> Hi Will, >>> >>> Could you just try a firedrake-clean and run it again ? it should then >>> work >>> >>> Thanks >>> >>> -- Fabio >>> >>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>> >>>> Hi firedrakers, >>>> >>>> I had this script working on an older version of firedrake (24th Aug), >>>> but when I updated today I now get the following error when I try to run it: >>>> >>>> Traceback (most recent call last): >>>> File "compressible_stratified.py", line 77, in <module> >>>> solve ( a_u_project == L_u_project , dHdu0 , >>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 119, in solve >>>> _solve_varproblem(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 147, in _solve_varproblem >>>> solver.solve() >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 198, in solve >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:170168) >>>> File "PETSc/petscsnes.pxi", line 261, in petsc4py.PETSc.SNES_Function >>>> (src/petsc4py.PETSc.c:33322) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 216, in form_function >>>> form_compiler_parameters=problem.form_compiler_parameters) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 81, in assemble >>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>> File "<decorator-gen-295>", line 2, in _assemble >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 444, in _assemble >>>> return thunk(bcs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>> line 357, in inner >>>> r = thunk(bcs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 394, in thunk >>>> op2.par_loop(*args, **kwargs) >>>> File "<decorator-gen-269>", line 2, in par_loop >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 154, in modifies_arguments >>>> retval = func(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>>> line 269, in par_loop >>>> return backends._BackendSelector._backend.par_loop(kernel, iterset, >>>> *args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>> line 4369, in par_loop >>>> return _make_object('ParLoop', kernel, it_space, *args, >>>> **kwargs).enqueue() >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>> line 72, in _make_object >>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>> File "<decorator-gen-262>", line 2, in __init__ >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>>> line 130, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>> line 3999, in __init__ >>>> fundecl = kernel._attached_info['fundecl'] >>>> TypeError: 'bool' object has no attribute '__getitem__' >>>> >>>> >>>> What needs to be changed to get it to compile again? >>>> >>>> Thanks >>>> Will >>>> >>>> >>>> >>>> >>>> >>>

2 1

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Hi Floriane, Sorry for taking a couple of days to get on to this. Unfortunately those files are not attached, they are on a University of Leeds sharepoint which my Imperial microsoft account cannot access. Could you please provide the files via an open route. Thanks, David On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec vous. > Pour les afficher, cliquez sur les liens ci-dessous. > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > horizontal.msh > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > BL.py > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > Dear David, > > > Attached is the "short" piece of code (BL.py), together with the mesh file > (horizontal.msh). When running it, I get the error below. However, if I > remove the weak formulations for eta(n+1) and phi(n+1) and solve only > phi_solver_half and q_solver_half, then the error is for the line > q_solver_half.solve(). If I also remove the solver for q_half and keeps > only phi_solver_half, then it works. > > Thank you, > > Floriane > > > Traceback (most recent call last): > File "BL.py", line 69, in <module> > phi_solver_half.solve() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 198, in solve > > self.snes.solve(None, v) > File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve > (src/petsc4py.PETSc.c:170168) > File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian > (src/petsc4py.PETSc.c:33847) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 261, in form_jacobian > ctx._jacs[lvl].force_evaluation() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", > line 248, in force_evaluation > self.assemble() > File "<decorator-gen-283>", line 2, in assemble > > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", > line 62, in wrapper > return f(*args, **kwargs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", > line 191, in assemble > self._assembly_callback(self.bcs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", > line 357, in inner > r = thunk(bcs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", > line 279, in thunk > zero_tensor() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", > line 219, in <lambda> > zero_tensor = lambda: tensor.zero() > File "<decorator-gen-300>", line 2, in zero > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", > line 126, in zeroes > _force_copies(self) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", > line 104, in _force_copies > c._cow_actual_copy(obj) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", > line 687, in _cow_actual_copy > self.handle = src.handle.duplicate(copy=True) > File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate > (src/petsc4py.PETSc.c:119330) > petsc4py.PETSc.Error: error code 1 > [0] SNESSolve() line 4060 in > /tmp/pip-xbPEGV-build/src/snes/interface/snes.c > [0] SNESSolve_NEWTONLS() line 228 in > /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c > [0] SNESComputeJacobian() line 2365 in > /tmp/pip-xbPEGV-build/src/snes/interface/snes.c > [0] MatDuplicate() line 4389 in > /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c > [0] MatDuplicate_SeqAIJ() line 4126 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] Out of memory. Allocated: 0, Used by process: 3556626432 > [0] Memory requested 422967946 > > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* mardi 20 septembre 2016 10:13:20 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Dear Floriane, > > Please provide a minimal failing example so we can see what is going on. > By a minimal failing example, we mean that you remove everything from the > example that is not related to the failure. Often this requires some trial > and error. The objective is to produce a very short piece of code which > illustrates the problem so that we can (a) check if we can reproduce it and > if so (b) find the problem easily. > > Regards, > > David > > On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear all, >> >> >> Some of my codes do not work either since I updated firedrake. I have run >> firedrake-clean but still have the same error when calling the nonlinear >> solvers. The error is pasted below. >> >> Any idea of what I could do ? >> >> Thanks, >> >> Floriane >> >> >> >> Traceback (most recent call last): >> File "3D_NL.py", line 232, in <module> >> wf1_solver = NonlinearVariationalSolver(wf1_problem) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >> line 137, in __init__ >> appctx=appctx) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 138, in __init__ >> for J, problem, ctx in zip(self.Js, problems, appctxs)) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 138, in <genexpr> >> for J, problem, ctx in zip(self.Js, problems, appctxs)) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 81, in assemble >> >> inverse=inverse, mat_type=mat_type, appctx=appctx) >> File "<decorator-gen-295>", line 2, in _assemble >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >> line 62, in wrapper >> return f(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 120, in _assemble >> inverse=inverse) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >> line 189, in compile_form >> number_map).kernels >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 198, in __new__ >> obj = make_obj() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 188, in make_obj >> obj.__init__(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >> line 119, in __init__ >> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >> line 118, in __call__ >> return t(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 198, in __new__ >> obj = make_obj() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 188, in make_obj >> obj.__init__(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >> 3778, in __init__ >> self._code = self._ast_to_c(self._ast, opts) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >> 60, in _ast_to_c >> ast_handler.plan_cpu(self._opts) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >> 119, in plan_cpu >> loop_opt.rewrite(rewrite) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >> line 142, in rewrite >> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >> line 181, in merge >> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >> line 74, in _merge_loops >> while isinstance(loop_b.children[0], (Block, For)): >> IndexError: list index out of range >> Exception AttributeError: "'NonlinearVariationalSolver' object has no >> attribute '_parameters'" in <bound method >> NonlinearVariationalSolver.__del__ of >> <firedrake.variational_solver.NonlinearVariationalSolver object at >> 0x595a250>> ignored >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de Fabio Luporini <f.luporini12(a)imperial.ac.uk> >> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> >> Hi Will, >> >> Could you just try a firedrake-clean and run it again ? it should then >> work >> >> Thanks >> >> -- Fabio >> >> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >> >>> Hi firedrakers, >>> >>> I had this script working on an older version of firedrake (24th Aug), >>> but when I updated today I now get the following error when I try to run it: >>> >>> Traceback (most recent call last): >>> File "compressible_stratified.py", line 77, in <module> >>> solve ( a_u_project == L_u_project , dHdu0 , >>> solver_parameters={'ksp_rtol': 1e-14} ) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>> line 119, in solve >>> _solve_varproblem(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>> line 147, in _solve_varproblem >>> solver.solve() >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 198, in solve >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:170168) >>> File "PETSc/petscsnes.pxi", line 261, in petsc4py.PETSc.SNES_Function >>> (src/petsc4py.PETSc.c:33322) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 216, in form_function >>> form_compiler_parameters=problem.form_compiler_parameters) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 81, in assemble >>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>> File "<decorator-gen-295>", line 2, in _assemble >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 444, in _assemble >>> return thunk(bcs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>> line 357, in inner >>> r = thunk(bcs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 394, in thunk >>> op2.par_loop(*args, **kwargs) >>> File "<decorator-gen-269>", line 2, in par_loop >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 154, in modifies_arguments >>> retval = func(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>> line 269, in par_loop >>> return backends._BackendSelector._backend.par_loop(kernel, iterset, >>> *args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>> line 4369, in par_loop >>> return _make_object('ParLoop', kernel, it_space, *args, >>> **kwargs).enqueue() >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>> line 72, in _make_object >>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>> File "<decorator-gen-262>", line 2, in __init__ >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>> line 130, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>> line 3999, in __init__ >>> fundecl = kernel._attached_info['fundecl'] >>> TypeError: 'bool' object has no attribute '__getitem__' >>> >>> >>> What needs to be changed to get it to compile again? >>> >>> Thanks >>> Will >>> >>> >>> >>> >>> >>

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