- firedrake - imperial.ac.uk

Specify boundary conditions at a corner
by Justin Chang 21 Aug '15

21 Aug '15

Hi all, If I create a mesh using UnitSquareMesh or UnitCubeMesh, is there a way to subject a single point (as opposed to an entire edge/face) to a DirichletBC? I want to subject the the location x=0,y=0 to some value. Thanks, Justin

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Re: [firedrake] Solve a Variational problem in a part of the domain
by Colin Cotter 17 Aug '15

17 Aug '15

Hi Anna, Not as written, no. I think that we would need to design a bespoke solver for that. all the best --cjc On 17 August 2015 at 12:18, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Hi all, > > I have to solve a problem with the bilinear form similar to the following: > > a = ( v*u + dt*inner(grad(u),grad(v)) )*dx + ( v*dt*assemble(u*dx) )*dx > > The last term is essentially the product of the integral of u and the > integral of test function v. > Is it even possible to solve this in Firedrake? > > Best, > > Anna. > > > On 14/08/15 15:43, Lawrence Mitchell wrote: > > On 14 Aug 2015, at 11:55, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> <a.kalogirou(a)leeds.ac.uk> wrote: > > Hi, > > I was planning to define the heavyside function as a DG0 function. > > Any ideas about solving equation (1b), which contains a time-update for both a function and a scalar? > > I haven't been fully following along, but it looks like the formulation in (1f) introduces, effectively, a global coupling. Is that right? Assuming you didn't have any implementation constraints, how would you go about solving this? > > Lawrence > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- > > Dr Anna Kalogirou > Research Fellow > School of Mathematics > University of Leeds > > http://www1.maths.leeds.ac.uk/~matak/ > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Solve a Variational problem in a part of the domain
by Colin Cotter 17 Aug '15

17 Aug '15

Hi Anna, It *was* interesting! How do you intend to compute the integrals against the Heaviside function? The Heaviside function is non-polynomial so can't be computed exactly by quadrature. You are right that our standard setup can't cope with this situation currently. What we really need are function spaces that are defined to be constant in an entire column. We should try to sketch out with David and Lawrence what might be required in the infrastructure to support this. I can see it being useful for many other free surface type problems as well. all the best --Colin On 13 August 2015 at 15:36, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Hi Colin, > > I attached a two-page document, where the system of equations I was > talking about in the previous email is (1a)-(1e). I am puzzled with > equation (1b) really. I can also eliminate (1b) & (1d) and solve for the > remaining (1a), (1c) & (1f), but in this case I still don't know how to > deal with (1f) since there is an integral into the integral, which contains > the unknown function lambda^{n+1/2}. > > Thanks, Anna. > > > On 13/08/15 13:47, Colin Cotter wrote: > > Hi Anna, > Sounds interesting. Please could you provide a bit more detail? > > all the best > --Colin > > On 13 August 2015 at 12:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > >> Dear all, >> >> I have a system of equations to solve, which involves three space >> dependent functions phi, eta, lambda and two constants/scalars Z, W. >> These need to be solved simultaneously because all the equations involve >> at least 2 unknowns. >> >> How do I solve that, considering that one of the scalar equations >> includes a spacial integral of one of the (still unknown) functions? Is >> it best to define the scalars as Constants? >> >> This problem goes away when I write down the system in a standard FEM >> formulation, introducing the mass matrix etc. In this case, it is clear >> that I could solve for that function and then consecutively solve each >> of the remaining 4 equations. It is not that obvious how I can do that >> using Firedrake, that is why I thought I would have to solve >> simultaneously, but then I have the problem described above. >> >> Regards, >> >> Anna. >> >> >> On 06/08/15 11:04, Lawrence Mitchell wrote: >> > -----BEGIN PGP SIGNED MESSAGE----- >> > Hash: SHA1 >> > >> > Hi Anna, >> > >> > On 06/08/15 10:37, Anna Kalogirou wrote: >> >> Dear all, >> >> >> >> I have a rather simple question but I would like to get some >> >> feedback from someone in the Firedrake team. >> >> >> >> I am now working on the problem which includes solving a >> >> variational problem in a part of the domain only (a water wave >> >> problem which includes a floating body). >> >> >> >> I can think of a couple of possible solutions on how to solve this: >> >> 1. Define two domains and solve the problem separately in each >> >> domain. However, I will have to deal with nonzero boundary >> >> conditions on the common boundary. >> >> >> >> 2. I prefer solving the problem in the whole domain, since most of >> >> the equations/functions are valid everywhere. Then I can define a >> >> Heavyside step function which will be 0 in one part and 1 in the >> >> part of the domain I am interested in (under the floating body). I >> >> will essentially write down a variational problem valid everywhere, >> >> but will actually be zero in a part of the domain. >> >> >> >> Is the 2nd step a good approach? The question essentially is how >> >> to split a mass matrix M_kl which is defined everywhere, and solve >> >> and integral form in a part of the domain only. >> > I think step two is a fine approach. However, note the following >> > issues at present. The way you would have to do this currently is as >> > follows: >> > >> > Define a DG0 field to hold your indicator function >> > >> > indicator = Function(DG0) >> > >> > # Set it to 1 in the appropriate part of the domain >> > indicator.interpolate(...) >> > >> > # Now use this extra field everywhere when defining your variational >> > # problem. >> > >> > However, all your integrals are still over the whole domain, you just >> > pick up lots of zeros. >> > >> > Steadily climbing our todo list (and at an increasing pace, I feel), >> > is the ability to define proper sub domains in a mesh, and then be >> > able to perform integrals over them. Until that time, I think >> > approach 2 is somewhat easier to do than approach 1. >> > >> > Cheers, >> > >> > LAwrence >> > -----BEGIN PGP SIGNATURE----- >> > Version: GnuPG v1 >> > >> > iQEcBAEBAgAGBQJVwzElAAoJECOc1kQ8PEYvGswIAN+Mr6hD+U0NmsnZAGminaq+ >> > j/SqmI+o7GlbXRSgPqEfrpyWwFiiFVN6DnPmTboRooZr3h93ZhGDhECQ/O12XKA/ >> > 00yNuCiDn4YBaXJamWBM6u8ILdZYGMyVNTG1JOaZZIMBoiIkrTyYpXatGApcE4sD >> > 4T+DoAYSUEY7u6MV4eJmRc1lzZEd8Rw43YP+Viy0itCs2jKV+HsDpvpvu1DU/FSQ >> > zMeE/cRR8It6aImk1L3OON8Zo2ZB0HNirK6YuD3sMkIoqLEYANnNl8qaeU3LL227 >> > 3TL4ddkALXQLGaYGo5ETgtMKI6afNDIsfjwGUcVRhTTxHM3GKOMQgWV6miNtgv4= >> > =wE25 >> > -----END PGP SIGNATURE----- >> > >> > _______________________________________________ >> > firedrake mailing list >> > firedrake(a)imperial.ac.uk >> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> -- >> >> Dr Anna Kalogirou >> Research Fellow >> School of Mathematics >> University of Leeds >> >> http://www1.maths.leeds.ac.uk/~matak/ >> >> >> _______________________________________________ >> 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 listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- > > Dr Anna Kalogirou > Research Fellow > School of Mathematics > University of Leeds > > http://www1.maths.leeds.ac.uk/~matak/ > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Solve a Variational problem in a part of the domain
by Colin Cotter 14 Aug '15

14 Aug '15

Hi Anna, Ah, I see. So you "snap" the Heaviside function to the nearest gridpoint. all the best --cjc On 14 August 2015 at 11:55, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Hi, > > I was planning to define the heavyside function as a DG0 function. > > Any ideas about solving equation (1b), which contains a time-update for > both a function and a scalar? > > Thanks, > Anna. > > > > On 13/08/15 18:35, Colin Cotter wrote: > > Hi Anna, > It *was* interesting! > > How do you intend to compute the integrals against the Heaviside function? > The Heaviside function is non-polynomial so can't be computed exactly by > quadrature. > > You are right that our standard setup can't cope with this situation > currently. What we really need are function spaces that are defined to be > constant in an entire column. We should try to sketch out with David and > Lawrence what might be required in the infrastructure to support this. I > can see it being useful for many other free surface type problems as well. > > all the best > --Colin > > On 13 August 2015 at 15:36, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > >> Hi Colin, >> >> I attached a two-page document, where the system of equations I was >> talking about in the previous email is (1a)-(1e). I am puzzled with >> equation (1b) really. I can also eliminate (1b) & (1d) and solve for the >> remaining (1a), (1c) & (1f), but in this case I still don't know how to >> deal with (1f) since there is an integral into the integral, which contains >> the unknown function lambda^{n+1/2}. >> >> Thanks, Anna. >> >> >> On 13/08/15 13:47, Colin Cotter wrote: >> >> Hi Anna, >> Sounds interesting. Please could you provide a bit more detail? >> >> all the best >> --Colin >> >> On 13 August 2015 at 12:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> >> wrote: >> >>> Dear all, >>> >>> I have a system of equations to solve, which involves three space >>> dependent functions phi, eta, lambda and two constants/scalars Z, W. >>> These need to be solved simultaneously because all the equations involve >>> at least 2 unknowns. >>> >>> How do I solve that, considering that one of the scalar equations >>> includes a spacial integral of one of the (still unknown) functions? Is >>> it best to define the scalars as Constants? >>> >>> This problem goes away when I write down the system in a standard FEM >>> formulation, introducing the mass matrix etc. In this case, it is clear >>> that I could solve for that function and then consecutively solve each >>> of the remaining 4 equations. It is not that obvious how I can do that >>> using Firedrake, that is why I thought I would have to solve >>> simultaneously, but then I have the problem described above. >>> >>> Regards, >>> >>> Anna. >>> >>> >>> On 06/08/15 11:04, Lawrence Mitchell wrote: >>> > -----BEGIN PGP SIGNED MESSAGE----- >>> > Hash: SHA1 >>> > >>> > Hi Anna, >>> > >>> > On 06/08/15 10:37, Anna Kalogirou wrote: >>> >> Dear all, >>> >> >>> >> I have a rather simple question but I would like to get some >>> >> feedback from someone in the Firedrake team. >>> >> >>> >> I am now working on the problem which includes solving a >>> >> variational problem in a part of the domain only (a water wave >>> >> problem which includes a floating body). >>> >> >>> >> I can think of a couple of possible solutions on how to solve this: >>> >> 1. Define two domains and solve the problem separately in each >>> >> domain. However, I will have to deal with nonzero boundary >>> >> conditions on the common boundary. >>> >> >>> >> 2. I prefer solving the problem in the whole domain, since most of >>> >> the equations/functions are valid everywhere. Then I can define a >>> >> Heavyside step function which will be 0 in one part and 1 in the >>> >> part of the domain I am interested in (under the floating body). I >>> >> will essentially write down a variational problem valid everywhere, >>> >> but will actually be zero in a part of the domain. >>> >> >>> >> Is the 2nd step a good approach? The question essentially is how >>> >> to split a mass matrix M_kl which is defined everywhere, and solve >>> >> and integral form in a part of the domain only. >>> > I think step two is a fine approach. However, note the following >>> > issues at present. The way you would have to do this currently is as >>> > follows: >>> > >>> > Define a DG0 field to hold your indicator function >>> > >>> > indicator = Function(DG0) >>> > >>> > # Set it to 1 in the appropriate part of the domain >>> > indicator.interpolate(...) >>> > >>> > # Now use this extra field everywhere when defining your variational >>> > # problem. >>> > >>> > However, all your integrals are still over the whole domain, you just >>> > pick up lots of zeros. >>> > >>> > Steadily climbing our todo list (and at an increasing pace, I feel), >>> > is the ability to define proper sub domains in a mesh, and then be >>> > able to perform integrals over them. Until that time, I think >>> > approach 2 is somewhat easier to do than approach 1. >>> > >>> > Cheers, >>> > >>> > LAwrence >>> > -----BEGIN PGP SIGNATURE----- >>> > Version: GnuPG v1 >>> > >>> > iQEcBAEBAgAGBQJVwzElAAoJECOc1kQ8PEYvGswIAN+Mr6hD+U0NmsnZAGminaq+ >>> > j/SqmI+o7GlbXRSgPqEfrpyWwFiiFVN6DnPmTboRooZr3h93ZhGDhECQ/O12XKA/ >>> > 00yNuCiDn4YBaXJamWBM6u8ILdZYGMyVNTG1JOaZZIMBoiIkrTyYpXatGApcE4sD >>> > 4T+DoAYSUEY7u6MV4eJmRc1lzZEd8Rw43YP+Viy0itCs2jKV+HsDpvpvu1DU/FSQ >>> > zMeE/cRR8It6aImk1L3OON8Zo2ZB0HNirK6YuD3sMkIoqLEYANnNl8qaeU3LL227 >>> > 3TL4ddkALXQLGaYGo5ETgtMKI6afNDIsfjwGUcVRhTTxHM3GKOMQgWV6miNtgv4= >>> > =wE25 >>> > -----END PGP SIGNATURE----- >>> > >>> > _______________________________________________ >>> > firedrake mailing list >>> > firedrake(a)imperial.ac.uk >>> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>> -- >>> >>> Dr Anna Kalogirou >>> Research Fellow >>> School of Mathematics >>> University of Leeds >>> >>> http://www1.maths.leeds.ac.uk/~matak/ >>> >>> >>> _______________________________________________ >>> 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 listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> >> -- >> >> Dr Anna Kalogirou >> Research Fellow >> School of Mathematics >> University of Leeds >> >> http://www1.maths.leeds.ac.uk/~matak/ >> >> > > > -- > http://www.imperial.ac.uk/people/colin.cotter > > www.cambridge.org/9781107663916 > > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Solve a Variational problem in a part of the domain
by Colin Cotter 13 Aug '15

13 Aug '15

Hi Anna, Sounds interesting. Please could you provide a bit more detail? all the best --Colin On 13 August 2015 at 12:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I have a system of equations to solve, which involves three space > dependent functions phi, eta, lambda and two constants/scalars Z, W. > These need to be solved simultaneously because all the equations involve > at least 2 unknowns. > > How do I solve that, considering that one of the scalar equations > includes a spacial integral of one of the (still unknown) functions? Is > it best to define the scalars as Constants? > > This problem goes away when I write down the system in a standard FEM > formulation, introducing the mass matrix etc. In this case, it is clear > that I could solve for that function and then consecutively solve each > of the remaining 4 equations. It is not that obvious how I can do that > using Firedrake, that is why I thought I would have to solve > simultaneously, but then I have the problem described above. > > Regards, > > Anna. > > > On 06/08/15 11:04, Lawrence Mitchell wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > Hi Anna, > > > > On 06/08/15 10:37, Anna Kalogirou wrote: > >> Dear all, > >> > >> I have a rather simple question but I would like to get some > >> feedback from someone in the Firedrake team. > >> > >> I am now working on the problem which includes solving a > >> variational problem in a part of the domain only (a water wave > >> problem which includes a floating body). > >> > >> I can think of a couple of possible solutions on how to solve this: > >> 1. Define two domains and solve the problem separately in each > >> domain. However, I will have to deal with nonzero boundary > >> conditions on the common boundary. > >> > >> 2. I prefer solving the problem in the whole domain, since most of > >> the equations/functions are valid everywhere. Then I can define a > >> Heavyside step function which will be 0 in one part and 1 in the > >> part of the domain I am interested in (under the floating body). I > >> will essentially write down a variational problem valid everywhere, > >> but will actually be zero in a part of the domain. > >> > >> Is the 2nd step a good approach? The question essentially is how > >> to split a mass matrix M_kl which is defined everywhere, and solve > >> and integral form in a part of the domain only. > > I think step two is a fine approach. However, note the following > > issues at present. The way you would have to do this currently is as > > follows: > > > > Define a DG0 field to hold your indicator function > > > > indicator = Function(DG0) > > > > # Set it to 1 in the appropriate part of the domain > > indicator.interpolate(...) > > > > # Now use this extra field everywhere when defining your variational > > # problem. > > > > However, all your integrals are still over the whole domain, you just > > pick up lots of zeros. > > > > Steadily climbing our todo list (and at an increasing pace, I feel), > > is the ability to define proper sub domains in a mesh, and then be > > able to perform integrals over them. Until that time, I think > > approach 2 is somewhat easier to do than approach 1. > > > > Cheers, > > > > LAwrence > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1 > > > > iQEcBAEBAgAGBQJVwzElAAoJECOc1kQ8PEYvGswIAN+Mr6hD+U0NmsnZAGminaq+ > > j/SqmI+o7GlbXRSgPqEfrpyWwFiiFVN6DnPmTboRooZr3h93ZhGDhECQ/O12XKA/ > > 00yNuCiDn4YBaXJamWBM6u8ILdZYGMyVNTG1JOaZZIMBoiIkrTyYpXatGApcE4sD > > 4T+DoAYSUEY7u6MV4eJmRc1lzZEd8Rw43YP+Viy0itCs2jKV+HsDpvpvu1DU/FSQ > > zMeE/cRR8It6aImk1L3OON8Zo2ZB0HNirK6YuD3sMkIoqLEYANnNl8qaeU3LL227 > > 3TL4ddkALXQLGaYGo5ETgtMKI6afNDIsfjwGUcVRhTTxHM3GKOMQgWV6miNtgv4= > > =wE25 > > -----END PGP SIGNATURE----- > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > -- > > Dr Anna Kalogirou > Research Fellow > School of Mathematics > University of Leeds > > http://www1.maths.leeds.ac.uk/~matak/ > > > _______________________________________________ > 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

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Solve a Variational problem in a part of the domain
by Anna Kalogirou 13 Aug '15

13 Aug '15

Dear all, I have a rather simple question but I would like to get some feedback from someone in the Firedrake team. I am now working on the problem which includes solving a variational problem in a part of the domain only (a water wave problem which includes a floating body). I can think of a couple of possible solutions on how to solve this: 1. Define two domains and solve the problem separately in each domain. However, I will have to deal with nonzero boundary conditions on the common boundary. 2. I prefer solving the problem in the whole domain, since most of the equations/functions are valid everywhere. Then I can define a Heavyside step function which will be 0 in one part and 1 in the part of the domain I am interested in (under the floating body). I will essentially write down a variational problem valid everywhere, but will actually be zero in a part of the domain. Is the 2nd step a good approach? The question essentially is how to split a mass matrix M_kl which is defined everywhere, and solve and integral form in a part of the domain only. Thank you. Regards, Anna.

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Grantham Institute talk, Mon 10th August 14:40
by Andrew McRae 07 Aug '15

07 Aug '15

Dear Firedrakers, I will be giving my Grantham third year presentation on Monday afternoon, with the title "Compatible finite element methods for atmospheric dynamical cores". I know that several people are currently on holiday, at a conference, or otherwise occupied, but I invite any of you still in SW7 to attend. As the Grantham Institute is multidisciplinary, my talk will not be particularly technical and should be accessible to a general audience. The schedule is below. Coffee will be served from 14:30. Feel free to leave immediately after my talk, or during the break, if the other talk titles don't appeal to you. Best, Andrew *Monday 10th August* *14:30-14:40* *Arr/coffee* Martin Siegert (chair) 14:40-15:10 Andrew McRae Compatible finite element methods for atmospheric dynamical cores 15:10-15:40 Ragnhild Noven Statistical Modelling of Tempo-Spatial Extrema and Dependencies *15:40-16:00* *Break* 16:00-16:30 Jonathan Ritson Peatland carbon sequestration and drinking water provision in an uncertain future 16:30-17:00 Joseph Yao Pressurised Carbonation Experiments in the presence of Steam in a Spouted Bed Reactor *17:00-18:00* *Drinks*

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Re: [firedrake] error installing PyOP2
by Fabio Luporini 06 Aug '15

06 Aug '15

If everything is up-to-date, you might have to clean the caches (run firedrake/scripts/firedrake-clean) -- Fabio 2015-08-06 2:19 GMT+01:00 Justin Chang <jychang48(a)gmail.com>: > Lawrence, > > Upgrading "six" resolved that issue. However, when I attempt to run my > mixed-poisson.py I get this error: > > Traceback (most recent call last): > > File "mixed-poisson.py", line 79, in <module> > > solver_parameters=selfp_parameters) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py", > line 231, in __init__ > > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py", > line 110, in __init__ > > ctx = solving_utils._SNESContext(problem) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py", > line 105, in __init__ > > for problem in problems) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py", > line 105, in <genexpr> > > for problem in problems) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py", > line 67, in assemble > > inverse=inverse, nest=nest) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py", > line 100, in _assemble > > inverse=inverse) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/ffc_interface.py", > line 285, in compile_form > > ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 201, in __new__ > > return cls._cache_lookup(key) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 253, in _cache_lookup > > return cls._cache.get(key) or cls._read_from_disk(key) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 279, in _read_from_disk > > val = cPickle.loads(val) > AttributeError: 'module' object has no attribute 'ColSparseArrayInit' > > This was after pulling the latest PyOP2 and firedrake repositories. > > Thanks, > Justin > > On Wed, Aug 5, 2015 at 3:50 AM, Lawrence Mitchell < > lawrence.mitchell(a)imperial.ac.uk> wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Hi Justin, >> >> On 04/08/15 23:05, Justin Chang wrote: >> > Coming back to this. >> > >> > I believe I have puled the latest petsc, petsc4py, and PyOP2 >> > repositories onto my laptop. Following through with all the >> > (re)installation, I come across this error when I run 'make test' >> > in PyOP2: >> > >> > Error in atexit._run_exitfuncs: >> >> Sorry for these continued pains! >> >> So PyOP2 imports cPickle elsewhere, so I think this module most exist. >> Plausibly the "six" module on your system is not sufficiently up-to-date. >> >> Does the following fail: >> >> python -c "from six.moves.cPickle import dumps" >> >> If that works, I'm very confused, but I suspect it won't. >> >> If it doesn't work, can you try installing an updated "six" module: >> >> pip install --user six >> >> and then go again. >> >> Lawrence >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1 >> >> iQEcBAEBAgAGBQJVwc5PAAoJECOc1kQ8PEYvSFwIALqHqS606QbklFGoQmmlFTJL >> zKzWvTk38907Jkz+028F5MrNSdrNAXSKUlkV/M90KWqBOKILk+n5mQfpz5P/rgbd >> ql/h2JTQMMBre3M9McacgdlHT5KIfOYPhmZcOudcgHo1hX03luOY4fzWM+shGpv9 >> woEooMJoIKXfyyxfiz8GO4xHakE4xnfzEiy3gJBoD1X0PyBo/ItKXEnMYwBcEF/1 >> 1/okUeJgmTI2y11CfA0zYpKCEMUkWa/ZK0iCD37tLnkawVtbc8s3+z/pKUeCnB2W >> jWKh2713ECCPBDCWMybXRDQsu1zFZL9HGh/VToVMT+uV+7V8/hSknRWVzSjIJxo= >> =gNYd >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > >

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error installing PyOP2
by Justin Chang 06 Aug '15

06 Aug '15

Hi everyone, I am trying to installing firedrake on my Ubuntu machine. Following the instructions for PyOP2, I get this error when I run "make test" cd test; py.test unit --backend=sequential Segmentation fault (core dumped) make: *** [unit_sequential] Error 139 I have installed everything via sudo pip install ... with the exception of petsc4py which was installed via pip install --user -U --no-deps ... python -c 'from pprint import pprint; import sys; pprint(sys.path)' gives the following: ['', '/usr/lib/python2.7/dist-packages', '/home/justin/.local/lib/python2.7/site-packages', '/home/justin/Software/firedrake-deps/PyOP2', '/home/justin/Software/firedrake-deps/firedrake', '/home/justin/.local/lib/python2.7/dist-packages', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client'] and py.test test/unit -vsx --tb=short --backend=sequential gives the following: [pacotaco-xps:29386] *** Process received signal *** [pacotaco-xps:29386] Signal: Segmentation fault (11) [pacotaco-xps:29386] Signal code: Address not mapped (1) [pacotaco-xps:29386] Failing at address: 0x44000098 [pacotaco-xps:29386] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f7eafdd8340] [pacotaco-xps:29386] [ 1] /usr/lib/libmpi.so.1(MPI_Comm_set_errhandler+0x4d) [0x7f7ead7fca1d] [pacotaco-xps:29386] [ 2] /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06(PetscInitialize+0x2a7) [0x7f7e9063f6b6] [pacotaco-xps:29386] [ 3] /home/justin/.local/lib/python2.7/site-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so(+0x11d3e8) [0x7f7e8e33c3e8] [pacotaco-xps:29386] [ 4] /usr/bin/python(PyEval_EvalFrameEx+0x40d) [0x49968d] [pacotaco-xps:29386] [ 5] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [ 6] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [ 7] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [ 8] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] [ 9] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [10] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [11] /usr/bin/python() [0x541510] [pacotaco-xps:29386] [12] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [13] /usr/bin/python(PyObject_Call+0x36) [0x505f96] [pacotaco-xps:29386] [14] /usr/bin/python() [0x536095] [pacotaco-xps:29386] [15] /usr/bin/python(PyObject_CallFunction+0xa5) [0x4ca095] [pacotaco-xps:29386] [16] /usr/bin/python(PyImport_Import+0xdd) [0x525e8d] [pacotaco-xps:29386] [17] /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(+0x770a) [0x7f7e915de70a] [pacotaco-xps:29386] [18] /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(initsparsity+0x1244) [0x7f7e915f91a4] [pacotaco-xps:29386] [19] /usr/bin/python(_PyImport_LoadDynamicModule+0x9b) [0x42266c] [pacotaco-xps:29386] [20] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [21] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [22] /usr/bin/python() [0x54111b] [pacotaco-xps:29386] [23] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [24] /usr/bin/python(PyEval_CallObjectWithKeywords+0x6b) [0x4dc9cb] [pacotaco-xps:29386] [25] /usr/bin/python(PyEval_EvalFrameEx+0x25fe) [0x49b87e] [pacotaco-xps:29386] [26] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [27] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [28] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [29] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] *** End of error message *** Segmentation fault (core dumped) Any idea what's going on? Thanks, Justin PS - this is a slightly separate issue from the petsc4py issue I posted in petsc-users (though it might be related?) But I figured I should try to resolve this one first.

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Counting FLOPS for assembling residual and Jacobian
by Justin Chang 05 Aug '15

05 Aug '15

Hi all, Is it possible to include manual/PETSc counts within the assembly of the FormResidual and FormJacobian routines? Because I think it would be nice to look at the performance of how firedrake is assembling these finite element discretization instead of always relying on hardware counters. Thanks, Justin

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