- firedrake - imperial.ac.uk

Re: [firedrake] building a function space for slice vector fields
by David Ham 15 Jun '15

15 Jun '15

Have you tried it? I think it might Just Work. The first thing which might break is the HDiv operator, but you never know.... On Mon, 15 Jun 2015 at 11:58 Cotter, Colin J <colin.cotter(a)imperial.ac.uk> wrote: > Dear all, > A lot of what we do in the vertical slice model would be a lot easier > if we could combine together our u-w components of our velocity field > (stored as an RT field in the slice) with our v component (stored as a DG > field in the slice) so that the basis functions are 3D vectors on a 2D x-z > plane. In particular, then I could assemble the inverse of the combined > u-w-v velocity mass matrix combined with Coriolis, and make things a lot > more implicit in the Coriolis term, leading to bigger timesteps when we > sent the Coriolis parameter to infinity (something we have to do in our > test case unfortunately). > > Is this supported by current code, if not, how much work would it take > for us to have this? > > all the best > --cjc >

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building a function space for slice vector fields
by Colin Cotter 15 Jun '15

15 Jun '15

Dear all, A lot of what we do in the vertical slice model would be a lot easier if we could combine together our u-w components of our velocity field (stored as an RT field in the slice) with our v component (stored as a DG field in the slice) so that the basis functions are 3D vectors on a 2D x-z plane. In particular, then I could assemble the inverse of the combined u-w-v velocity mass matrix combined with Coriolis, and make things a lot more implicit in the Coriolis term, leading to bigger timesteps when we sent the Coriolis parameter to infinity (something we have to do in our test case unfortunately). Is this supported by current code, if not, how much work would it take for us to have this? all the best --cjc

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30 June: Public lecture by FEniCS project founder Anders Logg
by David Ham 11 Jun '15

11 Jun '15

Tuesday 30 June at 1610 in Huxley 311. No registration required. Dear all, FEniCS is a system for automatically creating numerical simulations. As a part of the FEniCS '15 workshop at Imperial, FEniCS project founder Prof. Anders Logg of Chalmers University of Technology will be presenting a public lecture. This is an opportunity to hear about some of the latest advances in automated simulation technology from one of the leaders in the field. Prof. Logg's abstract is below, I look forward to seeing you there. Regards, David *Implementing mathematics: domain specific languages and automated computing* Computer simulation is today an indispensable tool for scientists and engineers in modeling, understanding and predicting nature. Having emerged as a complement to theory and experimentation, it is becoming increasingly more important as a result of advancements in hardware, software and algorithms. However, in spite of its success and ever increasing importance, simulation software is still largely written by hand, following a primitive, outdated and unsustainable pipeline: first express a model in the language of mathematics, then translate this model - using pen and paper - to a complex system of data structures and algorithms, then express those data structures and algorithms in a programming language. Even if those algorithms can today be expressed in high level programming languages, the pipeline still involves the translation (obfuscation) of the mathematical model to computer code. In this talk, I will argue that we should not strive to translate mathematical models or methods to computer code. Instead, we should strive to develop exact computer representations of mathematics that make the original mathematical model or method native to the mathematical / programming language. I will highlight three examples of ongoing work in this direction. First, the FEniCS Project, an ongoing effort to develop a domain specific language for expression and solution of partial differential equations; second, an application of the domain specific language of FEniCS for expressing the Einstein-Vlasov equations and computing the mass distribution of galaxies; third, a new effort to implement the abstractions of exterior calculus in a functional programming language (Haskell) to express and thereby compute all elements of the periodic table of finite elements. Acknowledgments: This talk is based on joint work with many people, in particular the developers of the FEniCS Project (http://fenicsproject.org) Håkan Andreasson and Ellery Ames (Einstein-Vlasov); Mary Sheeran, Patrik Jansson, Irene Lobo Valbuena, Simon Pfreundschuh and Andreas Rosén (functional finite element exterior calculus); and Douglas Arnold (periodic table of the finite elements).

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Re: [firedrake] Mapping nodal values from parent to extruded mesh
by David Ham 04 Jun '15

04 Jun '15

Hi Tuomas, Concerning the sets of spaces which this will work for, I think that the current implementation probably works for any horizontal space but only for vertical CG. One could just try relaxing the test in that case. The reason for the restriction to vertical CG is that fs.bt_masks uses the topological association of nodes with mesh entities in order to work out which nodes are on the top or bottom of the cell. In order to allow DG in the vertical, it would be necessary to support the geometric definition (ie which basis functions do not vanish on the top/bottom). If you look at functionspace.py:78 you can see where the bottom and top masks are generated. This uses entity_closure_dofs() from FIAT. In order to use the geometric definition of dofs one would need to support using facet_support_dofs() (which is how BC maps are set up at functionspace.py:375). Currently FIAT TensorFiniteElement objects do support entity_closure_dofs() but nobody has done the legwork to get them to support facet_support_dofs. Concerning documentation, COFFEE is deplorably underdocumented (although the author is on this list so maybe this will change ;). The actual available AST nodes are only "documented" by reading the source: https://github.com/coneoproject/COFFEE/blob/master/coffee/base.py However, you are fundamentally writing a PyOP2 kernel, and the C api for that *is* documented at: http://op2.github.io/PyOP2/kernels.html so that hopefully helps somewhat. Otherwise, keep asking here or in IRC (IRC tends to get faster responses, at least between about 10am and 8pm UK time). BTW, any chance of seeing you at FEniCS '15? Cheers, David On 10 April 2015 at 02:44, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > Hi all, > > A couple of questions regarding those extruded mesh -> parent mesh copy > operations, > > A while back I got the reverse 2d->3d copy working with a hard-coded pyop2 > kernel (like in mesh extrusion). I'm not familiar with COFFEE syntax, is > there documentation/examples somewhere? > > The 3d->2d copy routine in extrusion_extraction branch checks that the > function space is CG. Does this method easily generalize to other spaces? > DGxCG prisms seem to work OK. I'm also interested in using DGxDG and > RTxCG/DG spaces. > > > Cheers, > > Tuomas > > > On 03/05/2015 10:24 AM, Tuomas Karna wrote: > > Thanks David, > > This is great, I'll try doing the reverse operation. > > - Tuomas > > On 03/05/2015 08:20 AM, David Ham wrote: > > Hi Tuomas, > > This wasn't there this morning but I've implemented one of the cases > (pulling out the top and bottom maps). The result is in the > extrusion_extraction branches of both PyOP2 and Firedrake. The 2d->3d > operation would be rather similar except that you'd have to interrogate the > fiat_element on the extruded Function in order to determine which extruded > nodes are "on top of" the 2d nodes you have. Unfortunately I won't have > time to do that one soon (huge amounts to do before SIAM CSE next week) but > feel free to have a try and complain when it doesn't work! > > Cheers, > > David > > On 4 March 2015 at 22:23, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > >> Hi all, >> >> I'd need to copy nodal values between fields on parent and extruded >> meshes. For example, copy 2d->3d (constant over vertical) or 3d->2d >> (extract surface/bottom level). The horizontal function space is the >> same. Is there an easy way to do this? Is there a map of extruded nodes >> somewhere? >> >> Thanks, >> >> Tuomas >> >> >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > > > > -- > Dr David Ham > Departments of Mathematics and Computing > Imperial College London > > http://www.imperial.ac.uk/people/david.ham > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Projection on DG0 space fails on large core counts
by Eike Mueller 03 Jun '15

03 Jun '15

Dear firedrakers, I now re-ran my code on up to 1536 cores on ARCHER, but I get a problem when I try to project an expression onto a DG0 function space on an extruded grid. The full (very large) log is here https://gist.github.com/eikehmueller/83a5fc139e1fedb5306c but as far as I can tell the following crashes: r_p.project(expression,solver_parameters={'ksp_type':'cg','pc_type':'jacobi’}) and here is the relevant part of the trace that I attempted to reconstruct: File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/function.py", line 157, in project return projection.project(b, self, *args, **kwargs) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/projection.py", line 94, in project […] solving_utils.check_snes_convergence(self.snes) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/variational_solver.py", line 163, in solve File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/profiling.py", line 199, in wrapper %s""" % (snes.getIterationNumber(), msg)) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/solving_utils.py", line 62, in check_snes_convergence return f(*args, **kwargs) RuntimeError: Nonlinear solve failed to converge after 1 nonlinear iterations. It does work fine on smaller processor numbers. Maybe the PETSc integers overflow again, the number of cells is 5242880 x 64 = 335544320 ~ 2^{28}, which is not too far from 2^{32}, but I thought I check in case you’ve seen something similar before. I thought I had managed to run problems of this size in the past (i.e. earlier this year). Thanks, Eike

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EUCLID BoomerAMG smoother on ARCHER
by Eike Mueller 29 May '15

29 May '15

Hi, I just tried to run the PETSc fieldsplit solver with the EUCLID smoother for the BoomerAMG preconditioner on ARCHER, and I get this error message: ============= error stack trace ==================== [18] ERROR: global index 112 not found in map Numbering_dhGlobalToLocal file= Numbering_dh.c line= 175 [18] called from: Factor_dhSolveSetup file= Factor_dh.c line= 555 [18] called from: Euclid_dhSetup file= Euclid_dh.c line= 282 [18] called from: HYPRE_EuclidSetup file= HYPRE_parcsr_Euclid.c line= 278 any idea what might cause this? I can run this without problems on my laptop. Thanks, Eike

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FEniCS '15 registration. Imperial people: yes, you do have to register.
by David Ham 28 May '15

28 May '15

Dear Imperial FEniCS '15 participants (and apologies for spamming the other people on these lists), In response to a couple of enquiries this week, please be aware that Imperial staff and students who are intending to attend FEniCS '15 *do* have to register. The only exception is if you only plan to participate in the poster session and/or the public lecture. If you intend to attend the rest of the workshop then you need to register. Registration is comparatively cheap (given that you get food + beverages for 2.5 days) but it does get more expensive after this weekend! Register online at: http://bit.ly/1J5jIkJ Cheers, David

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Coordinates of nodes
by Colin Cotter 27 May '15

27 May '15

Dear all, What's the easiest way to get global coordinates evaluated at node points for normal evaluation nodes of H(div) spaces? Cheers Cjc

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FEniCS '15 Early registration closes on 31 May
by David Ham 27 May '15

27 May '15

Dear all, This is a gentle reminder that FEniCS '15 early registration closes this coming Sunday. From Monday, registration will cost £200 instead of £150. Note that this is not merely an attempt to fleece you: I need to make catering and other orders so I really need to know fairly firm numbers. If you haven't registered yet, please head to the link below and do so! http://bit.ly/1J5jIkJ Cheers, David

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Additional poster spaces, and poster board size.
by David Ham 22 May '15

22 May '15

Dear all, A few people have emailed me asking if they can submit a late poster abstract. I have now sourced the poster boards and there isn't a problem fitting in a few more posters. I have therefore emailed those people to tell them how to submit an abstract. If there is anyone else out there who would like to put in a poster and who has not yet done so, please email me and I'll make it possible for you to submit an abstract. For those of you who will be bringing posters to the workshop, the poster boards will accommodate an A0 portrait format poster. The boards are perhaps 2m tall and don't have legs, so there is plenty of vertical space, but A0 landscape posters won't fit. Regards, David

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