- firedrake - imperial.ac.uk

Fwd: Math Libraries
by Kelly, Paul H J 21 Jun '14

21 Jun '14

Meanwhile here is another - thank you to Freddie Witherden for both of these finds: "The Metalibm project provides a tool for the automatic implementation of mathematical (libm) functions. A function f is automatically transformed into Gappa-certified C code implementing an approximation polynomial in a given domain with given accuracy." Code: http://lipforge.ens-lyon.fr/www/metalibm/ Slides: http://tamadiwiki.ens-lyon.fr/tamadiwiki/images/d/d8/DeDinechin2013.pdf The context of this was the "STOKE" PLDI paper I mentioned last week, http://web.stanford.edu/~sharmar/pubs/fp.pdf The point being that MetaLibc produces approximated functions with proven properties, while STOKE stochastically searches for implementations that are "close enough" under testing. Paul Begin forwarded message: From: "Witherden, Freddie" <freddie.witherden08(a)imperial.ac.uk<mailto:freddie.witherden08@imperial.ac.uk>> Date: 21 June 2014 12:43:12 GMT+01:00 To: "Kelly, Paul H J" <p.kelly(a)imperial.ac.uk<mailto:p.kelly@imperial.ac.uk>> Subject: Math Libraries Hi Paul, With regards to our discussion last week on math libraries (and how you can apparently get away with flipping an instruction here and there) I am wondering if you have heard about metalibm: http://lipforge.ens-lyon.fr/www/metalibm/ http://tamadiwiki.ens-lyon.fr/tamadiwiki/images/d/d8/DeDinechin2013.pdf It is from the same group that developed crlibm. Regards, Freddie.

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Re: [firedrake] bcs
by Andrew McRae 17 Jun '14

17 Jun '14

Can you elaborate? 'top' and 'bottom' are there by default, otherwise you rely on markers on the base mesh (1 to 4 on a square) On 17 Jun 2014 12:30, "Cotter, Colin J" <colin.cotter(a)imperial.ac.uk> wrote: > So, what if I want to do the same for an extruded mesh? > > --cjc > ________________________________________ > From: Cotter, Colin J > Sent: 17 June 2014 09:14 > To: firedrake > Subject: RE: [firedrake] bcs > > doh! thanks. > ________________________________________ > From: firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Lawrence Mitchell [lawrence.mitchell(a)imperial.ac.uk] > Sent: 17 June 2014 09:00 > To: firedrake > Subject: Re: [firedrake] bcs > > > On 17 Jun 2014, at 09:45, "Cotter, Colin J" <colin.cotter(a)imperial.ac.uk> > wrote: > > > > from firedrake import * > > mesh = UnitSquareMesh(3,3,reorder=False) > > V = FunctionSpace(mesh,"CG",1) > > bc = DirichletBC(V,0.,"1") > > 1 not "1" > > > > print bc.nodes > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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bcs
by Cotter, Colin J 17 Jun '14

17 Jun '14

Dear firedrakers, The following code: from firedrake import * mesh = UnitSquareMesh(3,3,reorder=False) V = FunctionSpace(mesh,"CG",1) bc = DirichletBC(V,0.,"1") print bc.nodes produces: Traceback (most recent call last): File "test.py", line 5, in <module> print bc.nodes File "/home/cjc1/firedrake/firedrake/firedrake/utils.py", line 43, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/cjc1/firedrake/firedrake/firedrake/bcs.py", line 155, in nodes fs._mesh.exterior_facets.subset(self.sub_domain).indices, File "/home/cjc1/firedrake/firedrake/firedrake/mesh.py", line 185, in subset markers = as_tuple(markers, int) File "/home/cjc1/firedrake/PyOP2/pyop2/utils.py", line 62, in as_tuple raise TypeError("Items need to be of type %s" % type) TypeError: Items need to be of type <type 'int'> Is this a known bug? --cjc

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Demo illustrating more complicated forms
by Marie E. Rognes 16 Jun '14

16 Jun '14

Dear Firedrakers, Please consider the below if you ever need a more complicated variational form for stress testing and benchmarking. https://gist.github.com/meg-simula/3ab3fd63264c8cf1912b Best regards, Marie -- Marie E. Rognes, PhD Head of Department Biomedical Computing Department Simula Research Laboratory P.0.Box 134, 1325 Lysaker, Norway http://home.simula.no/~meg/ Skype: m.e.rognes Cell: +47 45 66 23 96

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Rob Kirby seminar 1200 TODAY!
by David Ham 13 Jun '14

13 Jun '14

Hi All, We have a really great seminar at Midday today in Huxley. I hope to see you all there! David "Mixed finite Element methods for wave equations" 13th June 2014, 12-13, 130 Huxley. Dr Robert Kirby, Department of Mathematics, Baylor University, USA Abstract: Wave equations model many important applications, such as acoustics and oceanic tides. Mixed finite element methods discretize the conservative first-order form of such equations and preserve important mathematical and physical structure. I will begin by surveying some of the basic features of these discretizations. Then, I will present new semi discrete energy estimates for linear tide models. These estimates give long-term stability and, in the absence of forcing terms, give exponential decay of solution profiles to a steady, solenoidal field. However, these results still leave important practical details related to algorithms and software open, such as time-stepping and enabling the right kinds of operations efficiently. I will conclude by surveying some of the challenges that thus presented to software tools such as FEniCS and Firedrake. http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/naturalscienc… -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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trying to set up nonlinear problem
by Cotter, Colin J 12 Jun '14

12 Jun '14

Dear Firedrakers, When I run the following script: https://gist.github.com/anonymous/32edd8c9c1614c1e2b67 I get: ufl.log.UFLException: All terms in form must have same rank. This is probably because I don't know how to set up nonlinear problems properly. Can anyone spot what is wrong? cheers --cjc

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latest
by Colin Cotter 03 Jun '14

03 Jun '14

Dear Firedrakers, Latest results, I have just done my first solution of a mixed Helmholtz equation on the extruded spherical annulus (the volume between two nested spheres, i.e. the geometry we need to solve for the atmosphere). This works thanks to: * extruded mesh iterators from Doru * extruded FEM spaces from Andrew * The "Hedgehog" mesh and help on how to use the preconditioner from Lawrence * everything else in Firedrake... See attached for a picture showing the solution a couple of slices through the solution (obviously the resolution is quite coarse!). For those in the know, this is actually using the "shallow atmosphere approximation" which neglects the increase in spherical surface area with radial direction (obviously a bad approximation for this O(1) mesh!). Next step is to use the hedgehog trick to add the curvature terms so that we remove this approximation, and of course some validation tests. Then we'll move on to building an atmosphere model using this setup. Keep up the good work! --cjc

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Seminar on mixed finite elements for wave equations by Rob Kirby 1200 on Friday 13 in Huxley 130
by David Ham 03 Jun '14

03 Jun '14

Hi All, Rob Kirby, of FIAT, FEniCS and Sundance fame, is visiting us next week. He'll be giving what promises to be a very interesting seminar at 1200 on Friday in Huxley 130. I'd encourage you all to attend. (And for those attending FEniCS '14 in Paris the next week, this is very different from his talk there!) Full seminar details are at: http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/naturalscienc… Cheers, David -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Fwd: Jan Vitek, today, 2nd June, R: a language for data analytics - ROOM 308 (changed)
by David Ham 02 Jun '14

02 Jun '14

A talk in 15 minutes time which Firedrake people might be interested in. *The once and future R: a language for data analytics* * Prof. Jan Vitek, Purdue* *TIME 2nd June, 11:00* *ROOM 308* Data analytics is all the rage. This talk overviews the state of the R programming language — a language designed by, and for, statisticians and data scientists of all stripes. With millions of users worldwide, R is a success story amongst domain specific programming languages, yet it is also misunderstood. R is both a lazy functional language and an imperative object-oriented one. It emphasizes rigorous mathematical development, yet it has not formal semantics and relies on unstructured reflective operations. It’s design is a puzzle; it’s performance is a tragedy. After conducting a large corpus study, we have gained a better understanding of the semantics R and of its real-world usage. Armed with this information, we have implemented FastR a self-optimizing interpreter for the language that yields an average 7x speed up. The techniques we are exploring are not limited to R but apply more widely to the family of dynamic language that includes JavaScript, Ruby, Lua, Python and PHP. Biography Jan Vitek is a Professor of Computer Science at Purdue University and University Faculty Scholar. Over the years, he worked on topics related to programming languages, their design, use, and implementation. With Noble and Potter, he proposed the notion of flexible alias control which became know as Ownership Types. He led the Ovm project which produced the first real-time Java virtual machine to be flight tested on a ScanEagle drone (he claims no one was harmed). Outcomes of this project include the Schism real-time garbage collector and the FijiVM – a production VM for embedded systems. More recently, Jan worked on dynamic languages, trying to make sense of JavaScript and to design a new language called, Thorn. Nowadays, he spends his time with statisticians and data scientists. Jan believes that his 2012 election as Chair of SIGPLAN was an accident; since has been busy trying to rock the boat to ensure this does not happen again. In his spare time, Jan enjoys organizing conferences and sitting on PCs (over 25 in the last decade). He founded the MOS (mobile objects), IWACO (alias control), STOP (gradual typing), and TRANSACT (transactional memory) workshop series. He was the first program chair of VEE and chaired ESOP, ECOOP, Coordination and TOOLS. He was the general chair of PLDI (in Beijing!), ISMM and LCTES. He may still be sitting on the steering committees of ECOOP, JTRES, ICFP, OOPLSA, POPL, PLDI, LCTES, ESOP. Jan will spend part of 2nd June at IC. Please let me know if you want to talk with him. Sophia -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Firedrake is now available on Archer
by Michael Lange 23 May '14

23 May '14

Hi, Firedrake is now available on Archer via the central system module 'firedrake'. To run Firedrake on the compute nodes please add the following to your .pbs file: module swap PrgEnv-cray PrgEnv-gnu module load anaconda module add firedrake and run your firedrake model with: aprun python my_firedrake_model.py Due to a known problem, Firedrake currently needs to be initialised in my_firedrake_model.py with: import pyop2 from firedrake import * If you have access to AUs on Archer, please give this a try and report any further problems you encounter. Thanks, Michael

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