- firedrake - imperial.ac.uk

.at() and PointNotInDomainError
by Floriane Gidel [RPG] 26 Oct '18

26 Oct '18

Dear all, When trying to evaluate a function u on some mesh points with mesh = Mesh('coarse/Omega_coarse.msh') V = FunctionSpace(mesh, "CG",1) V_Vec = VectorFunctionSpace(mesh, "CG", 1) u = Function(V) points = Function(V_vec).interpolate(SpatialCoordinate(mesh)) dat = u.at(points.dat.data_ro) I get the following error: File "lin_dyn_unicell.py", line 117, in <module> dat = u.at(points.dat.data_ro) File "/Users/gidel/Documents/Firedrake/firedrake/src/firedrake/firedrake/function.py", line 585, in at raise PointNotInDomainError(self.function_space().mesh(), points[i].reshape(-1)) firedrake.function.PointNotInDomainError: domain <Mesh #1> does not contain point [200. 66.66666667] How is that possible while both function spaces are defined on the same mesh? Note that in this example I am using the same domain to make sure the points are the same in the two cases, but I used to run this with different meshes and it worked on my laptop with an old firedrake version but not on my new machine on which I installed Firedrake yesterday. Thank you for your feedback, Floriane

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Sanity check
by Jon Hill 24 Oct '18

24 Oct '18

Hi folks, Can I just get a sanity check on this bit of code to check I'm not doing something insane (I probably am) or stupid (equally likely). The problem is a basic diffusion equation where a pile of sediment is eroded and transport by diffusion only. The un-erodable topographic surface (land) + sediment (phi) make up the land surface and the slope over which the sediment is moved. The attached figure might show it more clearly. phi is therefore moved according to the 2nd order (phi+land). However, I've also had to "turn off" diffusion by setting the diffusion coefficient (nu) to zero where there is no sediment or volume is definitely not conserved. The equation is set up using: tiny = 1e-10 surface.interpolate((((land+phi) + land)+abs((land+phi)-land)) / 2) thickness.interpolate(surface-land) limit.interpolate((surface - land)/(surface-land+tiny)) F = (inner((phi - phi_)/timestep, v) + limit*nu*inner(grad(phi+land), grad(v)))*dx And then simply solved: solve(F == 0, phi) in the time loop, updating limit and surface as we go. Hopefully, the above is understandable, but if anyone has any opinions on my (in)sanity, then I'm happy to hear them! Cheers, J. -- I'm currently in Australia and replies will not be in standard UK business hours. Please do not feel you have to respond outside your normal work hours. Dr Jon Hill Senior Lecturer in Physical Geography Department of Environment and Geography University of York M: +44(0)7748254812 P: +44(0)1904 324480 Twitter: @jonxhill Web: https://jonxhill.wordpress.com/ Web: https://envmodellinggroup.github.io/

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problems updating
by Francis Poulin 23 Oct '18

23 Oct '18

Hello, I have tried updating firedrake for the first time in months but it seems to fail. The output suggests doing a firedrake-clean, which I have tried but that seems to have failed. I am attaching the log file. Can anyone suggest something that I might be able to try to get this working? Cheers, Francis ------------------ Francis Poulin Associate Dean, Undergraduate Studies Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 [X]

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Re: [firedrake] Fix for problem with Monge-Ampere demo
by Ham, David A 11 Oct '18

11 Oct '18

Hi Dave, This is really rather odd. Do you happen to have the exception lying around somewhere? E.g. does the problem occur when the demo is run, or maybe when pylit is run on the input rst file? We ought to be able to fix this within Firedrake in an environment-independent way but it depends a bit on where the issue occurs. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Acreman, David" <D.M.Acreman(a)exeter.ac.uk> Reply-To: firedrake <firedrake(a)imperial.ac.uk> Date: Thursday, 11 October 2018 at 11:28 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] Fix for problem with Monge-Ampere demo Hi all, I ran into a slightly odd problem running one of the demos and thought it would be useful to post the solution in case anyone else is having the same problem. The problem was triggered by a non-ascii character in the Monge-Ampere demo (ma-demo) which showed up as a failure when running the test suite. The resulting error message is: UnicodeDecodeError: ’ascii’ codec can’t decode byte 0xc3 in position 41: ordinal not in range(128) This can be fixed by setting the LC_ALL environment variable e.g. for bash-like shells export LC_ALL=en_US.utf-8 You can check the encoding by running python3 -c 'import sys; print(sys.stdin.encoding)’ which should report "UTF-8” with the environment variable set. The encoding usually seems to work correctly but didn’t on our local cluster. Regards, Dave Dr. David Acreman, Senior Research Fellow, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4QL

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Fix for problem with Monge-Ampere demo
by Acreman, David 11 Oct '18

11 Oct '18

Hi all, I ran into a slightly odd problem running one of the demos and thought it would be useful to post the solution in case anyone else is having the same problem. The problem was triggered by a non-ascii character in the Monge-Ampere demo (ma-demo) which showed up as a failure when running the test suite. The resulting error message is: UnicodeDecodeError: ’ascii’ codec can’t decode byte 0xc3 in position 41: ordinal not in range(128) This can be fixed by setting the LC_ALL environment variable e.g. for bash-like shells export LC_ALL=en_US.utf-8 You can check the encoding by running python3 -c 'import sys; print(sys.stdin.encoding)’ which should report "UTF-8” with the environment variable set. The encoding usually seems to work correctly but didn’t on our local cluster. Regards, Dave Dr. David Acreman, Senior Research Fellow, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4QL

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local discontinuity
by Floriane Gidel [RPG] 05 Oct '18

05 Oct '18

Dear Firedrakers, I would like to solve equations in a domain made of two subdomains: - a disk, inside which test functions are continuous (Omega_d) - a plane around the disk, in which test functions are continuous (Omega_p) However, I would like the test functions to be discontinuous across the interface Gamma between the disk and the surrounding plane. This is to solve Laplace equation in each domain, augmented by a dynamic boundary condition on the jump between the two domains, that is Delta u = 0 in Omega_d Delta u = 0 in Omega_p partial_t [u] = ... on Gamma, where [u]= u(+)-u(-) is the jump Is there a way to define a functionspace on the full mesh, with continuous basis functions in each subdomain but discontinuous across the interface ? Or is there any better way to solve this kind of system ? Thank you for your help, Floriane

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Further complex simplifications
by Ham, David A 04 Oct '18

04 Oct '18

Dear Firedrakers, We have now merged the PyOP2 and COFFEE complex branches too. This means that the only special branches you need for complex are Firedrake and tsfc. The installation instructions have been updated accordingly: https://github.com/firedrakeproject/firedrake/projects/4 Existing firedrake complex installations should be updated with: cd src/COFFEE git checkout master cd ../PyOP2 git checkout master firedrake-update You should run firedrake-status to check that only the firedrake and tsfc components are still on the complex branch. Regards, David

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UFL complex branch is merged
by Ham, David A 03 Oct '18

03 Oct '18

Dear Firedrakers, Since FEniCS have merged the UFL complex branch upstream, this branch is now obsolete and has been deleted from github. Users of the (experimental) complex branches should therefore switch to ufl master. From an existing Firedrake complex installation, type: cd src/ufl git checkout master The installation instructions for complex have been updated: https://github.com/firedrakeproject/firedrake/projects/4 Regards, David

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Back full time
by Ham, David A 27 Sep '18

27 Sep '18

Dear Firedrakers, This is just a brief note to let everyone know that I’m now back full time after my 8 month stint on half-time parental leave. Hopefully you will find me more responsive to requests for help now, and I will be getting stuck in to finishing off complex. The time I’ve been able to spend with my son has been brilliant and I appreciate the understanding that the Firedrake community has shown for my limited availability over most of this year. To celebrate being back full time and to say thank you, I’ll be buying beers in the Queen’s Arms from 1730 on Tuesday. Cheers, David

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Re: [firedrake] Installation on macOS Sierra
by Ham, David A 27 Sep '18

27 Sep '18

Dear Hiroe, This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken. Regards, David On 26/09/2018, 17:33, "firedrake-bounces(a)imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces(a)imperial.ac.uk on behalf of h.yamazaki(a)imperial.ac.uk> wrote: Dear Firedrakers, I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this? All the best, Hiroe

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