September 2018 - firedrake

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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Creating indicator functions for Gmsh physical points/curves/surfaces in Firedrake
by Terenin, Alexander 27 Sep '18

27 Sep '18

I have a Gmsh mesh which has physical points/curves/surfaces. I need to create indicator functions for these that are equal to 1 for nodes in the given physical entity and zero everywhere else. The tutorial https://www.firedrakeproject.org/demos/linear_fluid_structure_interaction.p… says that this can be done via ``` fn = Function(fnspace) par_loop( 'for (int i=0; i < f.dofs; i++) f[i][0] = 1.0;', dx(subdomain_id), {'f': (fn, WRITE)} ) `` where subdomain_id is the numerical id of the physical entity in Gmsh. Unfortunately, this only works for physical surfaces and not points or lines. The error I get is ``` File "firedrake/dmplex.pyx", line 1022, in firedrake.dmplex.get_cell_markers ValueError: Invalid subdomain_id 5 not in [3 4] ``` where 5 is a physical line, 1,2 are physical points, and 3,4 are physical surfaces. Is there a different way I can create the necessary indicator function?

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Installation on macOS Sierra
by Yamazaki, Hiroe 26 Sep '18

26 Sep '18

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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installing the complex branch
by Shipton, Jemma 25 Sep '18

25 Sep '18

Hi All, I am attempting to use the complex branch of Firedrake but I'm having problems - I hope someone can help! I installed Firedrake using the firedrake-install script from the complex branch, using the command: python3 firedrake-install --disable-ssh --complex --minimal-petsc --adjoint --slope --install gusto --package-branch ufl complex --package-branch tsfc complex --package-branch PyOP2 complex --package-branch COFFEE complex --venv complex-firedrake I have activated the correct virtual environment and checked out the complex branch of firedrake: (complex-firedrake) jshipton@JSMac~/complex-firedrake/src/firedrake $ git branch * complex master I'm not sure which of the tests are supposed to work on this branch so I just tried the following: from firedrake import * mesh = UnitSquareMesh(10, 10) V = FunctionSpace(mesh, "CG", 1) and got the error: Traceback (most recent call last): File "test_complex.py", line 4, in <module> V = FunctionSpace(mesh, "CG", 1) File "<decorator-gen-716>", line 2, in FunctionSpace File "/Users/jshipton/complex-firedrake/src/PyOP2/pyop2/profiling.py", line 60, in wrapper return f(*args, **kwargs) File "/Users/jshipton/complex-firedrake/src/firedrake/firedrake/functionspace.py", line 118, in FunctionSpace element = make_scalar_element(mesh, family, degree, vfamily, vdegree) File "/Users/jshipton/complex-firedrake/src/firedrake/firedrake/functionspace.py", line 40, in make_scalar_element mesh.init() File "/Users/jshipton/complex-firedrake/src/firedrake/firedrake/mesh.py", line 993, in init self._callback(self) File "/Users/jshipton/complex-firedrake/src/firedrake/firedrake/mesh.py", line 1335, in callback (self.num_vertices(), geometric_dim)) File "firedrake/dmplex.pyx", line 851, in firedrake.dmplex.reordered_coords ELSE: ValueError: Buffer dtype mismatch, expected 'PetscReal' but got 'complex double' Did I miss a step or is this currently broken? I've attached the install log just incase that has any useful information but it looks happy with everything... Thanks! Jemma

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Help me
by Emmanuel Yarleque Medina 19 Sep '18

19 Sep '18

The installation error is attached in ubuntu 17.04LTS

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