November 2018 - firedrake - imperial.ac.uk

Re: [firedrake] Periodic domain with imported mesh
by Ham, David A 29 Nov '18

29 Nov '18

Hi Floriane, The short version is “no” because the right smarts tying together the gmsh, dmplex and Firedrake concepts of periodicity have not been done. Could you give a little detail of what sort of domain and mesh you want, and we can give some thought to whether we can do that for you. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Floriane Gidel [RPG]" <mmfg(a)leeds.ac.uk> Date: Wednesday, 7 November 2018 at 10:40 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] Periodic domain with imported mesh Dear all, Is there a way to force an imported mesh (created with Gmsh) to be x- and y-periodic ? (maybe something similar to the option 'constrained_domain' when defining a FunctionSpace in FeniCs ?) Thank you, Floriane

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replacing indexed mixed coefficients
by Cotter, Colin J 23 Nov '18

23 Nov '18

Dear Firedrake, In the Gusto equations rewrite project we are bumping into an issue with replacing components of mixed coefficients/test functions. The setup is that we want to write down a UFL form describing a mixed problem, and extract the subproblem for one of the components. The code that describes this is: from firedrake import * mesh = UnitSquareMesh(10,10) V = FunctionSpace(mesh,"CG",1) W = V * V w1, w2 = TestFunctions(W) u = Function(W) u1, u2 = split(u) F = (u1*w1 + u2*w2)*dx w = TestFunction(V) u0 = Function(V) F1 = replace(F, {w1:0}) F2 = replace(F1, {w2:w}) F3 = replace(F2, {u2,u0}) This does not work because w1 is not a terminal, it is an indexed mixed test function. I think what is happening is that the index is the terminal, but I don't really know what I am talking about. What is the solution to this? We have a workaround but I don't like it very much, which is to describe the equations in the mixed system individually, and then use replace to build the equivalent monolithic coupled system if we want to just apply implicit midpoint to the whole thing, but generating the individual equations from the monolithic coupled system would be much tidier. all the best --Colin

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Re: [firedrake] replacing indexed mixed coefficients
by Ham, David A 23 Nov '18

23 Nov '18

I think indexed is what is referred to as a modified terminal. Can you raise this as an issue and I’ll try to work out what we need to do. From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Cotter, Colin J" <colin.cotter(a)imperial.ac.uk> Date: Friday, 23 November 2018 at 09:20 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] replacing indexed mixed coefficients Dear Firedrake, In the Gusto equations rewrite project we are bumping into an issue with replacing components of mixed coefficients/test functions. The setup is that we want to write down a UFL form describing a mixed problem, and extract the subproblem for one of the components. The code that describes this is: from firedrake import * mesh = UnitSquareMesh(10,10) V = FunctionSpace(mesh,"CG",1) W = V * V w1, w2 = TestFunctions(W) u = Function(W) u1, u2 = split(u) F = (u1*w1 + u2*w2)*dx w = TestFunction(V) u0 = Function(V) F1 = replace(F, {w1:0}) F2 = replace(F1, {w2:w}) F3 = replace(F2, {u2,u0}) This does not work because w1 is not a terminal, it is an indexed mixed test function. I think what is happening is that the index is the terminal, but I don't really know what I am talking about. What is the solution to this? We have a workaround but I don't like it very much, which is to describe the equations in the mixed system individually, and then use replace to build the equivalent monolithic coupled system if we want to just apply implicit midpoint to the whole thing, but generating the individual equations from the monolithic coupled system would be much tidier. all the best --Colin

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20 Nov '18

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14 Nov '18

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Simple code failing in parallel
by Chris Eldred 13 Nov '18

13 Nov '18

Hey Firedrakers, The attached simple code is failing in parallel but works fine in serial. Specifically, when I run mpirun -n 1 python3 failing_example.py everything is fine. However, using mpirun -n 2 python3 failing_example.py fails with a segfault in PETSc. As far as I can tell (by adding print statements to various parts of the Firedrake src), the segfault is occurring in the set_function method of the _SNESContext class from solving_utils.py, specifically line 130: with self._F.dat.vec_wo as v: I don't know enough about the internals of Firedrake to diagnose the issue beyond that. Any ideas what could be going wrong? I am running a new copy of Firedrake on Ubuntu 18.04. Regards, Chris Eldred -- Chris Eldred https://www.math.univ-paris13.fr/~eldred/ Research Scientist, INRIA/Laboratoire Jean Kuntzmann Postdoctoral Fellow, LAGA, University of Paris 13 PhD, Atmospheric Science, Colorado State University, 2015 DOE Computational Science Graduate Fellow (Alumni) B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com

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firedrake_adjoint error
by Cotter, Colin J 09 Nov '18

09 Nov '18

Dear all, I'm getting the following error when I run the attached code (uses firedrake_adjoint). Did I do something silly or should I file a bug report? all the best --Colin Traceback (most recent call last): File "outer.py", line 80, in <module> z0Solver.solve() File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/variational_solver.py", line 48, in solve **sb_kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/solving.py", line 56, in __init__ self._init_dependencies(*args, **kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/solving.py", line 137, in _init_dependencies self.add_dependency(bc.block_variable, no_duplicates=True) File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/block.py", line 38, in add_dependency dep.will_add_as_dependency() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/block_variable.py", line 61, in will_add_as_dependency overwrite = self.output._ad_will_add_as_dependency() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/overloaded_type.py", line 332, in _ad_will_add_as_dependency self._ad_annotate_block() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/overloaded_type.py", line 349, in _ad_annotate_block block = self.block_class(*self._ad_args, **self._ad_kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/types/dirichletbc.py", line 90, in __init__ self.collapsed_space = self.function_space.collapse() File "/Users/colincotter/firedrake/src/firedrake/firedrake/functionspaceimpl.py", line 212, in __getattr__ return getattr(self.topological, name) AttributeError: 'ProxyFunctionSpace' object has no attribute 'collapse'

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Preconditioning grad(ln(c)) term
by Justin Chang 07 Nov '18

07 Nov '18

Hi everyone, I am attempting to solve the electrolyte domain of li-ion battery model. The concentration problem is somewhat like a nonlinear diffusion/heat equation but it gets messy because it has a div(grad(ln(c))) term. So I would be looking at something like this: -div(k1*grad(c)) + div(k2*grad(ln(c))) = 0 Which we can rewrite as: -div((k1 - k2/c)*grad(c)) = 0 If k2 is relatively small enough, the newton solver should converge with little problem. The problem I am having is with the linear solve. If I discretize the above using CG1, no solver works so long as k2 >> 0. With DG1, I can only use direct solvers like LU to solve the resulting linear system of equations. I can't seem to find a good iterative solver/pc to solve this - HYPRE gives me a DIVERGED_NANORINF, and jacobi/bjacobi do not converge at all. I've attached the code for you guys to play around with. I don't know what is a good PC for grad(ln(c)), my guess is that I'm going to need to provide an assembled preconditioner which approximates the inverse of the k2/c*grad(c) term but it doesn't seem clear to me how I can provide an explicit PC to the nonlinear solver without resorting to hacking at petsc4py. Any thoughts appreciated Justin

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Offline installs
by Lawrence Mitchell 07 Nov '18

07 Nov '18

Dear Andrew, > Begin forwarded message: > > From: mailman-bounces(a)imperial.ac.uk > Subject: Uncaught bounce notification > Date: 7 November 2018 at 14:19:04 GMT > To: firedrake-owner(a)imperial.ac.uk > > From: "Little, Andrew B" <a.little14(a)imperial.ac.uk <mailto:a.little14@imperial.ac.uk>> > Subject: Offline Install > Date: 7 November 2018 at 14:19:02 GMT > To: firedrake-bounces <firedrake-bounces(a)imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk>> > > > I have a requirement to install firedrake & thetis offline on a cluster - before I start bumbling around does anyone have any advice on how best to install firedrake & thetis: > a) Offline > b) On a cluster > > I appreciate this is too little info to give any detailed advice but I just wanted to test the water for what I am getting myself into! PETSc, which is a major part of this, allows providing local paths to the packages it installs. In theory this might be possible via firedrake-install. Chasing all the python dependencies is going to be tricky. If the system is "standard" you could install on a machine that has internet access in the same directory structure you're eventually going to use, zip it up, and transfer it over. One asks why you need to do this. If you have ssh access to the machine in question, I would set up a reverse-tunnelled proxy to send everything through. Cheers, Lawrence

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Help me
by Emmanuel Yarleque Medina 07 Nov '18

07 Nov '18

This is my installation error: Building extension modules Traceback (most recent call last): File "setup.py", line 8, in <module> import petsc4py ImportError: No module named 'petsc4py' Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests Traceback (most recent call last): File "/usr/lib/python3.5/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.5/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/emmanuel/firedrake/lib/python3.5/site-packages/pytest.py", line 7, in <module> from _pytest.assertion import register_assert_rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/__init__.py", line 12, in <module> from _pytest.assertion import rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/rewrite.py", line 24, in <module> from _pytest.pathlib import fnmatch_ex File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/pathlib.py", line 26, in <module> from pathlib2 import Path, PurePath ImportError: No module named 'pathlib2' Makefile:60: recipe for target 'test' failed make: *** [test] Error 1 (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ sudo su [sudo] senha para emmanuel: root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# make alltest Building extension modules Traceback (most recent call last): File "setup.py", line 31, in <module> import versioneer File "/home/emmanuel/firedrake/src/firedrake/versioneer.py", line 1658 file=sys.stderr) ^ SyntaxError: invalid syntax Linting firedrake codebase /usr/bin/python: No module named flake8 Makefile:8: recipe for target 'lint' failed make: *** [lint] Error 1

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