- firedrake - imperial.ac.uk

Mapping nodal values from parent to extruded mesh
by Tuomas Karna 04 Mar '15

04 Mar '15

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

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Re: [firedrake] Problem with nonlinear solver on extruded mesh
by Andrew McRae 04 Mar '15

04 Mar '15

You may or may not need to do the whole chain: PETSc, petsc4py, FIAT, UFL, FFC, COFFEE, PyOP2, and Firedrake Good luck! On 4 March 2015 at 18:16, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > I haven't updated after the new year, so that might be it. Thanks! > > Anna. > > > > On 04/03/15 18:14, Andrew McRae wrote: > > Is your Firedrake completely up-to-date? > > It sounds not-unrelated to > https://github.com/firedrakeproject/firedrake/issues/472, which was fixed > recently. > > On 4 March 2015 at 18:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > >> Dear all, >> >> I am experiencing a problem with extruded meshes. When I try to solve >> the nonlinear VP: >> >> m = IntervalMesh(N,L) >> mesh = ExtrudedMesh(m, layers=10) >> >> F = ( v*(p1-p0)/dt + v*(h0-1) + sigma*inner(grad(v),grad(h0)) + >> 0.5*inner(grad(p0_5),grad(p0_5))*v )*dx + E_t*v*ds_v(1) >> >> I get the error >> >> File >> >> "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/variational_solver.py", >> line 97, in __init__ >> form_compiler_parameters=self._problem.form_compiler_parameters) >> File >> "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", >> line 58, in assemble >> form_compiler_parameters=form_compiler_parameters) >> File >> "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", >> line 79, in _assemble >> kernels = ffc_interface.compile_form(f, "form", >> parameters=form_compiler_parameters) >> File >> >> "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/ffc_interface.py", >> line 273, in compile_form >> ((kernel, needs_orientations), ) = ffc_kernel.kernels >> ValueError: need more than 0 values to unpack >> >> However, this problem does not arise when I switch to a RectangleMesh ( >> and change the ds_v(1) to ds(1) ), OR when I solve the corresponding >> linear VP. >> Anyone has any ideas why this is happening? >> >> Thank you. >> >> Best, Anna. >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > > > -- > > Dr Anna Kalogirou > Research Fellow > School of Mathematics > University of Leeds > >

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Re: [firedrake] Problem with nonlinear solver on extruded mesh
by Andrew McRae 04 Mar '15

04 Mar '15

Is your Firedrake completely up-to-date? It sounds not-unrelated to https://github.com/firedrakeproject/firedrake/issues/472, which was fixed recently. On 4 March 2015 at 18:09, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I am experiencing a problem with extruded meshes. When I try to solve > the nonlinear VP: > > m = IntervalMesh(N,L) > mesh = ExtrudedMesh(m, layers=10) > > F = ( v*(p1-p0)/dt + v*(h0-1) + sigma*inner(grad(v),grad(h0)) + > 0.5*inner(grad(p0_5),grad(p0_5))*v )*dx + E_t*v*ds_v(1) > > I get the error > > File > > "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 97, in __init__ > form_compiler_parameters=self._problem.form_compiler_parameters) > File > "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", > line 58, in assemble > form_compiler_parameters=form_compiler_parameters) > File > "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", > line 79, in _assemble > kernels = ffc_interface.compile_form(f, "form", > parameters=form_compiler_parameters) > File > > "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/ffc_interface.py", > line 273, in compile_form > ((kernel, needs_orientations), ) = ffc_kernel.kernels > ValueError: need more than 0 values to unpack > > However, this problem does not arise when I switch to a RectangleMesh ( > and change the ds_v(1) to ds(1) ), OR when I solve the corresponding > linear VP. > Anyone has any ideas why this is happening? > > Thank you. > > Best, Anna. > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Problem with nonlinear solver on extruded mesh
by Anna Kalogirou 04 Mar '15

04 Mar '15

Dear all, I am experiencing a problem with extruded meshes. When I try to solve the nonlinear VP: m = IntervalMesh(N,L) mesh = ExtrudedMesh(m, layers=10) F = ( v*(p1-p0)/dt + v*(h0-1) + sigma*inner(grad(v),grad(h0)) + 0.5*inner(grad(p0_5),grad(p0_5))*v )*dx + E_t*v*ds_v(1) I get the error File "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/variational_solver.py", line 97, in __init__ form_compiler_parameters=self._problem.form_compiler_parameters) File "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", line 58, in assemble form_compiler_parameters=form_compiler_parameters) File "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/assemble.py", line 79, in _assemble kernels = ffc_interface.compile_form(f, "form", parameters=form_compiler_parameters) File "/opt/firedrake/2.0/lib/python2.7/site-packages/firedrake/ffc_interface.py", line 273, in compile_form ((kernel, needs_orientations), ) = ffc_kernel.kernels ValueError: need more than 0 values to unpack However, this problem does not arise when I switch to a RectangleMesh ( and change the ds_v(1) to ds(1) ), OR when I solve the corresponding linear VP. Anyone has any ideas why this is happening? Thank you. Best, Anna.

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Re: [firedrake] Perturbing mesh extrusion at runtime
by David Ham 04 Mar '15

04 Mar '15

Hi Tuomas, I suspect you may be hitting a bug in the assembly cache. Does the issue go away if you specify: parameters["assembly_cache"]["enabled"] = False ? David On 3 March 2015 at 23:17, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > Hi all, > > Custom mesh extrusions can be generated by manipulating mesh.coordinates > directly. This works fine as long as the coordinates are changed prior > to the first solve. After that changing the coordinates has no effect as > precomputed mesh properties do not get updated. > > What do I need to do to force a mesh update? I need to update the > extrusion only, not the parent mesh. Can this be done efficiently? > > > Cheers, > > 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

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Perturbing mesh extrusion at runtime
by Tuomas Karna 03 Mar '15

03 Mar '15

Hi all, Custom mesh extrusions can be generated by manipulating mesh.coordinates directly. This works fine as long as the coordinates are changed prior to the first solve. After that changing the coordinates has no effect as precomputed mesh properties do not get updated. What do I need to do to force a mesh update? I need to update the extrusion only, not the parent mesh. Can this be done efficiently? Cheers, Tuomas

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FEniCS '15 @ Imperial College London 29 June - 1 July 2015
by David Ham 25 Feb '15

25 Feb '15

The 2015 FEniCS workshop will be held at Imperial College London from 29 June - 1 July. This is the annual opportunity for developers, users and anyone else interested in FEniCS, and its relatives such as dolfin-adjoint and Firedrake, to communicate results and ideas formally and informally, face to face. Registration and abstract submission are now open via the workshop webpage: http://firedrakeproject.org/fenics_15 The abstract deadline (yes, this year we're having one of these!) is 30 April. The early registration deadline is 31 May. I look forward to seeing you all in London! 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: [CMSE-Membership] Research talk - boundary integral equation problems - Timo Betcke - Thu Feb 26
by David Ham 24 Feb '15

24 Feb '15

This AMMP seminar may be of interest to a broader CMSE audience: Timo Betcke (UCL): BEM++ - Efficient solution of boundary integral equation problems The BEM++ boundary element library is a software project that was started in 2010 at University College London to provide an open-source general purpose BEM library for a variety of application areas. In this talk we introduce the underlying design concepts of the library and discuss several applications, including high-frequency preconditioning for ultrasound applications, the solution of time-domain problems via convolution quadrature, light-scattering from ice crystals, and the solution of coupled FEM/BEM problems with FEniCS and BEM++. Date: 26 Feb 2015 Time: 16:00 - 17:00 Venue: Huxley 340 Campus: South Kensington Campus Speaker: Timo Betcke, UCL Contact: Pavel Berloff -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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PETSc error when projecting onto DG space
by Eike Mueller 19 Feb '15

19 Feb '15

Dear firedrakers, having just updated both petsc and petsc4py on my laptop (pulled latest revision of mapdes/firedrake branch in both cases, and I use the origin/multigrid-extrusion branch of firedrake), I get the error message below when I try to project an expression onto a DG function: r_p = Function(W3) expression = Expression('exp(-0.5*(x[0]*x[0]+x[1]*x[1])/(0.25*0.25))') r_p.project(expression) This issue only came up with the PETSc update I did, never seen it before. Thanks a lot, Eike Error message: Number of cells on finest grid = 5120 dx = 364.458 km, dt = 2429.717 s Traceback (most recent call last): File "driver.py", line 485, in <module> main(parameter_filename) File "driver.py", line 288, in main r_p.project(expression) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/function.py", line 135, in project return projection.project(b, self, *args, **kwargs) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/projection.py", line 94, in project form_compiler_parameters=form_compiler_parameters) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/solving.py", line 119, in solve _solve_varproblem(*args, **kwargs) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/solving.py", line 143, in _solve_varproblem solver.solve() File "<string>", line 2, in solve File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/profiling.py", line 197, in wrapper return f(*args, **kwargs) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/variational_solver.py", line 292, in solve self.snes.solve(None, v) File "SNES.pyx", line 516, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:153742) File "petscsnes.pxi", line 251, in petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:30058) File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/variational_solver.py", line 138, in form_function v.array[:] = X_.array[:] File "Vec.pyx", line 815, in petsc4py.PETSc.Vec.array.__get__ (src/petsc4py.PETSc.c:91905) File "arraynpy.pxi", line 67, in petsc4py.PETSc.asarray (src/petsc4py.PETSc.c:7333) File "petscvec.pxi", line 469, in petsc4py.PETSc._Vec_buffer.__getreadbuffer__ (src/petsc4py.PETSc.c:19630) File "petscvec.pxi", line 459, in petsc4py.PETSc._Vec_buffer.getbuffer (src/petsc4py.PETSc.c:19460) petsc4py.PETSc.Error: error code 73 [0] SNESSolve() line 3832 in /Users/eikemueller/PostDocBath/EllipticSolvers/petsc/src/snes/interface/snes.c [0] SNESSolve_KSPONLY() line 24 in /Users/eikemueller/PostDocBath/EllipticSolvers/petsc/src/snes/impls/ksponly/ksponly.c [0] SNESComputeFunction() line 2035 in /Users/eikemueller/PostDocBath/EllipticSolvers/petsc/src/snes/interface/snes.c [0] VecGetArray() line 1646 in /Users/eikemueller/PostDocBath/EllipticSolvers/petsc/src/vec/vec/interface/rvector.c [0] Object is in wrong state [0] Vec is locked read only, argument # 1 -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5803 e.mueller(a)bath.ac.uk http://people.bath.ac.uk/em459/

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Re: [firedrake] Crash when running at higher order on ARCHER: resolved now
by Fabio Luporini 16 Feb '15

16 Feb '15

I, however, recommend to always run with COFFEE on, because that'd be useful not just for performance, but also (and, at this stage, especially) for bug fixing. Then of course if you see something weird is going on, just turn off COFFEE. Thanks -- Fabio 2015-02-16 10:33 GMT+00:00 Homolya, Miklós <m.homolya14(a)imperial.ac.uk>: > Hi Eike, > > I think, in general, when you want to disable COFFEE, probably the best > place to do so is very soon after "from firedrake import *". > Or, alternatively, you may merge caffeine_withdrawal branch with whatever > branch you are using, and use that version of Firedrake. > > Regards, > Miklos > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Eike Mueller [e.mueller(a)bath.ac.uk] > *Sent:* 14 February 2015 10:53 > *To:* firedrake > *Subject:* Re: [firedrake] Crash when running at higher order on ARCHER: > resolved now > > Dear firedrakers, > > I finally got to the bottom of this. It turns out that I had set > parameters[“COFFEE”][“O2”]= False around the parloop which executes the > kernel, but not around the bit of code which actually compiles the UFL > form. Stupid mistake… So this caused a horrible segfault, since the kernel > expected data of size A[8][20], but it was passed A[6][18]. It was quite > tricky to find this kind of bug, though, since it only segfaults without > much information. I finally managed to run interactively on ARCHER, > inspected the core dump with gdb and looked at the generated c-code. I was > wondering whether this kind of issue can be detected when you generate the > wrapper code? Don’t you know both the signature of the function and the > passed data at this point? > > Or has the COFFEE optimisation issue been resolved? I pulled the latest > version of COFFEE, though. > > Thanks, > > Eike > > -- > > Dr Eike Hermann Mueller > Research Associate (PostDoc) > > Department of Mathematical Sciences > University of Bath > Bath BA2 7AY, United Kingdom > > +44 1225 38 5803 > e.mueller(a)bath.ac.uk > http://people.bath.ac.uk/em459/ > > On 5 Feb 2015, at 16:28, Eike Mueller <E.Mueller(a)bath.ac.uk> wrote: > > Thanks, I tried the atp and also inspected the core dump with > > gdb python core > > There is no backtrace in the core dump, and ATP does not generate any > information either. > > I still only get the segfault in my output file. I hope I can localise > this a bit more tomorrow. > > Eike > > On 05/02/15 15:23, Patrick Farrell wrote: > > On 05/02/15 14:37, Lawrence Mitchell wrote: > > > Number of cells on finest grid = 5120 dx = 364.458 km, dt = > 2429.717 s _pmiu_daemon(SIGCHLD): [NID 01160] [c6-0c0s2n0] [Thu Feb > 5 14:22:05 2015] PE RANK 11 exit signal Segmentation fault [NID > 01160] 2015-02-05 14:22:05 Apid 12880356: initiated application > termination Application 12880356 exit codes: 139 Application > 12880356 resources: utime ~31s, stime ~19s, Rss ~318352, inblocks > ~104428, outblocks ~788 Finished atThu Feb 5 14:22:10 GMT 2015 > > > Hmm, that's not a lot of useful information. > > > Try running again with > > module load atp > export ATP_ENABLED=1 > > Sometimes it gives useful information about abnormal terminations; > http://www.archer.ac.uk/documentation/best-practice-guide/debug.php > > Patrick > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

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