April 2015 - firedrake - imperial.ac.uk

Possible bug with perturbed extruded mesh?
by Tuomas Karna 14 Apr '15

14 Apr '15

Hi all, Encountered this issue with extruded mesh where the coordinates have been deformed. The first form a==L just evaluates div(u), the second a==L2 is the same but div(u) integrated in parts. Thus the results should be equivalent, but that's not what I see: a == L: 0.999999886488 1.0000001092 a == L2: -0.235329928101 3.47882106918 Without the mesh deformation the two forms give the correct solution (1.0). Am I missing something? Cheers, Tuomas --- from firedrake import * mesh2d = UnitSquareMesh(10,10) layers = 6 mesh = ExtrudedMesh(mesh2d, layers, -1.0/layers) P1 = FunctionSpace(mesh, 'CG', 1, vfamily='CG', vdegree=1) P2 = FunctionSpace(mesh, 'CG', 2, vfamily='CG', vdegree=1) P1v = VectorFunctionSpace(mesh, 'CG', 1, vfamily='CG', vdegree=1) # deform mesh scalar = Function(P1).interpolate(Expression('1.0+x[0]')) coords = mesh.coordinates coords.dat.data[:,2] *= scalar.dat.data[:] u = Function(P1v) w = Function(P2) u.interpolate(Expression(('x[0]', '0.0', '0.0'))) tri = TrialFunction(P2) test = TestFunction(P2) normal = FacetNormal(mesh) a = test*tri*dx L = div(u)*test*dx L2 = -dot(u, grad(test))*dx + dot(u, normal)*test*(ds_v+ds_t+ds_b) solve(a == L, w) print 'a == L:', w.dat.data.min(), w.dat.data.max() solve(a == L2, w) print 'a == L2:', w.dat.data.min(), w.dat.data.max()

1 0

Re: [firedrake] Mapping nodal values from parent to extruded mesh
by Fabio Luporini 11 Apr '15

11 Apr '15

Hi Tuomas Yes, the point of having ASTs instead of C code is for optimisation. However, you can stick to C strings and care about optimisation only at the very hand, if you saw a particular hand-written kernel is a bottleneck. In the future, we hope to integrate a parser to avoid writing ASTs Thanks -- Fabio 2015-04-11 0:50 GMT+01:00 Tuomas Karna <tuomas.karna(a)gmail.com>: > Hi David, > > Thanks for the clarification, this all makes sense. I think for the time > being I can live with CG in vertical. The pyop2 kernel documentation is > great. Is there a reason to prefer AST over hard-coded kernels? > Optimization? > > BTW, any chance of seeing you at FEniCS '15? > > Yes, I'm planning to attend, will submit abstract shortly. > > - Tuomas > > > On 04/10/2015 03:23 AM, David Ham wrote: > > Hi Tuomas, > > Concerning the sets of spaces which this will work for, I think that the > current implementation probably works for any horizontal space but only for > vertical CG. One could just try relaxing the test in that case. > > The reason for the restriction to vertical CG is that fs.bt_masks uses > the topological association of nodes with mesh entities in order to work > out which nodes are on the top or bottom of the cell. In order to allow DG > in the vertical, it would be necessary to support the geometric definition > (ie which basis functions do not vanish on the top/bottom). > > If you look at functionspace.py:78 you can see where the bottom and top > masks are generated. This uses entity_closure_dofs() from FIAT. In order to > use the geometric definition of dofs one would need to support using > facet_support_dofs() (which is how BC maps are set up at > functionspace.py:375). Currently FIAT TensorFiniteElement objects do > support entity_closure_dofs() but nobody has done the legwork to get them > to support facet_support_dofs. > > Concerning documentation, COFFEE is deplorably underdocumented (although > the author is on this list so maybe this will change ;). The actual > available AST nodes are only "documented" by reading the source: > https://github.com/coneoproject/COFFEE/blob/master/coffee/base.py > However, you are fundamentally writing a PyOP2 kernel, and the C api for > that *is* documented at: http://op2.github.io/PyOP2/kernels.html so that > hopefully helps somewhat. > > Otherwise, keep asking here or in IRC (IRC tends to get faster > responses, at least between about 10am and 8pm UK time). > > BTW, any chance of seeing you at FEniCS '15? > > Cheers, > > David > > > > On 10 April 2015 at 02:44, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > >> Hi all, >> >> A couple of questions regarding those extruded mesh -> parent mesh copy >> operations, >> >> A while back I got the reverse 2d->3d copy working with a hard-coded >> pyop2 kernel (like in mesh extrusion). I'm not familiar with COFFEE syntax, >> is there documentation/examples somewhere? >> >> The 3d->2d copy routine in extrusion_extraction branch checks that the >> function space is CG. Does this method easily generalize to other spaces? >> DGxCG prisms seem to work OK. I'm also interested in using DGxDG and >> RTxCG/DG spaces. >> >> >> Cheers, >> >> Tuomas >> >> >> On 03/05/2015 10:24 AM, Tuomas Karna wrote: >> >> Thanks David, >> >> This is great, I'll try doing the reverse operation. >> >> - Tuomas >> >> On 03/05/2015 08:20 AM, David Ham wrote: >> >> Hi Tuomas, >> >> This wasn't there this morning but I've implemented one of the cases >> (pulling out the top and bottom maps). The result is in the >> extrusion_extraction branches of both PyOP2 and Firedrake. The 2d->3d >> operation would be rather similar except that you'd have to interrogate the >> fiat_element on the extruded Function in order to determine which extruded >> nodes are "on top of" the 2d nodes you have. Unfortunately I won't have >> time to do that one soon (huge amounts to do before SIAM CSE next week) but >> feel free to have a try and complain when it doesn't work! >> >> Cheers, >> >> David >> >> On 4 March 2015 at 22:23, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: >> >>> 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 >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> firedrake mailing listfiredrake@imperial.ac.ukhttps://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 > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

1 0

FEniCS '15 Abstract deadline is 30 April
by David Ham 10 Apr '15

10 Apr '15

Dear all, a friendly reminder that the abstract deadline for FEniCS '15 is creeping up on us. Go on - surprise yourself: submit an abstract well in advance of the deadline and look forward to your blissful serenity while your colleagues frantically bang something out at the last second. http://www.firedrakeproject.org/fenics_15 Regards, David -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

1 0

Re: [firedrake] Mapping nodal values from parent to extruded mesh
by David Ham 10 Apr '15

10 Apr '15

Hi Tuomas, This wasn't there this morning but I've implemented one of the cases (pulling out the top and bottom maps). The result is in the extrusion_extraction branches of both PyOP2 and Firedrake. The 2d->3d operation would be rather similar except that you'd have to interrogate the fiat_element on the extruded Function in order to determine which extruded nodes are "on top of" the 2d nodes you have. Unfortunately I won't have time to do that one soon (huge amounts to do before SIAM CSE next week) but feel free to have a try and complain when it doesn't work! Cheers, David On 4 March 2015 at 22:23, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > 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 > > > > _______________________________________________ > 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

2 2

Measure fieldsplit/AMG setup time separately
by Eike Mueller 08 Apr '15

08 Apr '15

Dear firedrakers, how can I enforce the setup of the entire PETSc solver when the object is created? I use the fieldsplit preconditioner with AMG for the pressure space. What I currently do is up_problem = LinearVariationalProblem(a_up, L_up, vmixed, bcs=bcs) up_solver = LinearVariationalSolver(up_problem, solver_parameters=sparams) ksp = up_solver.snes.getKSP() ksp.setUp() pc = ksp.getPC() pc.setUp() But that does not seem to work, since I still see that the first iteration of the subsequent solve call is much larger. I also noticed that on ARCHER the setup time is ridiculously large (200x larger than 1 iteration), and I don’t observe this on my laptop. Has anyone seem similar behaviour on ARCHER? Thanks a lot, Eike

3 2

Re: [firedrake] Firedrake Installation
by Andrew McRae 06 Apr '15

06 Apr '15

Hi all, Suet [cc'd], one of Colin's project students, is encoutering the following error when using the PyOP2 'quick install' script. Can anyone help? IIRC, this is running in a (32-bit?) Ubuntu 14.04 virtual machine. (Last night, she was getting an mpi4py error, but I believe this <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927> fixed that). Cheers, Andrew On 16 November 2014 13:28, Lee, Suet <suet.lee11(a)imperial.ac.uk> wrote: > I ran the install mpi4py commange but I have a new error now: > > > mosh@ubuntu:~$ wget -O - > https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash > --2014-11-16 13:20:14-- > https://github.com/OP2/PyOP2/raw/master/install.sh > Resolving github.com (github.com) 192.30.252.131 > Connecting to github.com (github.com)|192.30.252.131|:443... connected. > HTTP request sent, awaiting response... 302 Found > Location: https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > [following] > --2014-11-16 13:20:16-- > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > Resolving raw.githubusercontent.com (raw.githubusercontent.com) > 185.31.18.133 > Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.18.133|:443... > connected. > HTTP request sent, awaiting response... 200 OK > Length: 3667 (3.6K) [text/plain] > Saving to: ‘STDOUT’ > > 100%[======================================>] 3,667 --.-K/s in > 0s > > 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667] > > PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014 > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC > 2014 i686 i686 i686 GNU/Linux > > *** Privileged installation *** > Running unprivileged commands as mosh > > *** Preparing system *** > > *** Installing dependencies *** > > *** Installing PETSc *** > > *** Installing PyOP2 *** > > [ubuntu:31603] *** Process received signal *** > [ubuntu:31603] Signal: Floating point exception (8) > [ubuntu:31603] Signal code: Integer divide-by-zero (1) > [ubuntu:31603] Failing at address: 0xb74d6da0 > [ubuntu:31603] [ 0] [0xb779a40c] > [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0) > [0xb74d6da0] > [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c) > [0xb74d871c] > [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b) > [0xb74d8a8b] > [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6) > [0xb74b38f6] > [ubuntu:31603] [ 5] > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6) > [0xb74b48ec] > [ubuntu:31603] [ 6] /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) > [0xb76fa881] > [ubuntu:31603] [ 7] /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) > [0xb7488445] > [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf) [0xb76cfb3f] > [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256) > [0xb76ec1c6] > [ubuntu:31603] [10] orted() [0x80485b3] > [ubuntu:31603] [11] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) > [0xb7504a83] > [ubuntu:31603] [12] orted() [0x80485f8] > [ubuntu:31603] *** End of error message *** > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 343 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 140 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file runtime/orte_init.c at line 128 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_set_name failed > --> Returned value Unable to start a daemon on the local node (-128) > instead of ORTE_SUCCESS > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init failed > --> Returned "Unable to start a daemon on the local node" (-128) instead > of "Success" (0) > -------------------------------------------------------------------------- > [ubuntu:31601] *** An error occurred in MPI_Init_thread > [ubuntu:31601] *** on a NULL communicator > [ubuntu:31601] *** Unknown error > [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > -------------------------------------------------------------------------- > An MPI process is aborting at a time when it cannot guarantee that all > of its peer processes in the job will be killed properly. You should > double check that everything has shut down cleanly. > > Reason: Before MPI_INIT completed > Local host: ubuntu > PID: 31601 > -------------------------------------------------------------------------- > PyOP2 installation failed > See /home/mosh/PyOP2/pyop2_install.log for details > > > Any idea what's going on? > > > Suet >

6 14

Crash in projection on ARCHER
by Eike Mueller 03 Apr '15

03 Apr '15

Dear firedrakers, I just updated all modules on ARCHER and tried to run my code there. However, I get the error below. Thanks, Eike Traceback (most recent call last): File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 619, in <module> main(parameter_filename) File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 585, in main expression) File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 400, in solve_matrixfree r_p.project(expression) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/function.py", line 146, in project return projection.project(b, self, *args, **kwargs) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/projection.py", line 94, in project form_compiler_parameters=form_compiler_parameters) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/solving.py", line 119, in solve _solve_varproblem(*args, **kwargs) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/solving.py", line 144, in _solve_varproblem solver.solve() File "<string>", line 2, in solve File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/profiling.py", line 197, in wrapper return f(*args, **kwargs) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/variational_solver.py", line 153, in solve self.snes.solve(None, v) File "SNES.pyx", line 516, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:158929) File "petscsnes.pxi", line 251, in petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:30207) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/solving_utils.py", line 170, in form_function with ctx._xs[lvl].dat.vec as v: IndexError: tuple index out of range

3 6

Fwd: New College regulations on Lectures start today
by David Ham 01 Apr '15

01 Apr '15

Dear All, I feel duty-bound to forward to you this morning's Imperial College policy change. David ---------- Forwarded message ---------- From: Director of Mathematics Undergraduate Studies <ma.dug(a)imperial.ac.uk> Date: 1 April 2015 at 08:52 Subject: New College regulations on Lectures start today To: Maths - All Research Associates <ma-all-ras-dl(a)imperial.ac.uk>, Maths - All Academic Staff <ma-all-academic-staff-dl(a)imperial.ac.uk> Dear All, In an attempt to combat plagiarism and inadequate referencing in student projects, the College has decreed that academic staff should lead by example. It is now a strict College regulation that “whenever a lecturer mentions a source by name, an appropriate reference must be supplied.” This sounds reasonable, but I am afraid it will have some unfortunate consequences for us all. >From the start of this month, whenever in lectures we use the name of a mathematician (or other scientist) whether living or dead, we must also provide a full reference. So for example “Poisson’s equation” must henceforth be accompanied by a written reference such as: S.D. Poisson d’Avril, "Remarques sur une équation qui se présente dans la théorie des attractions des sphéroïdes" Nouveau Bull. Soc. Philomathique de Paris, 3 (1813) 388–392. Notes and Clarifications: (1) When citing a dual source, BOTH authors must be credited. So for example Cayley-Hamilton, Euler-Lagrange, Bolzano-Weirstrass, Bose-Einstein each require two references. (2) If a topic is sufficiently standard that the name does not require a capital letter, then no reference need be supplied. Thus “Cartesian coordinates” requires a reference to René Descartes, but “cartesian coordinates” does not. (3) Adjectives, such as Bayesian or Jacobian, will require referencing to the appropriate author. (4) The Head of Dept has been asked to report any failure to comply with these regulations to the pro-rector for Quality Assurance in the Communication of Knowledge (QUACK). Usually, I manage to insulate the department from foolishness of this sort, but alas, not today. If you feel you wish to express concern about these changes, the heads of department or faculty, r.craster(a)ic.ac.uk or fonsdean(a)ic.ac.uk always welcome any constructive criticism. All the best, Jonathan, April 1st 2015 ------------------------------------------------------------- Jonathan Mestel, Professor of Applied Mathematics Director of Undergraduate Studies Mathematics Dept, Imperial College London Tel: 0207 594 8513 Room: Huxley 630 ma.dug(a)ic.ac.uk -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

1 0