December 2014 - firedrake - imperial.ac.uk

Re: [firedrake] Nullspace & VectorSpaceBasis
by Andrew McRae 29 Apr '15

29 Apr '15

Four comments: 1) If I understand correctly, PETSc insists that the diagonal entries of the sparse matrix are filled in. Usually, the LHS form will cause this to happen; however, that obviously isn't the case for your form! 2) It should be possible to build the nullspace you want, but I'm clueless on the actual syntax. This wouldn't get around (1) without further fixes from our end. 3) Could the equations given not be included in the weak form for the rest of the problem? 4) If not, there might be a hacky "add-a-weighted-mass-matrix-to-the-LHS" fix you could use?.... Andrew On 11 December 2014 at 12:46, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I am trying to solve a simple problem (linear water wave equations), > where I have the Laplace equation in a square domain with Neumann > boundary conditions on the three sides and on the top boundary two > equations are satisfied. > > I have the following code: > -------------------------------------- > V = FunctionSpace(mesh,"CG",1) > > eta0 = Function(V).interpolate(Expression("cos(2*pi*x[0])")) > phi0 = Function(V) > eta1 = Function(V) > phi1 = Function(V) > eta = TrialFunction(V) > phi = TrialFunction(V) > v = TestFunction(V) > > aeta = v*eta*ds(4) > Leta = v*eta0*ds(4) + dt*inner(grad(v),grad(phi0))*dx > > eta_problem = LinearVariationalProblem(aeta,Leta,eta1) > eta_solver = LinearVariationalSolver(eta_problem) > > aphi = v*phi*ds(4) > Lphi = (v*phi0 - g*dt*v*eta1)*ds(4) > > phi_problem = LinearVariationalProblem(aphi,Lphi,phi1) > phi_solver = LinearVariationalSolver(phi_problem) > -------------------------------------- > > The error I get tells me that Object is in wrong state, and Matrix is > missing diagonal entry 39. > > I thought this had to do with the problem being singular, so I tried to > build the nullspace but I don't know how to define the VectorSpaceBasis. > Any help would be appreciated. > > Thank you very much. > > Regards, Anna. > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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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 >

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Configure error on ARCHER
by Jacobs, Christian T 05 Jan '15

05 Jan '15

I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps: cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py firedrake.env contains: module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda # Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules # Load build environment module load fdrake-build-env module load fdrake-python-env export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2

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Issues with LMA of vertical derivative on extruded meshes
by Eike Mueller 05 Jan '15

05 Jan '15

Dear firedrakers, I came across a problem when doing a local matrix assembly of the weak derivative matrix from a DG space (W3) to a vertical-only HDiv space (W2_vert), i.e.: order_vertical = 0 U2 = FiniteElement('DG',interval,0) V0 = FiniteElement('CG',interval,1) V1 = FiniteElement('DG',interval,order_vertical) W2_vert = FunctionSpace(mesh,HDiv(OuterProductElement(U2,V0))) W3 = FunctionSpace(mesh,OuterProductElement(U2,V1)) phi = TestFunction(W3) psi = TrialFunction(W3) u = TestFunction(W2_vert) w = TrialFunction(W2_vert) form_D = phi*div(w)*dx form_DT = div(u)*psi*dx I work with an extruded mesh with one vertical layer, for details, see the attached code which exposes the issue. When I do a local matrix assembly for form_D and form_DT, I get the following entries of the LMA's (the grid has three cells, and I attach a 2x1 or 1x2 matrix representing the LMA at each cell, hence the three entries in the arrays below). *** D: W2_vert -> W3 *** [[-1. 1.] [-1. 1.] [ 1. -1.]] *** DT: W3 -> W2_vert *** [[-1. -1.] [-1. -1.] [ 1. 1.]] i.e. it looks fine for D, but the result is clearly wrong for DT, which should be the transpose of D. It does not even contain the same number of +1's and -1's. I can't really see what I'm doing wrong here. Furthermore, it does seem to work if I change set order_vertical from 0 to 1. I have to admit that I copied the code in build_lma() method from Lawrence, without trying to understand it in detail, but I thought it was sufficiently generic to deal with any UFL forms? Thanks a lot for any help, I'm lost as to what is going wrong here, Eike

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operations on matrices
by Cotter, Colin J 05 Jan '15

05 Jan '15

Dear Firedrakers, I've been recently revisiting the "algebraic flux correction" schemes of Dmitri Kuzmin, with the aim of getting a conservative+bounded advection scheme for temperature in our NWP setup. These schemes involve the following steps: 1) Forming the consistent mass matrix (which is column-diagonal) M_C for the temperature space. 2) Constructing the following matrix with the same sparsity as M_C: A_{ij} = (M_C)_{ij}(T_i-T_j) where T_i is the value of temperature at node i. 3) "Limiting" the matrix by replacing A_{ij} -> A_{ij}\alpha_{ij} where \alpha_{ij} depends on various field values at nodes i and j (only needs to be evaluated when nodes i and j share an element). 4) Evaluating Ax where x is the vector containing 1s, and adding x to the RHS of mass-matrix projection equation before solving. My question is: how to implement this in an efficient and parallel-safe way in the Firedrake/PyOP2 framework? In particular, step (3) involves looping over elements, and correcting matrix entries. Also, I'm not sure of the best way to assemble A. all the best --Colin

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BCs on velocity for mixed gravity wave system solver
by Eike Mueller 30 Dec '14

30 Dec '14

Dear firedrakers, I’ve got a first, lowest-order version of the matrix-free solver for the mixed 3d gravity-wave problem working now (pushed to “vertical" branch of firedrake-helmholtzsolver). I precondition with the matrix-free multigrid in pressure space, and it all converges nicely (although it is probably horribly inefficient in places). The equations for velocity u, pressure p and buoyancy b are du/dt = \grad(p) + b*\hat{z} dp/dt = -c^2 \div(u) db/dt = -N^2 u.\hat{z} Full details on the solver are in GravityWaves.tex in the directory https://github.com/firedrakeproject/firedrake-helmholtzsolver/tree/vertical… <https://github.com/firedrakeproject/firedrake-helmholtzsolver/tree/vertical…> However, I’m struggling to incorporate the boundary condition u.n=0 at the bottom and top of the domain (this is a spherical shell in my case - but should all also work for a 2d annulus) into the solver. I presume it is a Dirichlet BC, but of the form n_0*u_0 + n_1*u_1 + n_2*u_2 = 0, and I do not set the values explicity as in, for example, (u_0,u_1,u_2) = (0,0,0). How can I specify this? Also, where in the solver do I actually have to enforce it? In the mixed solver I apply the mixed operator, so I think I need to enforce it in the u-equation there. Also, in the mixed preconditioner I do a back-substitution for u after the pressure solve, so I think I have to do it there as well. Thanks a lot, 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/

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Re: [firedrake] BCs on velocity for mixed gravity wave system solver
by Andrew McRae 28 Dec '14

28 Dec '14

Hi Eike, In general, we don't actually have proper functionality for that. However, assuming you're using some H(div) space for u, including an HDiv(U2xV0) + HDiv(U1xV1) sort of thing, you can obtain the BC u.n=0 by doing, for example, bcs = [DirichletBC(W2, 0.0, "bottom"), DirichletBC(W2, 0.0, "top")] Why does this work? Well, this causes any degrees of freedom on the 'bottom' and 'top' boundaries to be set to 0. But the degrees of freedom on the boundary in an H(div) space are precisely u.n (technically with some sort of scaling, but scaled 0 is still 0). And any interior DOFs, or DOFs on other facets, have vanishing normal component on the original facet. So indeed, this does the right thing. If your velocity was in something like VectorFunctionSpace(mesh, "CG", n), unfortunately this approach wouldn't work, and I think you'd have to apply the BC weakly by adding on a surface integral. But in the H(div) case, what I described above happens to work. Hope this helps! Best, Andrew On 27 December 2014 at 14:14, Eike Mueller <e.mueller(a)bath.ac.uk> wrote: > Dear firedrakers, > > I’ve got a first, lowest-order version of the matrix-free solver for the > mixed 3d gravity-wave problem working now (pushed to “vertical" branch of > firedrake-helmholtzsolver). I precondition with the matrix-free multigrid > in pressure space, and it all converges nicely (although it is probably > horribly inefficient in places). The equations for velocity u, pressure p > and buoyancy b are > > du/dt = \grad(p) + b*\hat{z} > dp/dt = -c^2 \div(u) > db/dt = -N^2 u.\hat{z} > > Full details on the solver are in GravityWaves.tex in the directory > https://github.com/firedrakeproject/firedrake-helmholtzsolver/tree/vertical… > > However, I’m struggling to incorporate the boundary condition u.n=0 at > the bottom and top of the domain (this is a spherical shell in my case - > but should all also work for a 2d annulus) into the solver. I presume it is > a Dirichlet BC, but of the form n_0*u_0 + n_1*u_1 + n_2*u_2 = 0, and I do > not set the values explicity as in, for example, (u_0,u_1,u_2) = (0,0,0). > How can I specify this? Also, where in the solver do I actually have to > enforce it? > > In the mixed solver I apply the mixed operator, so I think I need to > enforce it in the u-equation there. > Also, in the mixed preconditioner I do a back-substitution for u after the > pressure solve, so I think I have to do it there as well. > > Thanks a lot, > > 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/ > >

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1+1 dimensional hierarchical meshes and function spaces
by Eike Mueller 22 Dec '14

22 Dec '14

Dear firedrakers, do the hierarchical meshes and function spaces currently only work in 2+1 dimension and not for 1+1? If I run the code below it works for dimension=3, but if I replace this by dimension=2 it crashes with [0]PETSC ERROR: DMPlexGetCellRefiner_Internal() line 6777 in /Users/eikemueller/PostDocBath/EllipticSolvers/petsc/src/dm/impls/plex/plexrefine.c Unknown dimension 1 for cell refiner -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 62. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- I want to work in dimension=2+1, but having dimension=1+1 would be useful for testing. Thanks a lot, Eike from firedrake import * dimension = 2 D = 0.1 nlayers=4 nlevel = 4 if (dimension == 2): ncells=3 host_mesh = CircleManifoldMesh(ncells) else: refcount = 0 host_mesh = UnitIcosahedralSphereMesh(refcount) host_mesh_hierarchy = MeshHierarchy(host_mesh,nlevel) mesh_hierarchy = ExtrudedMeshHierarchy(host_mesh_hierarchy, layers=nlayers, extrusion_type='radial', layer_height=D/nlayers) if (dimension == 2): U2 = FiniteElement('DG',interval,1) V1 = FiniteElement('DG',interval,1) else: U2 = FiniteElement('DG',triangle,0) V1 = FiniteElement('DG',interval,0) W3_elt = OuterProductElement(U2,V1) W3 = FunctionSpaceHierarchy(mesh_hierarchy,W3_elt) f = FunctionHierarchy(W3) f[-1].interpolate(Expression('x[0]*x[1]')) print norm(f[-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] Problem with Nonlinear solvers after update
by Fabio Luporini 22 Dec '14

22 Dec '14

Hi Anna, Yes, this problem is clearly caused by coffee; I'll work on this after the holidays. Thanks. -- Fabio 2014-12-22 15:28 GMT+01:00 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk>: > Thank you very much Andrew. That fixed my problems! > > Anna. > > P.S. Happy holidays and Merry Christmas to all of you :) > > > On 22 Dec 2014, at 14:22, Eike Mueller <e.mueller(a)bath.ac.uk<mailto: > e.mueller(a)bath.ac.uk>> wrote: > > Oh, I should have done what Andrew suggests before sending my email... > > op2.init() > parameters["coffee"]["O2"] = False > > seems to fix at least part of my problem :-) > > Sorry for the noise, > > 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<mailto:e.mueller@bath.ac.uk> > http://people.bath.ac.uk/em459/ > > On 22 Dec 2014, at 13:58, Andrew McRae <a.mcrae12(a)imperial.ac.uk<mailto: > a.mcrae12(a)imperial.ac.uk>> wrote: > > Ugh, one of the recent changes we made was to turn on COFFEE's > optimisations by default. Unfortunately, this has led to some teething > problems. > > I assume that all components -- COFFEE, Firedrake, PyOP2, FFC, UFL, and > FIAT -- are up to date, and that you're running with a clean cache (from > the Firedrake base directory, run "./scripts/firedrake-clean"). > > If the problem persists, as a short-term workaround, can you add > > op2.init() > parameters["coffee"]["O2"] = False > > to the start of your file, just after the imports? This will result in > sub-optimal performance during the assembly stage, so isn't ideal in the > long-term. > > Fabio, our resident barista, will have some fixes after the new year, I'm > sure. > > Andrew > > On 22 December 2014 at 13:47, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk > <mailto:A.Kalogirou@leeds.ac.uk>> wrote: > Dear all, > > I very recently updated firedrake, pyop2 and installed coffee, but since > then none of my codes include nonlinear solvers don’t work (they used to > work fine before the update). > > I even tried to run the burgers.py code from the demo and even that > diverges. > > I get something like: > > Traceback (most recent call last): > File "benney-luke.py", line 57, in <module> > phi_solver = solver_phi(phi1, phi1, phi0, eta0, etaR, phi, gamma, dt, > mu, epsilon, is_linear); > File "/Users/matak/Documents/Firedrake/modules/solvers.py", line 26, in > solver_phi > phi_solver = > NonlinearVariationalSolver(phi_problem,solver_parameters={'snes_monitor': > True,'ksp_monitor': True,'snes_linesearch_monitor': True}) > File "/Users/matak/firedrake/firedrake/variational_solver.py", line 97, > in __init__ > form_compiler_parameters=self._problem.form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/assemble.py", line 58, in assemble > form_compiler_parameters=form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/assemble.py", line 79, in > _assemble > kernels = ffc_interface.compile_form(f, "form", > parameters=form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/ffc_interface.py", line 268, in > compile_form > ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 202, in __new__ > obj = make_obj() > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 192, in make_obj > obj.__init__(*args, **kwargs) > File "/Users/matak/firedrake/firedrake/ffc_interface.py", line 194, in > __init__ > (name, it.integral_type(), it.subdomain_id()), opts, inc), > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/backends.py", > line 118, in __call__ > return t(*args, **kwargs) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 202, in __new__ > obj = make_obj() > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 192, in make_obj > obj.__init__(*args, **kwargs) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/base.py", > line 3632, in __init__ > self._code = self._ast_to_c(code, opts) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/host.py", > line 63, in _ast_to_c > ast_handler.plan_cpu(opts) > File "/usr/local/lib/python2.7/site-packages/coffee/plan.py", line 405, > in plan_cpu > loop_opts = _generate_cpu_code(self, **params) > File "/usr/local/lib/python2.7/site-packages/coffee/plan.py", line 241, > in _generate_cpu_code > loop_opt.rewrite(rewrite) > File "/usr/local/lib/python2.7/site-packages/coffee/optimizer.py", line > 110, in rewrite > ew.expand() > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 168, in expand > ee.expand(self.stmt.children[1], self.stmt, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 567, in expand > l_node, l_type = self.expand(node.children[0], node, itvars_occs, > itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 599, in expand > l_node, l_type = self.expand(node.children[0], node, itvars_occs, > itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 608, in expand > raise RuntimeError("Expansion error: unknown node: %s" % str(node)) > RuntimeError: Expansion error: unknown node: (LI_IPK_1_0[k] * > LI_IPJ_1_1[j]) / LI_C_1_0 > > > Thank you. > > Anna. > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk<mailto:firedrake@imperial.ac.uk> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk<mailto:firedrake@imperial.ac.uk> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk<mailto:firedrake@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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Re: [firedrake] Problem with Nonlinear solvers after update
by Andrew McRae 22 Dec '14

22 Dec '14

Ugh, one of the recent changes we made was to turn on COFFEE's optimisations by default. Unfortunately, this has led to some teething problems. I assume that all components -- COFFEE, Firedrake, PyOP2, FFC, UFL, and FIAT -- are up to date, and that you're running with a clean cache (from the Firedrake base directory, run "./scripts/firedrake-clean"). If the problem persists, as a short-term workaround, can you add op2.init() parameters["coffee"]["O2"] = False to the start of your file, just after the imports? This will result in sub-optimal performance during the assembly stage, so isn't ideal in the long-term. Fabio, our resident barista, will have some fixes after the new year, I'm sure. Andrew On 22 December 2014 at 13:47, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I very recently updated firedrake, pyop2 and installed coffee, but since > then none of my codes include nonlinear solvers don’t work (they used to > work fine before the update). > > I even tried to run the burgers.py code from the demo and even that > diverges. > > I get something like: > > Traceback (most recent call last): > File "benney-luke.py", line 57, in <module> > phi_solver = solver_phi(phi1, phi1, phi0, eta0, etaR, phi, gamma, dt, > mu, epsilon, is_linear); > File "/Users/matak/Documents/Firedrake/modules/solvers.py", line 26, in > solver_phi > phi_solver = > NonlinearVariationalSolver(phi_problem,solver_parameters={'snes_monitor': > True,'ksp_monitor': True,'snes_linesearch_monitor': True}) > File "/Users/matak/firedrake/firedrake/variational_solver.py", line 97, > in __init__ > form_compiler_parameters=self._problem.form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/assemble.py", line 58, in assemble > form_compiler_parameters=form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/assemble.py", line 79, in > _assemble > kernels = ffc_interface.compile_form(f, "form", > parameters=form_compiler_parameters) > File "/Users/matak/firedrake/firedrake/ffc_interface.py", line 268, in > compile_form > ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 202, in __new__ > obj = make_obj() > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 192, in make_obj > obj.__init__(*args, **kwargs) > File "/Users/matak/firedrake/firedrake/ffc_interface.py", line 194, in > __init__ > (name, it.integral_type(), it.subdomain_id()), opts, inc), > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/backends.py", > line 118, in __call__ > return t(*args, **kwargs) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 202, in __new__ > obj = make_obj() > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/caching.py", > line 192, in make_obj > obj.__init__(*args, **kwargs) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/base.py", > line 3632, in __init__ > self._code = self._ast_to_c(code, opts) > File > "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_148_g8a1955c-py2.7-macosx-10.9-x86_64.egg/pyop2/host.py", > line 63, in _ast_to_c > ast_handler.plan_cpu(opts) > File "/usr/local/lib/python2.7/site-packages/coffee/plan.py", line 405, > in plan_cpu > loop_opts = _generate_cpu_code(self, **params) > File "/usr/local/lib/python2.7/site-packages/coffee/plan.py", line 241, > in _generate_cpu_code > loop_opt.rewrite(rewrite) > File "/usr/local/lib/python2.7/site-packages/coffee/optimizer.py", line > 110, in rewrite > ew.expand() > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 168, in expand > ee.expand(self.stmt.children[1], self.stmt, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 567, in expand > l_node, l_type = self.expand(node.children[0], node, itvars_occs, > itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 599, in expand > l_node, l_type = self.expand(node.children[0], node, itvars_occs, > itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 565, in expand > return self.expand(node.children[0], node, itvars_occs, itvar_exp) > File "/usr/local/lib/python2.7/site-packages/coffee/rewriter.py", line > 608, in expand > raise RuntimeError("Expansion error: unknown node: %s" % str(node)) > RuntimeError: Expansion error: unknown node: (LI_IPK_1_0[k] * > LI_IPJ_1_1[j]) / LI_C_1_0 > > > Thank you. > > Anna. > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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