May 2016 - firedrake - imperial.ac.uk

Elastoplastic problems
by Chaitanya Raj Goyal 12 May '16

12 May '16

Hello, I was curious if Firedrake is capable of solving elastoplastic problems. Right now I am trying to create a simple wave using Fenics Solid Mechanics app in elastoplastic media (without any success). I was wondering is Firedrake has a more user friendly platform for such problems. Thank you, Sincerely, Chaitanya

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Error with constant DG basis
by William Booker 12 May '16

12 May '16

Dear Firedrakers, The attached code runs and gives good convergence for linear and quadratic DG basis. But when I run the scheme with a constant basis I get the following error: This integral is missing an integration domain. Traceback (most recent call last): File "compressible_acoustic.py", line 98, in <module> L1 = -div_u(dFdu_vec, dHdrho0) File "compressible_acoustic.py", line 94, in div_u return (dot(u, grad(p)))*dx + (jump(p)*dot((u('-')*(1-theta)+u('+')*theta), n('-')))*(dS) File "/usr/not-backed-up/firedrake/2016-05-11/firedrake/lib/python2.7/site-packages/ufl/measure.py", line 398, in __rmul__ error("This integral is missing an integration domain.") File "/usr/not-backed-up/firedrake/2016-05-11/firedrake/lib/python2.7/site-packages/ufl/log.py", line 158, in error raise self._exception_type(self._format_raw(*message)) ufl.log.UFLException: This integral is missing an integration domain. I've had a working version, including a constant basis, when I had the terms separately instead of being a definition. So I'm not quite sure where the error is. Regards, Will

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Trying to print discrete divergence
by William Booker 11 May '16

11 May '16

Dear all, I'm trying to assert that my projection in my incompressible case leaves my initial velocity to be discrete divergence free. I've tried print an L2 norm but must be writing it wrong as it causes causes the compiler to break. The relevant lines solve(DIVU_perp == DIVU, u_perp, solver_parameters={'ksp_rtol': 1e-14, 'pc_type' : 'none', 'ksp_type': 'lsqr'} ) u0 += u_perp # Print statement to verify initial velocity is divergence free u_div = assemble( div_u( u0 , dFdPproject ) ) u_div_norm = norm (u_div, norm_type="L2") print "l2 norm of discrete divergence on initial velocity is " % u_div_norm How would I go about getting the script to print that the velocity is verified as divergence free? Regards, Will

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Re: [firedrake] periodic boundary conditions?
by Colin Cotter 11 May '16

11 May '16

Hi Francis, I'm very sceptical that it is anything to do with the solver. Either: (1) The input to the solver is already bad, or, (2) The mesh is messed up somehow, or (3) The equations are messed up somehow. Just checking, you didn't keep non-zero beta did you? That would not work with double periodic. all the best --cjc On 7 May 2016 at 22:33, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > Sorry Lawrence for sending my email to the wrong address but thanks for > forwarding it. I will be more careful in the future. > > Thanks for the suggestion Colin. I had tried reducing it by a factor of > 10 and it still failed. Now I tried a factor of 10^5 and it still fails. > > If my implementation is correct, which is a big if, then I wonder if the > Helmholtz problem that I'm solving is much more poorly conditioned on a > doubly periodic domain than just a periodic domain. > > Is there another solver that might be a bit better at converging? > > Cheers, Francis > > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > > ________________________________________ > From: firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Lawrence Mitchell [lawrence.mitchell(a)imperial.ac.uk] > Sent: Saturday, May 07, 2016 11:41 AM > To: <firedrake(a)imperial.ac.uk> > Subject: [firedrake] periodic boundary conditions? > > This message reached me as a list administrator from Francis Poulin (but I > couldn't figure out how to release it onto the list, so instead, it's > copied below). > > Lawrence > > > Hello, > > Glad to see the posters are looking great. Sorry that I won't get to see > them in person this year but glad I could contribute a little. Hopefully > I'll get to attend next year with a grad student. > > I have a question on how to convert the QG code from a channel to periodic > boundary conditions. You can find a demo version of the code at > > > https://github.com/francispoulin/firedrake/blob/qg_demo/demos/quasigeostrop… > > I have removed the jet and only have random initial conditions. > > The good news is that 2D turbulence does happen and structures merge but > in a channel. To reproduce classical results I would like it to be doubly > periodic. > > I made two changes: > > 1) I asked it to be periodic in this line by switching "x" to "both". > > mesh = PeriodicRectangleMesh(n0, n0, Lx, Ly, direction="both", > quadrilateral=True, reorder=None > ) > > > 2) We should not impose Dirichlet boundary conditions. To do this I > removed bcs=bc1 in the following > > psi_problem = > LinearVariationalProblem(Apsi,Lpsi,psi0) > > > It occurs to me that perhaps one needs to explicitly impose periodic > boundary conditions. Is that the case? If yes then do I need to change > the following somehow? > > bc1 = [DirichletBC(Vcg, 0., 1 > ), > DirichletBC(Vcg, > 0., 2 > )] > > > When I run the code it does run but it doesn't converge (after 42 steps) > and dies. This is for the same resolution and everything else that does > converge for the channel case. Could it be that the periodic case is not > as well conditioned if it is periodic in both directions? > > I hope to make a nice simulation of this to see the structures merging and > increasing in size. > > What's really nice is that if I wanted to do 3D turbulence in the context > of 3D the changes are pretty small. I need to define the grid to be 3D and > impose Neumann BCs at the top and bottom. That I will ask about at a later > time. > > Cheers, Francis > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] installation Linux
by David Ham 11 May '16

11 May '16

Hi Floriane, It looks like you are trying to use the automatic package installation features on a linux distribution which is not based on apt. Which distro is this? Is it CentOS (like many of the Leeds machines)? If so, you should call: firedrake-install --no-package-manager In that case, you need to ensure that the following packages are installed: * A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * MPI * Blas and Lapack * Git, Mercurial * Python version 2.7 * pip and the Python headers * CMake * libspatialindex and headers * zlib Regards, David On Tue, 10 May 2016 at 07:59 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear all, > > > I am working on a Linux machine on which the IT team tried to install > Firedrake, but got the following error: > > > Traceback (most recent call last): > File "firedrake-install", line 766, in <module> > check_call(["apt-get", "--version"]) > File "firedrake-install", line 205, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call > retcode = call(*popenargs, **kwargs) > File "/usr/lib64/python2.7/subprocess.py", line 524, in call > return Popen(*popenargs, **kwargs).wait() > File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > > Do you know what the issue is? > > > Best, > > > Floriane >

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Re: [firedrake] (no subject)
by Fabio Luporini 10 May '16

10 May '16

I know some people had a similar issue with non-cleaned cache. If the problem persists, I'll fix it as soon as I have a failing test case. Thanks -- Fabio 2016-05-10 12:11 GMT+02:00 Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk>: > > > On 10 May 2016, at 11:02, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote: > > > > I did do the updates and all went through well it seems, but > > both with the codes of Fryderyk and Will matters crash at the solve > stage; I also attache d F's code he just send me. > > I run on an macbook and they run under linux. > > The code runs for Fryderyk, he said. > > > > mtob$ python ns_plane_poiseuille.py > > ... > > Traceback (most recent call last): > > File "ns_plane_poiseuille.py", line 104, in <module> > > solve(F_u == 0, u, bcs = [bc0,bc1,bc2],solver_parameters={'pc_type': > 'lu', 'pc_factor_mat_solver_package': 'mumps'} ) # > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", > line 120, in solve > > _solve_varproblem(*args, **kwargs) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", > line 164, in _solve_varproblem > > solver.solve() > > File "<decorator-gen-295>", line 2, in solve > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/profiling.py", > line 203, in wrapper > > return f(*args, **kwargs) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 190, in solve > > solving_utils.check_snes_convergence(self.snes) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 62, in check_snes_convergence > > %s""" % (snes.getIterationNumber(), msg)) > > RuntimeError: Nonlinear solve failed to converge after 0 nonlinear > iterations. > > Reason: > > Inner linear solve failed to converge after 0 iterations with reason: > unknown reason (petsc4py enum incomplete? > > This looks like the jacobian is singular, please follow the advice here: > http://firedrakeproject.org/solving-interface.html#debugging-convergence-fa… > > To try and get an idea as to what is going on. > > I get: > Linear solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0 > PCSETUP_FAILED due to FACTOR_NUMERIC_ZEROPIVOT > > > > > Similar problem for Will's code: > > ast_handler.plan_cpu(self._opts) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/plan.py", > line 184, in plan_cpu > > _generate_cpu_code(self, kernel, **params) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/plan.py", > line 110, in _generate_cpu_code > > loop_opt.eliminate_zeros() > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", > line 163, in eliminate_zeros > > self.nz_syms = zls.reschedule(self.header) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", > line 844, in reschedule > > self.exprs.update(elf.fission(stmt, expr_info)) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", > line 463, in fission > > split, splittable = self.cutter.cut(*splittable) > > File > "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", > line 300, in cut > > index = expr_info.parent.children.index(node) > > ValueError: <coffee.base.Incr object at 0x10e4186d0> is not in list > > This may be a bug in coffee, but it runs for Will? Please try running > firedrake-clean and then try again if so. Otherwise, please provide a > failing test case and report it as a github issue ( > https://github.com/firedrakeproject/firedrake/issues) > > Thanks, > > Lawrence >

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Meeting today 3pm
by Lawrence Mitchell 10 May '16

10 May '16

Hi all, we're in the WPL fishbowl at 3 today. Lawrence

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(no subject)
by Onno Bokhove 10 May '16

10 May '16

I did do the updates and all went through well it seems, but both with the codes of Fryderyk and Will matters crash at the solve stage; I also attache d F's code he just send me. I run on an macbook and they run under linux. The code runs for Fryderyk, he said. mtob$ python ns_plane_poiseuille.py COFFEE finished in 0.00192809 seconds (flops: 0 -> 0) COFFEE finished in 0.00323701 seconds (flops: 0 -> 0) COFFEE finished in 0.00282502 seconds (flops: 300 -> 300) pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done L2norm = 0.182574185835 compute_form_data finished in 0.203755 seconds. compile_integral finished in 0.122444 seconds. compile_integral finished in 0.047055 seconds. compile_integral finished in 0.0981019 seconds. compile_integral finished in 0.0492978 seconds. TSFC finished in 0.520766 seconds. COFFEE finished in 0.126961 seconds (flops: 27327 -> 24555) COFFEE finished in 0.0907421 seconds (flops: 3882 -> 1722) COFFEE finished in 0.0888281 seconds (flops: 3882 -> 1722) COFFEE finished in 0.087405 seconds (flops: 3882 -> 1722) compute_form_data finished in 0.177042 seconds. compile_integral finished in 0.077399 seconds. compile_integral finished in 0.028666 seconds. compile_integral finished in 0.0420549 seconds. compile_integral finished in 0.028265 seconds. TSFC finished in 0.353534 seconds. COFFEE finished in 0.046375 seconds (flops: 1196 -> 1196) compute_form_data finished in 0.196338 seconds. compile_integral finished in 0.0776689 seconds. compile_integral finished in 0.0208788 seconds. compile_integral finished in 0.034956 seconds. compile_integral finished in 0.0276241 seconds. TSFC finished in 0.357583 seconds. COFFEE finished in 0.0538301 seconds (flops: 1322 -> 1250) compute_form_data finished in 0.187414 seconds. compile_integral finished in 0.0602942 seconds. compile_integral finished in 0.0215549 seconds. compile_integral finished in 0.030211 seconds. compile_integral finished in 0.0244799 seconds. TSFC finished in 0.324083 seconds. COFFEE finished in 0.00157189 seconds (flops: 0 -> 0) COFFEE finished in 0.00145602 seconds (flops: 0 -> 0) pyop2:INFO Solving nonlinear variational problem... COFFEE finished in 0.00165892 seconds (flops: 0 -> 0) pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done COFFEE finished in 0.00231886 seconds (flops: 0 -> 0) COFFEE finished in 0.001647 seconds (flops: 0 -> 0) pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done compute_form_data finished in 0.166336 seconds. compile_integral finished in 0.0847039 seconds. compile_integral finished in 0.055573 seconds. compile_integral finished in 0.056812 seconds. compile_integral finished in 0.065223 seconds. TSFC finished in 0.428837 seconds. COFFEE finished in 0.122875 seconds (flops: 4752 -> 1616) COFFEE finished in 0.0609031 seconds (flops: 594 -> 270) COFFEE finished in 0.0570309 seconds (flops: 594 -> 270) COFFEE finished in 0.058157 seconds (flops: 594 -> 270) compute_form_data finished in 0.139532 seconds. compile_integral finished in 0.0625341 seconds. compile_integral finished in 0.022583 seconds. compile_integral finished in 0.0320051 seconds. compile_integral finished in 0.024895 seconds. TSFC finished in 0.281678 seconds. COFFEE finished in 0.0402429 seconds (flops: 842 -> 410) COFFEE finished in 0.00145102 seconds (flops: 0 -> 0) COFFEE finished in 0.00148582 seconds (flops: 0 -> 0) COFFEE finished in 0.00240588 seconds (flops: 0 -> 0) pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done compute_form_data finished in 0.167164 seconds. compile_integral finished in 0.101004 seconds. compile_integral finished in 0.053689 seconds. compile_integral finished in 0.106863 seconds. compile_integral finished in 0.0500929 seconds. TSFC finished in 0.478959 seconds. COFFEE finished in 0.11501 seconds (flops: 26991 -> 24219) COFFEE finished in 0.0758209 seconds (flops: 3786 -> 1626) COFFEE finished in 0.0740719 seconds (flops: 3786 -> 1626) COFFEE finished in 0.074147 seconds (flops: 3786 -> 1626) compute_form_data finished in 0.147847 seconds. compile_integral finished in 0.0788112 seconds. compile_integral finished in 0.028301 seconds. compile_integral finished in 0.0441599 seconds. compile_integral finished in 0.028101 seconds. TSFC finished in 0.327342 seconds. compute_form_data finished in 0.157457 seconds. compile_integral finished in 0.072794 seconds. compile_integral finished in 0.0211651 seconds. compile_integral finished in 0.0256679 seconds. compile_integral finished in 0.0287292 seconds. TSFC finished in 0.305935 seconds. COFFEE finished in 0.0498259 seconds (flops: 1178 -> 1178) compute_form_data finished in 0.14918 seconds. compile_integral finished in 0.0586369 seconds. compile_integral finished in 0.0208559 seconds. compile_integral finished in 0.0232871 seconds. compile_integral finished in 0.0236769 seconds. TSFC finished in 0.275756 seconds. pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done pyop2:INFO Compiling wrapper... pyop2:INFO Compiling wrapper...done Traceback (most recent call last): File "ns_plane_poiseuille.py", line 104, in <module> solve(F_u == 0, u, bcs = [bc0,bc1,bc2],solver_parameters={'pc_type': 'lu', 'pc_factor_mat_solver_package': 'mumps'} ) # File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 120, in solve _solve_varproblem(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 164, in _solve_varproblem solver.solve() File "<decorator-gen-295>", line 2, in solve File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/profiling.py", line 203, in wrapper return f(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", line 190, in solve solving_utils.check_snes_convergence(self.snes) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 62, in check_snes_convergence %s""" % (snes.getIterationNumber(), msg)) RuntimeError: Nonlinear solve failed to converge after 0 nonlinear iterations. Reason: Inner linear solve failed to converge after 0 iterations with reason: unknown reason (petsc4py enum incomplete?) Similar problem for Will's code: pyop2:INFO Compiling wrapper...done compute_form_data finished in 0.171724 seconds. compile_integral finished in 0.0246358 seconds. compile_integral finished in 0.105376 seconds. compile_integral finished in 0.145405 seconds. TSFC finished in 0.447226 seconds. Traceback (most recent call last): File "incompressible_acoustic.py", line 92, in <module> solve(DIVUdagger == DIVU, udagger, solver_parameters={'ksp_rtol': 1e-20, 'pc_type' : 'none', 'ksp_type': 'lsqr'} File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 120, in solve _solve_varproblem(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 147, in _solve_varproblem solver.solve() File "<decorator-gen-295>", line 2, in solve File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/profiling.py", line 203, in wrapper return f(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", line 188, in solve self.snes.solve(None, v) File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:172525) File "PETSc/petscsnes.pxi", line 253, in petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33588) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 187, in form_function nest=problem._nest) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 66, in assemble inverse=inverse, nest=nest) File "<decorator-gen-296>", line 2, in _assemble File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 100, in _assemble inverse=inverse) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 243, in compile_form number_map).kernels File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 174, in __init__ kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/backends.py", line 118, in __call__ return t(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 3847, in __init__ self._code = self._ast_to_c(self._ast, self._opts) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/pyop2/host.py", line 60, in _ast_to_c ast_handler.plan_cpu(self._opts) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/plan.py", line 184, in plan_cpu _generate_cpu_code(self, kernel, **params) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/plan.py", line 110, in _generate_cpu_code loop_opt.eliminate_zeros() File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", line 163, in eliminate_zeros self.nz_syms = zls.reschedule(self.header) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 844, in reschedule self.exprs.update(elf.fission(stmt, expr_info)) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 463, in fission split, splittable = self.cutter.cut(*splittable) File "/Users/amtob/werk/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 300, in cut index = expr_info.parent.children.index(node) ValueError: <coffee.base.Incr object at 0x10e4186d0> is not in list

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firedrake & gmsh 3d hexahedron mesh
by Tomasz Salwa [RPG] 10 May '16

10 May '16

Dear all, Can anybody familiar with gmsh tell me why firedrake protests when loading the attached mesh? How can it be corrected? Thank you, Tomasz Error listing: ... File "/home/tommy/work/programs/lin_coupled_3d/lib/coupled_system.py", line 23, in __init__ self.mesh = fd.Mesh("L_domain.msh") File "<decorator-gen-275>", line 2, in Mesh File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/pyop2/profiling.py", line 203, in wrapper return f(*args, **kwargs) File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 1075, in Mesh plex = _from_gmsh(meshfile) File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 159, in _from_gmsh gmsh_plex = PETSc.DMPlex().createGmsh(gmsh_viewer) File "PETSc/DMPlex.pyx", line 109, in petsc4py.PETSc.DMPlex.createGmsh (src/petsc4py.PETSc.c:222051) petsc4py.PETSc.Error: error code 62 [0] DMPlexCreateGmsh() line 247 in /tmp/pip-5Zhs5M-build/src/dm/impls/plex/plexgmsh.c [0] Invalid argument [0] Could not determine Plex facet for element 913

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installation Linux
by Floriane Gidel [RPG] 10 May '16

10 May '16

Dear all, I am working on a Linux machine on which the IT team tried to install Firedrake, but got the following error: Traceback (most recent call last): File "firedrake-install", line 766, in <module> check_call(["apt-get", "--version"]) File "firedrake-install", line 205, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Do you know what the issue is? Best, Floriane

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