Hi Floriane, Sorry for taking a couple of days to get on to this. Unfortunately those files are not attached, they are on a University of Leeds sharepoint which my Imperial microsoft account cannot access. Could you please provide the files via an open route. Thanks, David On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg@leeds.ac.uk> wrote:
Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec vous. Pour les afficher, cliquez sur les liens ci-dessous.
<https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C3%A8ces%20jointes%20de%20courrier%20%C3%A9lectronique%201/horizontal.msh> horizontal.msh <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C3%A8ces%20jointes%20de%20courrier%20%C3%A9lectronique%201/horizontal.msh>
<https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C3%A8ces%20jointes%20de%20courrier%20%C3%A9lectronique%201/BL.py> BL.py <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C3%A8ces%20jointes%20de%20courrier%20%C3%A9lectronique%201/BL.py>
Dear David,
Attached is the "short" piece of code (BL.py), together with the mesh file (horizontal.msh). When running it, I get the error below. However, if I remove the weak formulations for eta(n+1) and phi(n+1) and solve only phi_solver_half and q_solver_half, then the error is for the line q_solver_half.solve(). If I also remove the solver for q_half and keeps only phi_solver_half, then it works.
Thank you,
Floriane
Traceback (most recent call last): File "BL.py", line 69, in <module> phi_solver_half.solve() File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", line 198, in solve
self.snes.solve(None, v) File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:170168) File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian (src/petsc4py.PETSc.c:33847) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 261, in form_jacobian ctx._jacs[lvl].force_evaluation() File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", line 248, in force_evaluation self.assemble() File "<decorator-gen-283>", line 2, in assemble
File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", line 191, in assemble self._assembly_callback(self.bcs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", line 357, in inner r = thunk(bcs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 279, in thunk zero_tensor() File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 219, in <lambda> zero_tensor = lambda: tensor.zero() File "<decorator-gen-300>", line 2, in zero File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", line 126, in zeroes _force_copies(self) File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", line 104, in _force_copies c._cow_actual_copy(obj) File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", line 687, in _cow_actual_copy self.handle = src.handle.duplicate(copy=True) File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate (src/petsc4py.PETSc.c:119330) petsc4py.PETSc.Error: error code 1 [0] SNESSolve() line 4060 in /tmp/pip-xbPEGV-build/src/snes/interface/snes.c [0] SNESSolve_NEWTONLS() line 228 in /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c [0] SNESComputeJacobian() line 2365 in /tmp/pip-xbPEGV-build/src/snes/interface/snes.c [0] MatDuplicate() line 4389 in /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c [0] MatDuplicate_SeqAIJ() line 4126 in /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c [0] Out of memory. Allocated: 0, Used by process: 3556626432 [0] Memory requested 422967946
------------------------------ *De :* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de David Ham <David.Ham@imperial.ac.uk> *Envoyé :* mardi 20 septembre 2016 10:13:20
*À :* firedrake *Objet :* Re: [firedrake] (no subject) Dear Floriane,
Please provide a minimal failing example so we can see what is going on. By a minimal failing example, we mean that you remove everything from the example that is not related to the failure. Often this requires some trial and error. The objective is to produce a very short piece of code which illustrates the problem so that we can (a) check if we can reproduce it and if so (b) find the problem easily.
Regards,
David
On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg@leeds.ac.uk> wrote:
Dear all,
Some of my codes do not work either since I updated firedrake. I have run firedrake-clean but still have the same error when calling the nonlinear solvers. The error is pasted below.
Any idea of what I could do ?
Thanks,
Floriane
Traceback (most recent call last): File "3D_NL.py", line 232, in <module> wf1_solver = NonlinearVariationalSolver(wf1_problem) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", line 137, in __init__ appctx=appctx) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 138, in __init__ for J, problem, ctx in zip(self.Js, problems, appctxs)) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 138, in <genexpr> for J, problem, ctx in zip(self.Js, problems, appctxs)) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 81, in assemble
inverse=inverse, mat_type=mat_type, appctx=appctx) File "<decorator-gen-295>", line 2, in _assemble File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 120, in _assemble inverse=inverse) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 189, in compile_form number_map).kernels File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 198, in __new__ obj = make_obj() File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 188, in make_obj obj.__init__(*args, **kwargs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 119, in __init__ kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", line 118, in __call__ return t(*args, **kwargs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 198, in __new__ obj = make_obj() File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 188, in make_obj obj.__init__(*args, **kwargs) File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 3778, in __init__ self._code = self._ast_to_c(self._ast, opts) File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line 60, in _ast_to_c ast_handler.plan_cpu(self._opts) File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line 119, in plan_cpu loop_opt.rewrite(rewrite) File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", line 142, in rewrite merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 181, in merge merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", line 74, in _merge_loops while isinstance(loop_b.children[0], (Block, For)): IndexError: list index out of range Exception AttributeError: "'NonlinearVariationalSolver' object has no attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ of <firedrake.variational_solver.NonlinearVariationalSolver object at 0x595a250>> ignored
------------------------------ *De :* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Fabio Luporini <f.luporini12@imperial.ac.uk> *Envoyé :* jeudi 15 septembre 2016 14:14:44 *À :* firedrake *Objet :* Re: [firedrake] (no subject)
Hi Will,
Could you just try a firedrake-clean and run it again ? it should then work
Thanks
-- Fabio
2016-09-15 14:07 GMT+02:00 William Booker <scwb@leeds.ac.uk>:
Hi firedrakers,
I had this script working on an older version of firedrake (24th Aug), but when I updated today I now get the following error when I try to run it:
Traceback (most recent call last): File "compressible_stratified.py", line 77, in <module> solve ( a_u_project == L_u_project , dHdu0 , solver_parameters={'ksp_rtol': 1e-14} ) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 119, in solve _solve_varproblem(*args, **kwargs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", line 147, in _solve_varproblem solver.solve() File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", line 198, in solve self.snes.solve(None, v) File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:170168) File "PETSc/petscsnes.pxi", line 261, in petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33322) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", line 216, in form_function form_compiler_parameters=problem.form_compiler_parameters) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 81, in assemble inverse=inverse, mat_type=mat_type, appctx=appctx) File "<decorator-gen-295>", line 2, in _assemble File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 444, in _assemble return thunk(bcs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", line 357, in inner r = thunk(bcs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", line 394, in thunk op2.par_loop(*args, **kwargs) File "<decorator-gen-269>", line 2, in par_loop File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", line 154, in modifies_arguments retval = func(*args, **kwargs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", line 269, in par_loop return backends._BackendSelector._backend.par_loop(kernel, iterset, *args, **kwargs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 4369, in par_loop return _make_object('ParLoop', kernel, it_space, *args, **kwargs).enqueue() File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", line 72, in _make_object return _BackendSelector._backend.__dict__[obj](*args, **kwargs) File "<decorator-gen-262>", line 2, in __init__ File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line 130, in wrapper return f(*args, **kwargs) File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 3999, in __init__ fundecl = kernel._attached_info['fundecl'] TypeError: 'bool' object has no attribute '__getitem__'
What needs to be changed to get it to compile again?
Thanks Will