Crash in projection on ARCHER
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
On 2 Apr 2015, at 13:48, Eike Mueller <E.Mueller@bath.ac.uk> wrote:
Dear firedrakers,
I just updated all modules on ARCHER and tried to run my code there. However, I get the error below.
Oops, my mistake. I've added a test for this behaviour and fixed it. Can you please update firedrake to latest master please? Cheers, Lawrence
Hi Lawrence, thanks, this fixes that problem, however I now get the error below. Cheers, 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 552, in main mesh_hierarchy = build_mesh_hierarchy(param_grid,param_orography) File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 160, in build_mesh_hierarchy host_mesh_hierarchy = MeshHierarchy(coarse_host_mesh,nlevel) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/mg/mesh.py", line 74, in __init__ m.init() File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/mesh.py", line 415, in init self._callback(self) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/mesh.py", line 382, in callback self._coordinate_fs = functionspace.VectorFunctionSpace(self, "Lagrange", 1) File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/caching.py", line 160, in __new__ obj = make_obj() File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/caching.py", line 141, in make_obj obj.__init__(*args, **kwargs) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/functionspace.py", line 582, in __init__ super(VectorFunctionSpace, self).__init__(mesh, element, name, dim=dim, rank=1) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/functionspace.py", line 111, in __init__ self._halo = halo.Halo(dm) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/halo.py", line 57, in __init__ self.sf = dmplex.prune_sf(sf) AttributeError: 'module' object has no attribute 'prune_sf' On 02/04/15 14:15, Lawrence Mitchell wrote:
On 2 Apr 2015, at 13:48, Eike Mueller <E.Mueller@bath.ac.uk> wrote:
Dear firedrakers,
I just updated all modules on ARCHER and tried to run my code there. However, I get the error below.
Oops, my mistake.
I've added a test for this behaviour and fixed it. Can you please update firedrake to latest master please?
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- Dr Eike Hermann Mueller Lecturer in Scientific Computing Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 6241 e.mueller@bath.ac.uk http://people.bath.ac.uk/em459/
On 2 Apr 2015, at 16:20, Eike Mueller <E.Mueller@bath.ac.uk> wrote:
Hi Lawrence,
thanks, this fixes that problem, however I now get the error below.
Please type make in the firedrake directory. But note in the mean time you must update to the current firedrake petsc branch (or else revert to prior to the sf-halos merge). Lawrence
Hi Lawrence, which PyOP2 branch do I want to use? If I use columnwise_kernel, I get error [1], if I use master, then the PyOP2 kernel does not support the cpp keyword [2]. Thanks, Eike [1] error with PyOP2 branch columnwise_kernels 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 398, in solve_matrixfree all_param) File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 294, in matrixfree_solver_setup omega_N) File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/pressuresolver/hierarchy.py", line 30, in __init__ self._data = [Type(*x,**kwargs) for x in arglist] File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/pressuresolver/operators.py", line 168, in __init__ assemble(div(TestFunction(self._W2_h))*TrialFunction(self._W3)*self._dx).M.handle File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/assemble.py", line 67, in assemble inverse=inverse, nest=nest) File "/work/n02/n02/eike/git_workspace/firedrake/firedrake/assemble.py", line 176, in _assemble nest=nest) File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/backends.py", line 118, in __call__ return t(*args, **kwargs) TypeError: __init__() got an unexpected keyword argument ‘nest’ [2] error with PyOP2 master keyword cpp not supported in kernel constructor. 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 398, in solve_matrixfree all_param) File "/work/n02/n02/eike//git_workspace/firedrake-helmholtzsolver/source/driver.py", line 294, in matrixfree_solver_setup omega_N) File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/pressuresolver/hierarchy.py", line 30, in __init__ self._data = [Type(*x,**kwargs) for x in arglist] File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/pressuresolver/operators.py", line 182, in __init__ vertical_bcs=True) File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/bandedmatrix/bandedmatrix.py", line 217, in assemble_ufl_form self._assemble_lma(lma,vertical_bcs) File "/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source/bandedmatrix/bandedmatrix.py", line 259, in _assemble_lma kernel = op2.Kernel(kernel_code % param_dict,'assemble_lma',cpp=True) File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/backends.py", line 118, in __call__ return t(*args, **kwargs) File "/work/n02/n02/eike/git_workspace/PyOP2/pyop2/caching.py", line 181, in __new__ key = cls._cache_key(*args, **kwargs) TypeError: _cache_key() got an unexpected keyword argument 'cpp'
On 2 Apr 2015, at 16:32, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:
On 2 Apr 2015, at 16:20, Eike Mueller <E.Mueller@bath.ac.uk> wrote:
Hi Lawrence,
thanks, this fixes that problem, however I now get the error below.
Please type make in the firedrake directory. But note in the mean time you must update to the current firedrake petsc branch (or else revert to prior to the sf-halos merge).
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 2 Apr 2015, at 19:50, Eike Mueller <e.mueller@bath.ac.uk> wrote:
which PyOP2 branch do I want to use? If I use columnwise_kernel, I get error [1], if I use master, then the PyOP2 kernel does not support the cpp keyword [2].
You can now use columnwise_kernel (I've rebased that on current master). Thanks, Lawrence
Hi Lawrence, I got it working again on ARCHER now, thanks a lot for your help. Eike
On 2 Apr 2015, at 22:23, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:
On 2 Apr 2015, at 19:50, Eike Mueller <e.mueller@bath.ac.uk> wrote:
which PyOP2 branch do I want to use? If I use columnwise_kernel, I get error [1], if I use master, then the PyOP2 kernel does not support the cpp keyword [2].
You can now use columnwise_kernel (I've rebased that on current master).
Thanks,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (3)
-
Eike Mueller
-
Eike Mueller
-
Lawrence Mitchell