May 2019 - firedrake - imperial.ac.uk

using AuxiliaryOperatorPC in MG
by Cotter, Colin J 03 Jun '19

03 Jun '19

Hi folks, The following set of options: ap_mg_params = {"mat_type": "matfree", "snes_type": "ksponly", "ksp_type": "gmres", "ksp_rtol": 1.0e-8, "ksp_atol": 0.0, "ksp_max_it": 1000, "ksp_monitor": None, "ksp_converged_reason": None, "ksp_norm_type": "unpreconditioned", "pc_type": "mg", "mg_coarse_ksp_type": "preonly", "mg_coarse_pc_type": "python", "mg_coarse_pc_python_type": "firedrake.AssembledPC", "mg_coarse_assembled_pc_type": "lu", "mg_coarse_assembled_pc_factor_mat_solver_type": "mumps", "mg_levels_ksp_type": "richardson", "mg_levels_ksp_max_it": 1, "mg_levels_ksp_richardson_scale": 1/3, "mg_levels_pc_type": "python", "mg_levels_pc_python_type": "__main__.Shifted", "mg_levels_aux_pc_type": "python", "mg_levels_aux_pc_python_type": "firedrake.PatchPC", "mg_levels_aux_patch_pc_patch_save_operators": True, "mg_levels_aux_patch_pc_patch_partition_of_unity": False, "mg_levels_aux_patch_pc_patch_sub_mat_type": "seqaij", "mg_levels_aux_patch_pc_patch_construct_type": "star", "mg_levels_aux_patch_pc_patch_multiplicative": False, "mg_levels_aux_patch_pc_patch_symmetrise_sweep": False, "mg_levels_aux_patch_pc_patch_construct_dim": 0, "mg_levels_aux_patch_sub_ksp_type": "preonly", "mg_levels_aux_patch_sub_pc_type": "lu"} causes the message at the bottom of this email (below which is my Shifted class). What am I doing wrong? all the best --cjc Traceback (most recent call last): File "libpetsc4py/libpetsc4py.pyx", line 1343, in libpetsc4py.PCApply_Python File "/Users/colincotter/firedrake/src/firedrake/firedrake/preconditioners/assembled.py", line 114, in apply push_appctx(dm, self._ctx_ref) AttributeError: 'Shifted' object has no attribute '_ctx_ref' The above exception was the direct cause of the following exception: SystemError: <built-in method insert of list object at 0x1125f5548> returned a result with an error set Exception ignored in: 'petsc4py.PETSc.traceback' SystemError: <built-in method insert of list object at 0x1125f5548> returned a result with an error set class Shifted(AuxiliaryOperatorPC): def form(self, pc, test, trial): ur, ui = split(trial) vr, vi = split(test) hrP = tau*H/(arP**2 + aiP**2)*(arP*div(ur) + aiP*div(ui)) hiP = tau*H/(arP**2 + aiP**2)*(-aiP*div(ur) + arP*div(ui)) aP = ( inner(arP*ur,vr) - inner(aiP*ui, vr) - tau*inner(f*perp(ur),vr) + tau*g*inner(hr,div(vr)) + inner(arP*ui,vi) + inner(aiP*ur, vi) - tau*inner(f*perp(ui),vi) + tau*g*inner(hi,div(vi)) )*dx bcs = None return (aP, bcs)

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GenericVector
by Cotter, Colin J 29 May '19

29 May '19

Dear Firedrake, Using firedrake-adjoint provokes the message at the bottom of this email. Is it expected? How can it be avoided? all the best --Colin File "edge_stable.py", line 106, in <module> z_opt = solver.solve()[0] File "/home/cjc1/firedrake/src/pyadjoint/pyadjoint/tape.py", line 46, in wrapper return function(*args, **kwargs) File "/home/cjc1/firedrake/src/pyadjoint/pyadjoint/optimization/rol_solver.py", line 217, in solve solver.solve() File "/home/cjc1/firedrake/src/pyadjoint/pyadjoint/optimization/rol_solver.py", line 24, in gradient g.dat = g.riesz_map(self.deriv) File "/home/cjc1/firedrake/src/pyadjoint/pyadjoint/optimization/rol_solver.py", line 52, in riesz_map dat.append(deriv._ad_convert_type(deriv, options=opts)) File "/home/cjc1/firedrake/src/pyadjoint/pyadjoint/tape.py", line 46, in wrapper return function(*args, **kwargs) File "/home/cjc1/firedrake/src/pyadjoint/fenics_adjoint/types/function.py", line 131, in _ad_convert_type if not isinstance(value, backend.GenericVector): AttributeError: module 'firedrake' has no attribute 'GenericVector'

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A lot of your incoming messages has been suspended
by Shadmehr Houriyeh (RSE) 23 May '19

23 May '19

MICROSOFT VERIFICATION NEEDED A lot of your incoming messages has been suspended because your email box account is not verify by Microsoft verification team. In order to receive your messages do verify<https://muioprew.wixsite.com/mysite> now, We apologise for any inconvenience and appreciate your understanding. Thank You. Microsoft Verification Team Copyright © 2019 Webmail .Inc . All rights reserved. RSE SpA ha adottato il Modello Organizzativo ai sensi del D.Lgs.231/2001, in forza del quale l'assunzione di obbligazioni da parte della Società avviene con firma di un procuratore, munito di idonei poteri. RSE adopts a Compliance Programme under the Italian Law (D.Lgs.231/2001). According to this RSE Compliance Programme, any commitment of RSE is taken by the signature of one Representative granted by a proper Power of Attorney. Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne e' vietata la diffusione in qualsiasi modo o forma. Qualora Lei non fosse la persona destinataria del presente messaggio, La invitiamo a non diffonderlo e ad eliminarlo, dandone gentilmente comunicazione al mittente. The information included in this e-mail and any attachments are confidential and may also be privileged. If you are not the correct recipient, you are kindly requested to notify the sender immediately, to cancel it and not to disclose the contents to any other person.

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Your kernel body contains a double indirection
by Jagir Hussan 20 May '19

20 May '19

Hi, I have installed firedrake under Windows Subsystem Linux (Ubuntu 18.04). I get the following error and segmentation fault. Kindly, could you let me know what the instructions are? Thanks Jagir firedrake:WARNING Your kernel body contains a double indirection. You should update it to single indirections. Mail firedrake(a)imperial.ac.uk for advice. firedrake:WARNING Your kernel body contains a double indirection. You should update it to single indirections. Mail firedrake(a)imperial.ac.uk for advice. Traceback (most recent call last): File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 197, in __new__ return cls._cache_lookup(key) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 205, in _cache_lookup return cls._cache[key] KeyError: ('c9930cddd7d7e4db4562d4b34b0960db', <class 'pyop2.base.Set'>, False, False, True, <class 'pyop2.base.Arg'>, Access('WRITE'), (<class 'pyop2.petsc_base.Dat'>, dtype('float64'), (<class 'pyop2.petsc_base.DataSet'>, (1,), (<class 'pyop2.base.Set'>,))), ((<class 'pyop2.base.Map'>, 1, None),), False, 0, None, <class 'pyop2.sequential.JITModule'>, 4) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 263, in get_so return ctypes.CDLL(soname) File "/usr/lib/python3.6/ctypes/__init__.py", line 348, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b.so: cannot open shared object file: No such file or directory During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 293, in get_so stdout=log) File "/usr/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-ffast-math', '-I/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/include', '-I/home/ftest/firedrake/firedrake/src/PyOP2/pyop2', '-o', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.so.tmp', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.c', '-shared', '-L/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-Wl,-rpath,/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-lpetsc', '-lm']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "start_computation.py", line 12, in <module> fn.time_evolution(parameters.parameters) File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/functions.py", line 88, in time_evolution CS = coupled_system.CoupledSystem(prm) File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/coupled_system.py", line 25, in __init__ self.W = water_mixed.Water_mixed( self.mesh, **parameters ) File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 13, in __init__ super(Water_mixed, self).__init__(**kwargs) File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water.py", line 28, in __init__ self.initialize() File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 19, in initialize self.beyond_fluid_BCs() File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 57, in beyond_fluid_BCs self.BC_exclude_beyond_fluid = MyBC( self.V, 0, self.I_cg ) File "/mnt/d/firedrake/Examples/FSI/lin_coupled_3d/lib/water_mixed.py", line 53, in __init__ self.nodes = np.unique(np.where(markers.dat.data_ro_with_halos == 0)[0]) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 1683, in data_ro_with_halos _trace.evaluate(set([self]), set()) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 192, in evaluate comp._run() File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 3740, in _run return self.compute() File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/base.py", line 3786, in compute fun = self._jitmodule File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/utils.py", line 62, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 207, in _jitmodule pass_layer_arg=self._pass_layer_arg) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 199, in __new__ obj = make_obj() File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/caching.py", line 189, in make_obj obj.__init__(*args, **kwargs) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 101, in __init__ self.compile() File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/sequential.py", line 159, in compile comm=self.comm) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 475, in load dll = compiler.get_so(code, extension) File "/home/ftest/firedrake/firedrake/src/PyOP2/pyop2/compilation.py", line 299, in get_so Compile errors in %s""" % (e.cmd, e.returncode, logfile, errfile)) pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-ffast-math', '-I/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/include', '-I/home/ftest/firedrake/firedrake/src/PyOP2/pyop2', '-o', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.so.tmp', '/home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.c', '-shared', '-L/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-Wl,-rpath,/home/ftest/firedrake/firedrake/lib/python3.6/site-packages/petsc/lib', '-lpetsc', '-lm']" return error status 1. Unable to compile code Compile log in /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.log Compile errors in /home/ftest/firedrake/firedrake/.cache/pyop2/3e/e8b6d36dedd774a83d03beb3c5ea2b_p524.err

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Internship in numerical multiphase modelling at IBM
by Robert Sawko 20 May '19

20 May '19

Hi, I realise this is a bit out of scope for this mailing list, but please let me advertise an internship programme we will be running at IBM this Autumn: https://www.research.ibm.com/labs/uk/internships.html# This is a paid 3-6 month internship for PhD students. The theme my colleague will be supervising is: "High-resolution numerical prediction of drop/bubble wall interaction" If you know anyone who might be interested please pass this message and the link forward. Best wishes, Robert -- Dr Robert Sawko Research Staff Member, IBM Daresbury Laboratory Keckwick Lane, Warrington WA4 4AD United Kingdom -- Email (IBM): RSawko(a)uk.ibm.com Email (STFC): robert.sawko(a)stfc.ac.uk Phone (office): +44 (0) 1925 60 3967 Phone (mobile): +44 759 301 0452 Profile page: http://researcher.watson.ibm.com/researcher/view.php?person=uk-RSawko --Unless stated otherwise above: IBM United Kingdom Limited - Registered in England and Wales with number 741598. Registered office: PO Box 41, North Harbour, Portsmouth, Hampshire PO6 3AU

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Firedrake '19 user and developer meeting
by Lawrence Mitchell 10 May '19

10 May '19

Dear firedrakers, I'm delighted to announce that the 2019 edition of the Firedrake user and developer meeting will this year be held in Durham on the 26th and 27th September. Following the model of the previous two iterations, the meeting will commence with a half-day introductory tutorial, finishing around lunchtime on the 26th. The scientific program will start after lunch on the 26th and run until the afternoon of the 27th. Abstract submission is now open on Easychair (https://easychair.org/conferences/?conf=firedrake19) and registration should open in the next week or so. For more details see https://firedrakeproject.org/firedrake_19.html Thanks, and looking forward to seeing you in Durham, Lawrence

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sub-matrix assembly
by Shawn W Walker 10 May '19

10 May '19

Hello. I would like to know if you can tell Firedrake to run the assembly over part of a mesh. For example, suppose I have a stiffness matrix (with variable coefficient) defined over a global mesh, but I want to do some domain decomposition where I solve on a sub-domain that may be changing with iteration. I don't want to assemble the entire matrix (then take a sub-matrix) because this can be inefficient. Is there a way to only assemble over a subset of elements, and solve using the corresponding sub-matrix? -Shawn

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two splittings
by Cotter, Colin J 01 May '19

01 May '19

Dear Firedrakers, Greetings from Montreal. I'm thinking about a double splitting method to solve the system (M + D + L)u = f, which as a preconditioner works out as (M + D)^{-1}M(M + L)^{-1} r, where r is a residual. In the absence of a better idea, I'll implement this through a Python preconditioner. But is there a smarter way to do this? all the best --cjc

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