December 2016 - firedrake - imperial.ac.uk

Re: [firedrake] Mixed system
by David Ham 02 Dec '16

02 Dec '16

On Fri, 2 Dec 2016 at 16:12 Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk> wrote: > > > On 2 Dec 2016, at 16:01, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > > > > Linear firedrake_0_fieldsplit_3_ solve did not converge due to > DIVERGED_DTOL iterations 35 > > > > The option > > > > "fieldsplit_3_pc_factor_shift_type": "nonzero" > > Given that LU with pivoting ought to invert the block unless it is > singular, I think something funky is going on. > > Can you additionally run with: > > "fieldsplit_3_ksp_monitor_true_residual": True > > (In passing, if you're using LU you should probably be setting the > ksp_type of these sub solves to "preonly", so you don't bother iterating). > > The function space is CG1. I believe that has diagonally dominant mass matrices so we shouldn't actually need pivotting. > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Re: [firedrake] Mixed system
by David Ham 02 Dec '16

02 Dec '16

Hi Anna, The issue is that (at least at the moment) you can't use lu on the real space block (that's fieldsplit_4 in your setup). You can switch this out for a ksp_type of cg and a preconditioner of none (it's a 1 * 1 block so from a straight maths point of view pretty much any solver will work). If you fix this then the solver fails to converge. Sticking fieldsplit_n_ksp_converged_reason on for n=0,1,2,3 reveals that lu fails on block 3 due to zero pivots. I'm not sure what this block is but it's apparently indefinite. I replaced the solver on that block with unpreconditioned cg too and the solver converged. That's almost certainly not the best choice of solver for that block, but it's progress. With CG in place, the F_solve converges. You then get a failure in the phi_solver. I haven't really looked into that case, but the error message suggests that you're trying to use a field split preconditioner on a case with only one field. Regards, David On Fri, 2 Dec 2016 at 12:21 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > The code is available here > <https://bitbucket.org/annakalog/buoy2d/src/02696bd962286ef8b67667c98bc1043c…>. > Note that you have to go to the directory: Buoy2D/Inequality > constraint/Mixed system. > > Thank you, > > Anna. > > > On 2 Dec 2016, at 12:10, David Ham <David.Ham(a)imperial.ac.uk> wrote: > > Hi Anna, > > Yes, you're using a preconditioner which is not legal for one of your > blocks. I suspect it's the global block. Can you push your code somewhere I > can see and I'll have a read of your PETSc options. > > Regards, > > David > > On Fri, 2 Dec 2016 at 10:04 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > Can advice on this error? > > File "/e/data1/users/matak/opt/firedrake/Ship/Modules/Inequality > constraint/Mixed system/solvers.py", line 182, in solvers_SV > F_solver.solve() > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/variational_solver.py", > line 196, in solve > self.snes.solve(None, v) > File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve > (src/petsc4py.PETSc.c:171835) > petsc4py.PETSc.Error: error code 1 > [0] SNESSolve() line 4128 in > /tmp/pip-P_wDAl-build/src/snes/interface/snes.c > [0] SNESSolve_KSPONLY() line 40 in > /tmp/pip-P_wDAl-build/src/snes/impls/ksponly/ksponly.c > [0] KSPSolve() line 677 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] KSPSolve_GMRES() line 239 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/impls/gmres/gmres.c > [0] KSPInitialResidual() line 69 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itres.c > [0] KSP_PCApply() line 263 in > /tmp/pip-P_wDAl-build/include/petsc/private/kspimpl.h > [0] PCApply() line 482 in > /tmp/pip-P_wDAl-build/src/ksp/pc/interface/precon.c > [0] PCApply_FieldSplit() line 996 in > /tmp/pip-P_wDAl-build/src/ksp/pc/impls/fieldsplit/fieldsplit.c > [0] KSPSolve() line 620 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] KSPSetUp() line 393 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] PCSetUp() line 968 in > /tmp/pip-P_wDAl-build/src/ksp/pc/interface/precon.c > [0] PCSetUp_LU() line 92 in > /tmp/pip-P_wDAl-build/src/ksp/pc/impls/factor/lu/lu.c > [0] MatGetOrdering() line 260 in > /tmp/pip-P_wDAl-build/src/mat/order/sorder.c > [0] MatGetOrdering_ND() line 19 in > /tmp/pip-P_wDAl-build/src/mat/order/spnd.c > [0] No support for this operation for this object type > [0] Cannot get rows for matrix type python > > Thanks, Anna. > > > > On 01/12/16 17:26, Anna Kalogirou wrote: > > Oh ok I am not using the globals_petsc_changes branch of PyOP2. I will > update again, thanks. > > Best, Anna. > > On 1 Dec 2016, at 17:22, David Ham <David.Ham(a)imperial.ac.uk> wrote: > > Hi Anna, > > I don't think that PyOP2 install is current. Are you sure you are on the > latest versions of the right branches? The most important lines from > firedrake-status are: > > |PyOP2 |globals_petsc_changes |ddca732 > |False | > |firedrake |real-function-space |e051f50 > |False | > |petsc4py |python_matrix_bug_fixes |2d3f08a > |False | > > Do your branches and revisions match the above? > > Regards, > > David > > On Thu, 1 Dec 2016 at 17:09 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > I am now running into the following error message: > > Traceback (most recent call last): > File "buoy-swe.py", line 84, in <module> > F_solver = solver_F(phi0_5, eta1, lambda0_5, mu0_5, I, w, phi0, eta0, > Z0, W0, etaR, phi_t, eta_t, lambda_t, mu_t, I_t, v1, v2, v3, v4, v5, dt, > Hb, H0, L, dR_dt, lambda_bar, (2/dt)*mu_bar, g, rho, Mass, solvers_print); > File > "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Inequality > constraint/Mixed system/solvers.py", line 52, in solver_F > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 262, in __init__ > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 132, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/solving_utils.py", > line 213, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 104, in allocate_matrix > allocate_only=True) > File "<decorator-gen-278>", line 2, in _assemble > File "/Users/matak/firedrake/src/firedrake/firedrake/utils.py", line 62, > in wrapper > return f(*args, **kwargs) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 261, in _assemble > "%s_%s_matrix" % fs_names) > File "/Users/matak/firedrake/src/firedrake/firedrake/matrix.py", line > 152, in __init__ > self._M = op2.Mat(*args, **kwargs) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 637, > in _init > self._init_nest() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 696, > in _init_nest > '_'.join([self.name, str(i), str(j)]))) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 642, > in _init > self._init_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 709, > in _init_block > self._init_global_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 773, > in _init_global_block > self._version_set_zero() > AttributeError: 'Mat' object has no attribute '_version_set_zero' > > Here is the relevant part of the code: > > aphi = v1*(phi - lambda_t)*dx > Lphi = v1*(phi0 - 0.5*dt*g*(eta0-etaR))*dx > > aeta = (v2*eta - dt*Hb*inner(grad(v2),grad(phi)))*dx > Leta = v2*eta0*dx + dt*H0*dR_dt*v2*ds(1) #ds_v(1) > > alambda = v3*(eta/dt + rho/Mass*I_t + mu_bar*mu_t)*dx > Llambda = v3*(Z0/dt + W0)*dx > > amu = v4*(mu_bar*lambda_t + lambda_bar*mu_t)*dx > > aI = v5*(I_t/L-lambda_t)*dx > > a_solve = aphi + aeta + alambda + amu + aI > L_solve = Lphi + Leta + Llambda > > Ap = v1*phi*dx + Hb*inner(grad(v1),grad(phi))*dx \ > + v2*eta*dx \ > + v3*(rho/Mass-mu_bar**2)*lambda_t*dx \ > + v4*lambda_bar*mu_t*dx \ > + v5*1.0/L*I_t*dx > > F_problem = LinearVariationalProblem(a_solve, L_solve, w, aP=Ap) > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > > Thank you, > > Anna. > > On 7 Nov 2016, at 17:23, David Ham <david.ham(a)imperial.ac.uk> wrote: > > Yes. This is because trace elements were very recently (after my email) > merged into other components of Firedrake and the globals branch needs to > catch up. > > I've just pushed the relevant commits to the real-function-space branch so > that might work now. > > Regards, > > David > > > On Mon, 7 Nov 2016 at 17:15 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > I have just updated firedrake using the branches you mention in the email > below but I now get some error related to the mesh (?), when running > various codes which were previously working. Any idea what this is? > > Thanks, Anna. > > > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 42, in make_scalar_element > mesh.init() > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 898, in init > self._callback(self) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 1245, in callback > dim=geometric_dim) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 174, in VectorFunctionSpace > return FunctionSpace(mesh, element, name=name) > File "<decorator-gen-280>", line 2, in FunctionSpace > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/PyOP2/pyop2/profiling.py", > line 59, in wrapper > return f(*args, **kwargs) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 127, in FunctionSpace > check_element(element) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 85, in check_element > ufl.TraceElement, ufl.HDivElement, ufl.HCurlElement): > AttributeError: 'module' object has no attribute 'TraceElement' > > > > > On 04/11/16 16:16, David Ham wrote: > > A brief status update on this: the real-function-spaces branch of > Firedrake taken together with the globals_petsc_changes branch of PyOP2 no > longer exhibits the direct crash observed. However I am also yet to > actually successfully solve using a block preconditioner. I need to consult > with Lawrence to establish whether the problem is another bug or pilot > error. > > Regards, > > David > > On Mon, 24 Oct 2016 at 11:37 Mitchell, Lawrence < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > On 24 Oct 2016, at 11:13, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > > > > Hi Lawrence, > > > > Any update regarding the bug reported below? > > This appears to be more involved than I had first thought. So no luck > yet, sorry! David and I need to find some time together to work out the > differences/corner cases. > > Cheers, > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > _______________________________________________ > firedrake mailing list > firedrake(a)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 > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://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] Mixed system
by David Ham 02 Dec '16

02 Dec '16

Hi Anna, Yes, you're using a preconditioner which is not legal for one of your blocks. I suspect it's the global block. Can you push your code somewhere I can see and I'll have a read of your PETSc options. Regards, David On Fri, 2 Dec 2016 at 10:04 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Dear David, > > Can advice on this error? > > File "/e/data1/users/matak/opt/firedrake/Ship/Modules/Inequality > constraint/Mixed system/solvers.py", line 182, in solvers_SV > F_solver.solve() > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/variational_solver.py", > line 196, in solve > self.snes.solve(None, v) > File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve > (src/petsc4py.PETSc.c:171835) > petsc4py.PETSc.Error: error code 1 > [0] SNESSolve() line 4128 in > /tmp/pip-P_wDAl-build/src/snes/interface/snes.c > [0] SNESSolve_KSPONLY() line 40 in > /tmp/pip-P_wDAl-build/src/snes/impls/ksponly/ksponly.c > [0] KSPSolve() line 677 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] KSPSolve_GMRES() line 239 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/impls/gmres/gmres.c > [0] KSPInitialResidual() line 69 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itres.c > [0] KSP_PCApply() line 263 in > /tmp/pip-P_wDAl-build/include/petsc/private/kspimpl.h > [0] PCApply() line 482 in > /tmp/pip-P_wDAl-build/src/ksp/pc/interface/precon.c > [0] PCApply_FieldSplit() line 996 in > /tmp/pip-P_wDAl-build/src/ksp/pc/impls/fieldsplit/fieldsplit.c > [0] KSPSolve() line 620 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] KSPSetUp() line 393 in > /tmp/pip-P_wDAl-build/src/ksp/ksp/interface/itfunc.c > [0] PCSetUp() line 968 in > /tmp/pip-P_wDAl-build/src/ksp/pc/interface/precon.c > [0] PCSetUp_LU() line 92 in > /tmp/pip-P_wDAl-build/src/ksp/pc/impls/factor/lu/lu.c > [0] MatGetOrdering() line 260 in > /tmp/pip-P_wDAl-build/src/mat/order/sorder.c > [0] MatGetOrdering_ND() line 19 in > /tmp/pip-P_wDAl-build/src/mat/order/spnd.c > [0] No support for this operation for this object type > [0] Cannot get rows for matrix type python > > Thanks, Anna. > > > > On 01/12/16 17:26, Anna Kalogirou wrote: > > Oh ok I am not using the globals_petsc_changes branch of PyOP2. I will > update again, thanks. > > Best, Anna. > > On 1 Dec 2016, at 17:22, David Ham <David.Ham(a)imperial.ac.uk> wrote: > > Hi Anna, > > I don't think that PyOP2 install is current. Are you sure you are on the > latest versions of the right branches? The most important lines from > firedrake-status are: > > |PyOP2 |globals_petsc_changes |ddca732 > |False | > |firedrake |real-function-space |e051f50 > |False | > |petsc4py |python_matrix_bug_fixes |2d3f08a > |False | > > Do your branches and revisions match the above? > > Regards, > > David > > On Thu, 1 Dec 2016 at 17:09 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > I am now running into the following error message: > > Traceback (most recent call last): > File "buoy-swe.py", line 84, in <module> > F_solver = solver_F(phi0_5, eta1, lambda0_5, mu0_5, I, w, phi0, eta0, > Z0, W0, etaR, phi_t, eta_t, lambda_t, mu_t, I_t, v1, v2, v3, v4, v5, dt, > Hb, H0, L, dR_dt, lambda_bar, (2/dt)*mu_bar, g, rho, Mass, solvers_print); > File > "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Inequality > constraint/Mixed system/solvers.py", line 52, in solver_F > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 262, in __init__ > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 132, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/solving_utils.py", > line 213, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 104, in allocate_matrix > allocate_only=True) > File "<decorator-gen-278>", line 2, in _assemble > File "/Users/matak/firedrake/src/firedrake/firedrake/utils.py", line 62, > in wrapper > return f(*args, **kwargs) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 261, in _assemble > "%s_%s_matrix" % fs_names) > File "/Users/matak/firedrake/src/firedrake/firedrake/matrix.py", line > 152, in __init__ > self._M = op2.Mat(*args, **kwargs) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 637, > in _init > self._init_nest() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 696, > in _init_nest > '_'.join([self.name, str(i), str(j)]))) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 642, > in _init > self._init_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 709, > in _init_block > self._init_global_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 773, > in _init_global_block > self._version_set_zero() > AttributeError: 'Mat' object has no attribute '_version_set_zero' > > Here is the relevant part of the code: > > aphi = v1*(phi - lambda_t)*dx > Lphi = v1*(phi0 - 0.5*dt*g*(eta0-etaR))*dx > > aeta = (v2*eta - dt*Hb*inner(grad(v2),grad(phi)))*dx > Leta = v2*eta0*dx + dt*H0*dR_dt*v2*ds(1) #ds_v(1) > > alambda = v3*(eta/dt + rho/Mass*I_t + mu_bar*mu_t)*dx > Llambda = v3*(Z0/dt + W0)*dx > > amu = v4*(mu_bar*lambda_t + lambda_bar*mu_t)*dx > > aI = v5*(I_t/L-lambda_t)*dx > > a_solve = aphi + aeta + alambda + amu + aI > L_solve = Lphi + Leta + Llambda > > Ap = v1*phi*dx + Hb*inner(grad(v1),grad(phi))*dx \ > + v2*eta*dx \ > + v3*(rho/Mass-mu_bar**2)*lambda_t*dx \ > + v4*lambda_bar*mu_t*dx \ > + v5*1.0/L*I_t*dx > > F_problem = LinearVariationalProblem(a_solve, L_solve, w, aP=Ap) > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > > Thank you, > > Anna. > > On 7 Nov 2016, at 17:23, David Ham <david.ham(a)imperial.ac.uk> wrote: > > Yes. This is because trace elements were very recently (after my email) > merged into other components of Firedrake and the globals branch needs to > catch up. > > I've just pushed the relevant commits to the real-function-space branch so > that might work now. > > Regards, > > David > > > On Mon, 7 Nov 2016 at 17:15 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > I have just updated firedrake using the branches you mention in the email > below but I now get some error related to the mesh (?), when running > various codes which were previously working. Any idea what this is? > > Thanks, Anna. > > > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 42, in make_scalar_element > mesh.init() > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 898, in init > self._callback(self) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 1245, in callback > dim=geometric_dim) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 174, in VectorFunctionSpace > return FunctionSpace(mesh, element, name=name) > File "<decorator-gen-280>", line 2, in FunctionSpace > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/PyOP2/pyop2/profiling.py", > line 59, in wrapper > return f(*args, **kwargs) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 127, in FunctionSpace > check_element(element) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 85, in check_element > ufl.TraceElement, ufl.HDivElement, ufl.HCurlElement): > AttributeError: 'module' object has no attribute 'TraceElement' > > > > > On 04/11/16 16:16, David Ham wrote: > > A brief status update on this: the real-function-spaces branch of > Firedrake taken together with the globals_petsc_changes branch of PyOP2 no > longer exhibits the direct crash observed. However I am also yet to > actually successfully solve using a block preconditioner. I need to consult > with Lawrence to establish whether the problem is another bug or pilot > error. > > Regards, > > David > > On Mon, 24 Oct 2016 at 11:37 Mitchell, Lawrence < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > On 24 Oct 2016, at 11:13, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > > > > Hi Lawrence, > > > > Any update regarding the bug reported below? > > This appears to be more involved than I had first thought. So no luck > yet, sorry! David and I need to find some time together to work out the > differences/corner cases. > > Cheers, > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > _______________________________________________ > firedrake mailing list > firedrake(a)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 > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > >

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Re: [firedrake] Mixed system
by David Ham 02 Dec '16

02 Dec '16

Hi Anna, I don't think that PyOP2 install is current. Are you sure you are on the latest versions of the right branches? The most important lines from firedrake-status are: |PyOP2 |globals_petsc_changes |ddca732 |False | |firedrake |real-function-space |e051f50 |False | |petsc4py |python_matrix_bug_fixes |2d3f08a |False | Do your branches and revisions match the above? Regards, David On Thu, 1 Dec 2016 at 17:09 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > Dear David, > > I am now running into the following error message: > > Traceback (most recent call last): > File "buoy-swe.py", line 84, in <module> > F_solver = solver_F(phi0_5, eta1, lambda0_5, mu0_5, I, w, phi0, eta0, > Z0, W0, etaR, phi_t, eta_t, lambda_t, mu_t, I_t, v1, v2, v3, v4, v5, dt, > Hb, H0, L, dR_dt, lambda_bar, (2/dt)*mu_bar, g, rho, Mass, solvers_print); > File > "/Users/matak/Documents/Simulations/Firedrake/Ship/Modules/Inequality > constraint/Mixed system/solvers.py", line 52, in solver_F > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 262, in __init__ > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > File > "/Users/matak/firedrake/src/firedrake/firedrake/variational_solver.py", > line 132, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/solving_utils.py", > line 213, in __init__ > appctx=appctx) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 104, in allocate_matrix > allocate_only=True) > File "<decorator-gen-278>", line 2, in _assemble > File "/Users/matak/firedrake/src/firedrake/firedrake/utils.py", line 62, > in wrapper > return f(*args, **kwargs) > File "/Users/matak/firedrake/src/firedrake/firedrake/assemble.py", line > 261, in _assemble > "%s_%s_matrix" % fs_names) > File "/Users/matak/firedrake/src/firedrake/firedrake/matrix.py", line > 152, in __init__ > self._M = op2.Mat(*args, **kwargs) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 637, > in _init > self._init_nest() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 696, > in _init_nest > '_'.join([self.name, str(i), str(j)]))) > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 626, > in __init__ > self._init() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 642, > in _init > self._init_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 709, > in _init_block > self._init_global_block() > File "/Users/matak/firedrake/src/PyOP2/pyop2/petsc_base.py", line 773, > in _init_global_block > self._version_set_zero() > AttributeError: 'Mat' object has no attribute '_version_set_zero' > > Here is the relevant part of the code: > > aphi = v1*(phi - lambda_t)*dx > Lphi = v1*(phi0 - 0.5*dt*g*(eta0-etaR))*dx > > aeta = (v2*eta - dt*Hb*inner(grad(v2),grad(phi)))*dx > Leta = v2*eta0*dx + dt*H0*dR_dt*v2*ds(1) #ds_v(1) > > alambda = v3*(eta/dt + rho/Mass*I_t + mu_bar*mu_t)*dx > Llambda = v3*(Z0/dt + W0)*dx > > amu = v4*(mu_bar*lambda_t + lambda_bar*mu_t)*dx > > aI = v5*(I_t/L-lambda_t)*dx > > a_solve = aphi + aeta + alambda + amu + aI > L_solve = Lphi + Leta + Llambda > > Ap = v1*phi*dx + Hb*inner(grad(v1),grad(phi))*dx \ > + v2*eta*dx \ > + v3*(rho/Mass-mu_bar**2)*lambda_t*dx \ > + v4*lambda_bar*mu_t*dx \ > + v5*1.0/L*I_t*dx > > F_problem = LinearVariationalProblem(a_solve, L_solve, w, aP=Ap) > F_solver = LinearVariationalSolver(F_problem, > solver_parameters=solvers_print) > > Thank you, > > Anna. > > On 7 Nov 2016, at 17:23, David Ham <david.ham(a)imperial.ac.uk> wrote: > > Yes. This is because trace elements were very recently (after my email) > merged into other components of Firedrake and the globals branch needs to > catch up. > > I've just pushed the relevant commits to the real-function-space branch so > that might work now. > > Regards, > > David > > > On Mon, 7 Nov 2016 at 17:15 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > wrote: > > Dear David, > > I have just updated firedrake using the branches you mention in the email > below but I now get some error related to the mesh (?), when running > various codes which were previously working. Any idea what this is? > > Thanks, Anna. > > > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 42, in make_scalar_element > mesh.init() > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 898, in init > self._callback(self) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", > line 1245, in callback > dim=geometric_dim) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 174, in VectorFunctionSpace > return FunctionSpace(mesh, element, name=name) > File "<decorator-gen-280>", line 2, in FunctionSpace > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/PyOP2/pyop2/profiling.py", > line 59, in wrapper > return f(*args, **kwargs) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 127, in FunctionSpace > check_element(element) > File > "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", > line 85, in check_element > ufl.TraceElement, ufl.HDivElement, ufl.HCurlElement): > AttributeError: 'module' object has no attribute 'TraceElement' > > > > > On 04/11/16 16:16, David Ham wrote: > > A brief status update on this: the real-function-spaces branch of > Firedrake taken together with the globals_petsc_changes branch of PyOP2 no > longer exhibits the direct crash observed. However I am also yet to > actually successfully solve using a block preconditioner. I need to consult > with Lawrence to establish whether the problem is another bug or pilot > error. > > Regards, > > David > > On Mon, 24 Oct 2016 at 11:37 Mitchell, Lawrence < > lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > On 24 Oct 2016, at 11:13, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> > wrote: > > > > Hi Lawrence, > > > > Any update regarding the bug reported below? > > This appears to be more involved than I had first thought. So no luck > yet, sorry! David and I need to find some time together to work out the > differences/corner cases. > > Cheers, > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://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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Best way to detect memory leaks
by Justin Chang 01 Dec '16

01 Dec '16

Hi all, What's the best way or tool to detect for potential memory leaks for Firedrake? Normally I use the PETSc log functions but in my Firedrake code I am doing lots of extra curricular programming which isn't seen by PETSc. Thanks, Justin

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Re: [firedrake] Mixed system
by David Ham 01 Dec '16

01 Dec '16

Yes. This is because trace elements were very recently (after my email) merged into other components of Firedrake and the globals branch needs to catch up. I've just pushed the relevant commits to the real-function-space branch so that might work now. Regards, David On Mon, 7 Nov 2016 at 17:15 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: Dear David, I have just updated firedrake using the branches you mention in the email below but I now get some error related to the mesh (?), when running various codes which were previously working. Any idea what this is? Thanks, Anna. File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", line 42, in make_scalar_element mesh.init() File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", line 898, in init self._callback(self) File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/mesh.py", line 1245, in callback dim=geometric_dim) File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", line 174, in VectorFunctionSpace return FunctionSpace(mesh, element, name=name) File "<decorator-gen-280>", line 2, in FunctionSpace File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/PyOP2/pyop2/profiling.py", line 59, in wrapper return f(*args, **kwargs) File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", line 127, in FunctionSpace check_element(element) File "/e/data1/users/matak/opt/firedrake-installation/firedrake/src/firedrake/firedrake/functionspace.py", line 85, in check_element ufl.TraceElement, ufl.HDivElement, ufl.HCurlElement): AttributeError: 'module' object has no attribute 'TraceElement' On 04/11/16 16:16, David Ham wrote: A brief status update on this: the real-function-spaces branch of Firedrake taken together with the globals_petsc_changes branch of PyOP2 no longer exhibits the direct crash observed. However I am also yet to actually successfully solve using a block preconditioner. I need to consult with Lawrence to establish whether the problem is another bug or pilot error. Regards, David On Mon, 24 Oct 2016 at 11:37 Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk> wrote: > On 24 Oct 2016, at 11:13, Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > > Hi Lawrence, > > Any update regarding the bug reported below? This appears to be more involved than I had first thought. So no luck yet, sorry! David and I need to find some time together to work out the differences/corner cases. Cheers, Lawrence _______________________________________________ firedrake mailing list firedrake(a)imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake

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eigenvalue problems with SLEPc
by Francis Poulin 01 Dec '16

01 Dec '16

Hello, A while ago someone pointed me towards test_slepc.py for an example on how to solve an eigenvalue problem. I have been using this as a model to compute Quasi-Geostrophic basin modes in a closed basin. We have a version working in FENicS and I am very keen to get it working in Firedrake as well. I have a good start, which can be found on github, https://github.com/francispoulin/firedrakeQG/blob/master/basin_modes_qg.py Unfortunately, I don't know how to do a lot of things. For example specify number of eigenvalues to determine, specify a target eigenvalue, what method to use, or even just look at the eigenvector. Are there any other examples that someone might be able to share that might to able to do this? 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

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