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Re: [firedrake] Solving adjoint equation
by Andrew McRae 30 Mar '16

30 Mar '16

The second and third of those links work for me, so perhaps there's an issue at your end. Anyway, let's bypass this for now by running in "minimal PETSc" mode. Can you edit your firedrake-update script (located at, I guess, /home/george/polygon/firedrake/bin/firedrake-update) by changing args.minimal_petsc from False to True (around line 120-130) and rerun? This should install PETSc without most third-party packages, including the one you're having trouble with, when you run firedrake-update. On 29 March 2016 at 20:18, George Ovchinnikov <lives9(a)gmail.com> wrote: > I'm trying to update firedrake, but getting > > TESTING: configureLibrary from > > config.packages.netcdf(/tmp/pip-YAhIai-build/config/BuildSystem/config/package.py:626) > > > =============================================================================== > Trying to download > ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz for NETCDF > > > =============================================================================== > > > > =============================================================================== > Trying to download > http://ftp.mcs.anl.gov/pub/petsc/externalpackages/netcdf-4.3.2.tar.gz > for NETCDF > > > =============================================================================== > > > > =============================================================================== > Trying to download > ftp://ftp.mcs.anl.gov/pub/petsc/externalpackages/netcdf-4.3.2.tar.gz for > NETCDF > > > =============================================================================== > > > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see > configure.log for details): > > > ------------------------------------------------------------------------------- > Unable to download NETCDF > Unable to download package NETCDF from: > ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz > * If URL specified manually - perhaps there is a typo? > * If your network is disconnected - please reconnect and rerun > ./configure > * Or perhaps you have a firewall blocking the download > * Alternatively, you can download the above URL manually, to > /yourselectedlocation/netcdf-4.3.2.tar.gz > and use the configure option: > --download-netcdf=/yourselectedlocation/netcdf-4.3.2.tar.gz > file could not be opened successfully > Downloaded package NETCDF from: > http://ftp.mcs.anl.gov/pub/petsc/externalpackages/netcdf-4.3.2.tar.gz is > not a tarball. > [or installed python cannot process compressed files] > * If you are behind a firewall - please fix your proxy and rerun > ./configure > For example at LANL you may need to set the environmental variable > http_proxy (or HTTP_PROXY?) to http://proxyout.lanl.gov > * Alternatively, you can download the above URL manually, to > /yourselectedlocation/netcdf-4.3.2.tar.gz > and use the configure option: > --download-netcdf=/yourselectedlocation/netcdf-4.3.2.tar.gz > Unable to download package NETCDF from: > ftp://ftp.mcs.anl.gov/pub/petsc/externalpackages/netcdf-4.3.2.tar.gz > * If URL specified manually - perhaps there is a typo? > * If your network is disconnected - please reconnect and rerun > ./configure > * Or perhaps you have a firewall blocking the download > * Alternatively, you can download the above URL manually, to > /yourselectedlocation/netcdf-4.3.2.tar.gz > and use the configure option: > --download-netcdf=/yourselectedlocation/netcdf-4.3.2.tar.gz > > > ******************************************************************************* > > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/tmp/pip-YAhIai-build/setup.py", line 302, in <module> > **metadata) > File "/usr/lib/python2.7/distutils/core.py", line 151, in setup > dist.run_commands() > File "/usr/lib/python2.7/distutils/dist.py", line 953, in > run_commands > self.run_command(cmd) > File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command > cmd_obj.run() > File "/tmp/pip-YAhIai-build/setup.py", line 218, in run > config(prefix, self.dry_run) > File "/tmp/pip-YAhIai-build/setup.py", line 148, in config > if status != 0: raise RuntimeError(status) > RuntimeError: 256 > > ---------------------------------------- > Command "/home/george/polygon/firedrake/bin/python -u -c "import > setuptools, > > tokenize;__file__='/tmp/pip-YAhIai-build/setup.py';exec(compile(getattr(tokenize, > 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, > 'exec'))" install --record /tmp/pip-OhlEEH-record/install-record.txt > --single-version-externally-managed --compile --install-headers > /home/george/polygon/firedrake/include/site/python2.7/petsc" failed with > error code 1 in /tmp/pip-YAhIai-build/ > Traceback (most recent call last): > File "firedrake-install", line 836, in <module> > install("petsc/") > File "firedrake-install", line 497, in install > run_pip_install(["--ignore-installed", package]) > File "firedrake-install", line 360, in run_pip_install > check_call(pipinstall + pipargs) > File "firedrake-install", line 211, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib/python2.7/subprocess.py", line 540, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command > '['/home/george/polygon/firedrake/bin/pip', 'install', '--no-deps', > '--ignore-installed', 'petsc/']' returned non-zero exit status 1 > > > On all of the abovementioned urls I'm getting 403 error when trying to > access manually. > > Sincerely, > George > > > On 29.03.2016 18:30, Andrew McRae wrote: > > I also note that your line numbers don't match up with the current > > codebase; e.g. > > > https://github.com/firedrakeproject/firedrake/blob/master/firedrake/linear_… > > > > On 29 March 2016 at 16:13, George Ovchinnikov <lives9(a)gmail.com > > <mailto:lives9@gmail.com>> wrote: > > > > Here it is > > > > > --------------------------------------------------------------------------- > > KeyError Traceback (most recent > > call last) > > <ipython-input-8-752634385ffb> in <module>() > > 22 > > 23 w_sol = Function(V) > > ---> 24 solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > > "preonly", "pc_type": "lu"}) > > 25 File("w_sol.pvd") << w_sol > > > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > > in solve(*args, **kwargs) > > 121 else: > > 122 # Solve pre-assembled system > > --> 123 return _la_solve(*args, **kwargs) > > 124 > > 125 > > > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > > in _la_solve(A, x, b, **kwargs) > > 209 options_prefix=options_prefix) > > 210 > > --> 211 solver.solve(x, b) > > 212 > > 213 > > > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/linear_solver.pyc > > in solve(self, x, b) > > 140 r = self.ksp.getConvergedReason() > > 141 if r < 0: > > --> 142 raise RuntimeError("LinearSolver failed to > converge > > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > > solving_utils.KSPReasons[r]) > > > > KeyError: -11 > > > > > > > > On 29.03.2016 18:10, Andrew McRae wrote: > > > What output do you get? > > > > > > On 29 March 2016 at 16:09, George Ovchinnikov <lives9(a)gmail.com > <mailto:lives9@gmail.com> > > > <mailto:lives9@gmail.com <mailto:lives9@gmail.com>>> wrote: > > > > > > Dear All, > > > > > > I have trilinear form a(w,u,v) and usually solve > > > a(w,u,v) = l(v), for u with fixed w. > > > > > > Here I have: > > > > > > a = w dot(grad(u), grad(v)) * dx, > > > and > > > l(v) = f * v * dx. > > > > > > Now, given u_tilde I want to solve for w, i.e. find > > > w_tilde such, that > > > a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. > > > > > > I'm trying the following: > > > > > > mesh = UnitSquareMesh(size, size) > > > V = FunctionSpace(mesh, "CG", 1) > > > > > > f = Function(V) > > > f.interpolate(Expression("1")) > > > > > > u_tilde = Function(V) > > > u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * > > > 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * > > 1/(1+exp(-1*(1-x[1])))" )) > > > > > > w_tilde = TrialFunction(V) > > > v = TestFunction(V) > > > > > > a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx > > > frm_tilde = assemble( a_tilde ) > > > > > > L = f * v * dx > > > rhs = assemble(L) > > > > > > w_sol = Function(V) > > > solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > > "preonly", > > > "pc_type": "lu"}) > > > File("w_sol.pvd") << w_sol > > > > > > > > > It fails to converge: > > > 140 r = self.ksp.getConvergedReason() > > > 141 if r < 0: > > > --> 142 raise RuntimeError("LinearSolver failed to > > converge > > > after %d iterations with reason: %s", > > self.ksp.getIterationNumber(), > > > solving_utils.KSPReasons[r]) > > > > > > KeyError: -11 > > > > > > I'm using direct method, not the iterative one, so what is > > happening > > > here? > > > > > > _______________________________________________ > > > firedrake mailing list > > > firedrake(a)imperial.ac.uk <mailto:firedrake@imperial.ac.uk> > > <mailto:firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk>> > > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > > > > > > > > > > > _______________________________________________ > > > firedrake mailing list > > > firedrake(a)imperial.ac.uk <mailto:firedrake@imperial.ac.uk> > > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk <mailto:firedrake@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 list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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confirm
by G. D. McBain 29 Mar '16

29 Mar '16

confirm 3659d40f27a64e5837a16cdd48c8f9d71f7b4df1

1 0

Re: [firedrake] Solving adjoint equation
by Andrew McRae 29 Mar '16

29 Mar '16

I also note that your line numbers don't match up with the current codebase; e.g. https://github.com/firedrakeproject/firedrake/blob/master/firedrake/linear_… On 29 March 2016 at 16:13, George Ovchinnikov <lives9(a)gmail.com> wrote: > Here it is > > --------------------------------------------------------------------------- > KeyError Traceback (most recent call last) > <ipython-input-8-752634385ffb> in <module>() > 22 > 23 w_sol = Function(V) > ---> 24 solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > "preonly", "pc_type": "lu"}) > 25 File("w_sol.pvd") << w_sol > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > in solve(*args, **kwargs) > 121 else: > 122 # Solve pre-assembled system > --> 123 return _la_solve(*args, **kwargs) > 124 > 125 > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > in _la_solve(A, x, b, **kwargs) > 209 options_prefix=options_prefix) > 210 > --> 211 solver.solve(x, b) > 212 > 213 > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/linear_solver.pyc > in solve(self, x, b) > 140 r = self.ksp.getConvergedReason() > 141 if r < 0: > --> 142 raise RuntimeError("LinearSolver failed to converge > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > solving_utils.KSPReasons[r]) > > KeyError: -11 > > > > On 29.03.2016 18:10, Andrew McRae wrote: > > What output do you get? > > > > On 29 March 2016 at 16:09, George Ovchinnikov <lives9(a)gmail.com > > <mailto:lives9@gmail.com>> wrote: > > > > Dear All, > > > > I have trilinear form a(w,u,v) and usually solve > > a(w,u,v) = l(v), for u with fixed w. > > > > Here I have: > > > > a = w dot(grad(u), grad(v)) * dx, > > and > > l(v) = f * v * dx. > > > > Now, given u_tilde I want to solve for w, i.e. find > > w_tilde such, that > > a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. > > > > I'm trying the following: > > > > mesh = UnitSquareMesh(size, size) > > V = FunctionSpace(mesh, "CG", 1) > > > > f = Function(V) > > f.interpolate(Expression("1")) > > > > u_tilde = Function(V) > > u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * > > 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * 1/(1+exp(-1*(1-x[1])))" > )) > > > > w_tilde = TrialFunction(V) > > v = TestFunction(V) > > > > a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx > > frm_tilde = assemble( a_tilde ) > > > > L = f * v * dx > > rhs = assemble(L) > > > > w_sol = Function(V) > > solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > "preonly", > > "pc_type": "lu"}) > > File("w_sol.pvd") << w_sol > > > > > > It fails to converge: > > 140 r = self.ksp.getConvergedReason() > > 141 if r < 0: > > --> 142 raise RuntimeError("LinearSolver failed to > converge > > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > > solving_utils.KSPReasons[r]) > > > > KeyError: -11 > > > > I'm using direct method, not the iterative one, so what is happening > > here? > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk <mailto:firedrake@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 list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Solving adjoint equation
by George Ovchinnikov 29 Mar '16

29 Mar '16

Dear All, I have trilinear form a(w,u,v) and usually solve a(w,u,v) = l(v), for u with fixed w. Here I have: a = w dot(grad(u), grad(v)) * dx, and l(v) = f * v * dx. Now, given u_tilde I want to solve for w, i.e. find w_tilde such, that a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. I'm trying the following: mesh = UnitSquareMesh(size, size) V = FunctionSpace(mesh, "CG", 1) f = Function(V) f.interpolate(Expression("1")) u_tilde = Function(V) u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * 1/(1+exp(-1*(1-x[1])))" )) w_tilde = TrialFunction(V) v = TestFunction(V) a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx frm_tilde = assemble( a_tilde ) L = f * v * dx rhs = assemble(L) w_sol = Function(V) solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": "preonly", "pc_type": "lu"}) File("w_sol.pvd") << w_sol It fails to converge: 140 r = self.ksp.getConvergedReason() 141 if r < 0: --> 142 raise RuntimeError("LinearSolver failed to converge after %d iterations with reason: %s", self.ksp.getIterationNumber(), solving_utils.KSPReasons[r]) KeyError: -11 I'm using direct method, not the iterative one, so what is happening here?

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Re: [firedrake] Solving adjoint equation
by Andrew McRae 29 Mar '16

29 Mar '16

I see; the syntax should be solve(frm_tilde, w_sol, rhs, solver_parameters=...) i.e. "solve(A, x, b)" rather than "solve(A, b, x)". On 29 March 2016 at 16:09, George Ovchinnikov <lives9(a)gmail.com> wrote: > Dear All, > > I have trilinear form a(w,u,v) and usually solve > a(w,u,v) = l(v), for u with fixed w. > > Here I have: > > a = w dot(grad(u), grad(v)) * dx, > and > l(v) = f * v * dx. > > Now, given u_tilde I want to solve for w, i.e. find > w_tilde such, that > a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. > > I'm trying the following: > > mesh = UnitSquareMesh(size, size) > V = FunctionSpace(mesh, "CG", 1) > > f = Function(V) > f.interpolate(Expression("1")) > > u_tilde = Function(V) > u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * > 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * 1/(1+exp(-1*(1-x[1])))" )) > > w_tilde = TrialFunction(V) > v = TestFunction(V) > > a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx > frm_tilde = assemble( a_tilde ) > > L = f * v * dx > rhs = assemble(L) > > w_sol = Function(V) > solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": "preonly", > "pc_type": "lu"}) > File("w_sol.pvd") << w_sol > > > It fails to converge: > 140 r = self.ksp.getConvergedReason() > 141 if r < 0: > --> 142 raise RuntimeError("LinearSolver failed to converge > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > solving_utils.KSPReasons[r]) > > KeyError: -11 > > I'm using direct method, not the iterative one, so what is happening here? > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Re: [firedrake] Solving adjoint equation
by Andrew McRae 29 Mar '16

29 Mar '16

Do you not get any PETSc output before that? The KeyError is weird; according to http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPConverge…, -11 is KSP_DIVERGED_PCSETUP_FAILED. I don't use the preassembly syntax normally; does it work if you remove the lines assembling frm_tilde and rhs, and simply call solve(a_tilde == L, w_sol, solver_parameters={...}) ? On 29 March 2016 at 16:13, George Ovchinnikov <lives9(a)gmail.com> wrote: > Here it is > > --------------------------------------------------------------------------- > KeyError Traceback (most recent call last) > <ipython-input-8-752634385ffb> in <module>() > 22 > 23 w_sol = Function(V) > ---> 24 solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > "preonly", "pc_type": "lu"}) > 25 File("w_sol.pvd") << w_sol > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > in solve(*args, **kwargs) > 121 else: > 122 # Solve pre-assembled system > --> 123 return _la_solve(*args, **kwargs) > 124 > 125 > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/solving.pyc > in _la_solve(A, x, b, **kwargs) > 209 options_prefix=options_prefix) > 210 > --> 211 solver.solve(x, b) > 212 > 213 > > > /home/george/polygon/firedrake_new/firedrake/local/lib/python2.7/site-packages/firedrake/linear_solver.pyc > in solve(self, x, b) > 140 r = self.ksp.getConvergedReason() > 141 if r < 0: > --> 142 raise RuntimeError("LinearSolver failed to converge > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > solving_utils.KSPReasons[r]) > > KeyError: -11 > > > > On 29.03.2016 18:10, Andrew McRae wrote: > > What output do you get? > > > > On 29 March 2016 at 16:09, George Ovchinnikov <lives9(a)gmail.com > > <mailto:lives9@gmail.com>> wrote: > > > > Dear All, > > > > I have trilinear form a(w,u,v) and usually solve > > a(w,u,v) = l(v), for u with fixed w. > > > > Here I have: > > > > a = w dot(grad(u), grad(v)) * dx, > > and > > l(v) = f * v * dx. > > > > Now, given u_tilde I want to solve for w, i.e. find > > w_tilde such, that > > a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. > > > > I'm trying the following: > > > > mesh = UnitSquareMesh(size, size) > > V = FunctionSpace(mesh, "CG", 1) > > > > f = Function(V) > > f.interpolate(Expression("1")) > > > > u_tilde = Function(V) > > u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * > > 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * 1/(1+exp(-1*(1-x[1])))" > )) > > > > w_tilde = TrialFunction(V) > > v = TestFunction(V) > > > > a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx > > frm_tilde = assemble( a_tilde ) > > > > L = f * v * dx > > rhs = assemble(L) > > > > w_sol = Function(V) > > solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": > "preonly", > > "pc_type": "lu"}) > > File("w_sol.pvd") << w_sol > > > > > > It fails to converge: > > 140 r = self.ksp.getConvergedReason() > > 141 if r < 0: > > --> 142 raise RuntimeError("LinearSolver failed to > converge > > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > > solving_utils.KSPReasons[r]) > > > > KeyError: -11 > > > > I'm using direct method, not the iterative one, so what is happening > > here? > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk <mailto:firedrake@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 list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Re: [firedrake] Solving adjoint equation
by Andrew McRae 29 Mar '16

29 Mar '16

What output do you get? On 29 March 2016 at 16:09, George Ovchinnikov <lives9(a)gmail.com> wrote: > Dear All, > > I have trilinear form a(w,u,v) and usually solve > a(w,u,v) = l(v), for u with fixed w. > > Here I have: > > a = w dot(grad(u), grad(v)) * dx, > and > l(v) = f * v * dx. > > Now, given u_tilde I want to solve for w, i.e. find > w_tilde such, that > a(w_tilde, u_tilde, v) = l(v), for any v in suitable subspace. > > I'm trying the following: > > mesh = UnitSquareMesh(size, size) > V = FunctionSpace(mesh, "CG", 1) > > f = Function(V) > f.interpolate(Expression("1")) > > u_tilde = Function(V) > u_tilde.interpolate(Expression("1/(1+exp(-1*x[0])) * > 1/(1+exp(-1*(1-x[0]))) *1/(1+exp(-1*x[1])) * 1/(1+exp(-1*(1-x[1])))" )) > > w_tilde = TrialFunction(V) > v = TestFunction(V) > > a_tilde = (w_tilde * dot(grad(u_tilde), grad(v))) * dx > frm_tilde = assemble( a_tilde ) > > L = f * v * dx > rhs = assemble(L) > > w_sol = Function(V) > solve(frm_tilde, rhs, w_sol, solver_parameters={"ksp_type": "preonly", > "pc_type": "lu"}) > File("w_sol.pvd") << w_sol > > > It fails to converge: > 140 r = self.ksp.getConvergedReason() > 141 if r < 0: > --> 142 raise RuntimeError("LinearSolver failed to converge > after %d iterations with reason: %s", self.ksp.getIterationNumber(), > solving_utils.KSPReasons[r]) > > KeyError: -11 > > I'm using direct method, not the iterative one, so what is happening here? > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Projecting function to finer mesh
by George Ovchinnikov 29 Mar '16

29 Mar '16

Dear All, I have a function w: mesh = UnitSquareMesh(size, size, quadrilateral = True) V0 = FunctionSpace(mesh, "DG", 0) w = Function(V0) ... w was calculated during my program run. Now, I want to project it to finer mesh, something like: mesh2 = UnitSquareMesh(2*size, 2*size, quadrilateral = True) V2_0 = FunctionSpace(mesh, "DG", 0) w2 = Function(V2_0) project(w, w2) but I'm getting errors about mesh being quadrilateral or something like RuntimeError: Can't project between mismatching meshes. What is the correct way to project function from one mesh to another? Sincerely, George

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Merging UFL and FIAT back to FEnICS
by David Ham 25 Mar '16

25 Mar '16

Hello Firedrakers (including Martin and Marie, whom I believe are on this list), I just want to touch base on our plans to get onto common UFL and FIAT with FEniCS - which would mean that we'll have come full circle and be in sync for everything which is in common. FIAT pull request #4 introduces Travis testing for FIAT, and fixes some Python 3 issues which hadn't previously been raised. When that lands (reviews please!), I think we have done all the things required for FEniCS to accept the pull. https://github.com/firedrakeproject/fiat/pull/4 FIAT pull request #3 implements Taylor basis for 2D and 3D. It could land either before or after merging to FEnICS. Tuomas probably wants it pronto so we could think of merging it sooner. https://github.com/firedrakeproject/fiat/pull/3 When we merge back into FEniCS, OuterProductFoo becomes TensorProductFoo as agreed in the wider FEniCS community. This has consequences for UFL which have landed for us but still need to change in FEniCS. I have just read the diff between our UFL and FEniCS UFL, and it appears that the diff consists of: * The rename * Various fixes for non-affine. I think we could therefore reasonably just put in a pull request to merge our UFL into theirs. Should we just do that, or is there something I am missing? Responses please. Regards, David

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Re: [firedrake] Compile error
by David Ham 18 Mar '16

18 Mar '16

Hi Will, Your error is occuring in FFC. FFC has not been a part of Firedrake for quite some time now, so your first issue is that your firedrake is old. Please run firedrake-update and try again. Regards, David On Fri, 18 Mar 2016 at 13:22 William Booker <scwb(a)leeds.ac.uk> wrote: > Dear all, > > I've been trying to compile the attached code for a compressible acoustic > wave, but I've been getting the following error. > > How do I fix this? > > Traceback (most recent call last): > File "compressible_acoustic.py", line 118, in <module> > solve(a == L, out) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", > line 120, in solve > _solve_varproblem(*args, **kwargs) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", > line 147, in _solve_varproblem > solver.solve() > File "<decorator-gen-277>", line 2, in solve > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/profiling.py", > line 203, in wrapper > return f(*args, **kwargs) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/variational_solver.py", > line 173, in solve > self.snes.solve(None, v) > File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve > (src/petsc4py.PETSc.c:169677) > File "PETSc/petscsnes.pxi", line 253, in petsc4py.PETSc.SNES_Function > (src/petsc4py.PETSc.c:33478) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving_utils.py", > line 187, in form_function > nest=problem._nest) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", > line 68, in assemble > inverse=inverse, nest=nest) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", > line 101, in _assemble > inverse=inverse) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/ffc_interface.py", > line 279, in compile_form > ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 203, in __new__ > obj = make_obj() > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 193, in make_obj > obj.__init__(*args, **kwargs) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/ffc_interface.py", > line 188, in __init__ > ffc_tree = ffc_compile_form(form, prefix=name, parameters=parameters) > File "build/bdist.linux-x86_64/egg/ffc/compiler.py", line 159, in > compile_form > File "build/bdist.linux-x86_64/egg/ffc/representation.py", line 108, in > compute_ir > File "build/bdist.linux-x86_64/egg/ffc/representation.py", line 351, in > _compute_integral_ir > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", > line 95, in compute_integral_ir > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", > line 191, in _transform_integrals_by_type > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", > line 223, in _transform_integrals > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 772, in generate_terms > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 548, in index_sum > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 511, in indexed > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 724, in component_tensor > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 103, in visit > r = h(o, *[self.visit(op) for op in o.ufl_operands]) > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 511, in indexed > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 668, in negative_restricted > File > "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", > line 107, in visit > r = h(o) > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 474, in coefficient > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/optimisedquadraturetransformer.py", > line 558, in create_function > File > "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", > line 1290, in _create_function_name > UnboundLocalError: local variable 'loop_index' referenced before assignment > > > >

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