- firedrake - imperial.ac.uk

firedrake_adjoint error
by Cotter, Colin J 09 Nov '18

09 Nov '18

Dear all, I'm getting the following error when I run the attached code (uses firedrake_adjoint). Did I do something silly or should I file a bug report? all the best --Colin Traceback (most recent call last): File "outer.py", line 80, in <module> z0Solver.solve() File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/variational_solver.py", line 48, in solve **sb_kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/solving.py", line 56, in __init__ self._init_dependencies(*args, **kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/solving.py", line 137, in _init_dependencies self.add_dependency(bc.block_variable, no_duplicates=True) File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/block.py", line 38, in add_dependency dep.will_add_as_dependency() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/block_variable.py", line 61, in will_add_as_dependency overwrite = self.output._ad_will_add_as_dependency() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/overloaded_type.py", line 332, in _ad_will_add_as_dependency self._ad_annotate_block() File "/Users/colincotter/firedrake/src/pyadjoint/pyadjoint/overloaded_type.py", line 349, in _ad_annotate_block block = self.block_class(*self._ad_args, **self._ad_kwargs) File "/Users/colincotter/firedrake/src/pyadjoint/fenics_adjoint/types/dirichletbc.py", line 90, in __init__ self.collapsed_space = self.function_space.collapse() File "/Users/colincotter/firedrake/src/firedrake/firedrake/functionspaceimpl.py", line 212, in __getattr__ return getattr(self.topological, name) AttributeError: 'ProxyFunctionSpace' object has no attribute 'collapse'

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Preconditioning grad(ln(c)) term
by Justin Chang 07 Nov '18

07 Nov '18

Hi everyone, I am attempting to solve the electrolyte domain of li-ion battery model. The concentration problem is somewhat like a nonlinear diffusion/heat equation but it gets messy because it has a div(grad(ln(c))) term. So I would be looking at something like this: -div(k1*grad(c)) + div(k2*grad(ln(c))) = 0 Which we can rewrite as: -div((k1 - k2/c)*grad(c)) = 0 If k2 is relatively small enough, the newton solver should converge with little problem. The problem I am having is with the linear solve. If I discretize the above using CG1, no solver works so long as k2 >> 0. With DG1, I can only use direct solvers like LU to solve the resulting linear system of equations. I can't seem to find a good iterative solver/pc to solve this - HYPRE gives me a DIVERGED_NANORINF, and jacobi/bjacobi do not converge at all. I've attached the code for you guys to play around with. I don't know what is a good PC for grad(ln(c)), my guess is that I'm going to need to provide an assembled preconditioner which approximates the inverse of the k2/c*grad(c) term but it doesn't seem clear to me how I can provide an explicit PC to the nonlinear solver without resorting to hacking at petsc4py. Any thoughts appreciated Justin

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Offline installs
by Lawrence Mitchell 07 Nov '18

07 Nov '18

Dear Andrew, > Begin forwarded message: > > From: mailman-bounces(a)imperial.ac.uk > Subject: Uncaught bounce notification > Date: 7 November 2018 at 14:19:04 GMT > To: firedrake-owner(a)imperial.ac.uk > > From: "Little, Andrew B" <a.little14(a)imperial.ac.uk <mailto:a.little14@imperial.ac.uk>> > Subject: Offline Install > Date: 7 November 2018 at 14:19:02 GMT > To: firedrake-bounces <firedrake-bounces(a)imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk>> > > > I have a requirement to install firedrake & thetis offline on a cluster - before I start bumbling around does anyone have any advice on how best to install firedrake & thetis: > a) Offline > b) On a cluster > > I appreciate this is too little info to give any detailed advice but I just wanted to test the water for what I am getting myself into! PETSc, which is a major part of this, allows providing local paths to the packages it installs. In theory this might be possible via firedrake-install. Chasing all the python dependencies is going to be tricky. If the system is "standard" you could install on a machine that has internet access in the same directory structure you're eventually going to use, zip it up, and transfer it over. One asks why you need to do this. If you have ssh access to the machine in question, I would set up a reverse-tunnelled proxy to send everything through. Cheers, Lawrence

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Help me
by Emmanuel Yarleque Medina 07 Nov '18

07 Nov '18

This is my installation error: Building extension modules Traceback (most recent call last): File "setup.py", line 8, in <module> import petsc4py ImportError: No module named 'petsc4py' Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests Traceback (most recent call last): File "/usr/lib/python3.5/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.5/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/emmanuel/firedrake/lib/python3.5/site-packages/pytest.py", line 7, in <module> from _pytest.assertion import register_assert_rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/__init__.py", line 12, in <module> from _pytest.assertion import rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/rewrite.py", line 24, in <module> from _pytest.pathlib import fnmatch_ex File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/pathlib.py", line 26, in <module> from pathlib2 import Path, PurePath ImportError: No module named 'pathlib2' Makefile:60: recipe for target 'test' failed make: *** [test] Error 1 (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ sudo su [sudo] senha para emmanuel: root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# make alltest Building extension modules Traceback (most recent call last): File "setup.py", line 31, in <module> import versioneer File "/home/emmanuel/firedrake/src/firedrake/versioneer.py", line 1658 file=sys.stderr) ^ SyntaxError: invalid syntax Linting firedrake codebase /usr/bin/python: No module named flake8 Makefile:8: recipe for target 'lint' failed make: *** [lint] Error 1

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Periodic domain with imported mesh
by Floriane Gidel [RPG] 07 Nov '18

07 Nov '18

Dear all, Is there a way to force an imported mesh (created with Gmsh) to be x- and y-periodic ? (maybe something similar to the option 'constrained_domain' when defining a FunctionSpace in FeniCs ?) Thank you, Floriane

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firedrake build failure.
by Balay, Satish 06 Nov '18

06 Nov '18

Hi, I'm attempted a build of firedrake - and get a failure. Attaching the log. thanks, Satish ------------- balay@asterix /home/balay/soft $ python3 firedrake-install --install pyadjoint --no-package-manager Running firedrake-install --install pyadjoint --no-package-manager apt-get not found or disabled. Proceeding on the rash assumption that your compiled dependencies are in place. If this is not the case, please install the following and try again: * A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * MPI * Blas and Lapack * Git, Mercurial * Python version >=3.5 * The Python headers * autoconf, automake, libtool * CMake * zlib Creating firedrake venv in '/home/balay/soft/firedrake'. Cloning firedrake Successfully cloned repository firedrake Checking out branch master Successfully checked out branch master Cloning the dependencies of firedrake Cloning ufl Successfully cloned repository ufl Checking out branch master Successfully checked out branch master Cloning fiat Successfully cloned repository fiat Checking out branch master Successfully checked out branch master Cloning FInAT Successfully cloned repository FInAT Checking out branch master Successfully checked out branch master Cloning tsfc Successfully cloned repository tsfc Checking out branch master Successfully checked out branch master Cloning PyOP2 Successfully cloned repository PyOP2 Checking out branch master Successfully checked out branch master Cloning the dependencies of PyOP2 Cloning petsc Successfully cloned repository petsc Checking out branch firedrake Successfully checked out branch firedrake Cloning petsc4py Successfully cloned repository petsc4py Checking out branch firedrake Successfully checked out branch firedrake Cloning COFFEE Successfully cloned repository COFFEE Checking out branch master Successfully checked out branch master Cloning pyadjoint Successfully cloned repository pyadjoint Checking out branch master Successfully checked out branch master Cloning the dependencies of pyadjoint Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Checking Eigen tarball integrity Eigen tarball hash valid Building PETSc. Depending on your platform, may take between a few minutes and an hour or more to build! Installing pip dependencies for petsc4py No dependencies found. Skipping. Installing pip dependencies for COFFEE Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for firedrake Installing pip dependencies for pyadjoint Traceback (most recent call last): File "firedrake-install", line 1124, in <module> pip_requirements(p) File "firedrake-install", line 614, in pip_requirements run_pip_install(["-r", "%s/requirements.txt" % package]) File "firedrake-install", line 597, in run_pip_install check_call(pipinstall + pipargs) File "firedrake-install", line 435, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib64/python3.7/subprocess.py", line 389, in check_output **kwargs).stdout File "/usr/lib64/python3.7/subprocess.py", line 481, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/balay/soft/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '-vvv', '-r', 'pyadjoint/requirements.txt']' returned non-zero exit status 1. Install log saved in firedrake-install.log balay@asterix /home/balay/soft

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Re: [firedrake] Installation with my own PETSc repository
by Andrew McRae 06 Nov '18

06 Nov '18

Line 5406 _configtest.c:2:10: fatal error: 'mpi.h' file not found On Wed, 31 Oct 2018 at 20:27, Matthew Knepley <knepley(a)gmail.com> wrote: > Thanks folks! I made it farther: > > :/PETSc3/fem$ ~/MacSoftware/bin/python3 ./firedrake-install > --honour-petsc-dir --verbose --no-package-manager > > Running ./firedrake-install --honour-petsc-dir --verbose > --no-package-manager > > Xcode and homebrew installation disabled. Proceeding on the rash > assumption that packaged dependencies are in place. > > Creating firedrake venv in '/PETSc3/fem/firedrake'. > > Cloning firedrake > > > Successfully cloned repository firedrake > > Checking out branch master > > Successfully checked out branch master > > Cloning the dependencies of firedrake > > Cloning ufl > > > Successfully cloned repository ufl > > Checking out branch master > > Successfully checked out branch master > > Cloning fiat > > > Successfully cloned repository fiat > > Checking out branch master > > Successfully checked out branch master > > Cloning FInAT > > > Successfully cloned repository FInAT > > Checking out branch master > > Successfully checked out branch master > > Cloning tsfc > > > Successfully cloned repository tsfc > > Checking out branch master > > Successfully checked out branch master > > Cloning PyOP2 > > > Successfully cloned repository PyOP2 > > Checking out branch master > > Successfully checked out branch master > > Cloning the dependencies of PyOP2 > > Using existing petsc installation > > > Cloning petsc4py > > > Successfully cloned repository petsc4py > > Checking out branch firedrake > > Successfully checked out branch firedrake > > Cloning COFFEE > > > Successfully cloned repository COFFEE > > Checking out branch master > > Successfully checked out branch master > > Installing pip dependencies for petsc4py > > No dependencies found. Skipping. > > Installing pip dependencies for COFFEE > > Installing pip dependencies for ufl > > No dependencies found. Skipping. > > Installing pip dependencies for fiat > > No dependencies found. Skipping. > > Installing pip dependencies for FInAT > > Installing pip dependencies for tsfc > > Installing pip dependencies for PyOP2 > > Traceback (most recent call last): > > File "./firedrake-install", line 1124, in <module> > > pip_requirements(p) > > File "./firedrake-install", line 607, in pip_requirements > > run_pip_install(["-r", "%s/requirements-ext.txt" % package]) > > File "./firedrake-install", line 597, in run_pip_install > > check_call(pipinstall + pipargs) > > File "./firedrake-install", line 435, in check_call > > log.debug(subprocess.check_output(arguments, > stderr=subprocess.STDOUT, env=env).decode()) > > File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line > 336, in check_output > > **kwargs).stdout > > File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line > 418, in run > > output=stdout, stderr=stderr) > > subprocess.CalledProcessError: Command > '['/PETSc3/fem/firedrake/bin/python', '-m', 'pip', 'install', > '--no-binary', 'mpi4py', '-vvv', '-r', 'PyOP2/requirements-ext.txt']' > returned non-zero exit status 1. > > > > Install log saved in firedrake-install.log > > 1:/PETSc3/fem$ vi firedrake-install.log > > > It looks like mpi4py is failing, but I do not know where to look for the > actual error message. Log attached. > > Thanks, > > Matt > > On Tue, Oct 30, 2018 at 12:51 PM Lawrence Mitchell <wence(a)gmx.li> wrote: > >> >> >> > On 30 Oct 2018, at 16:30, Matthew Knepley <knepley(a)gmail.com> wrote: >> > >> > On Fri, Oct 26, 2018 at 11:26 AM Matthew Knepley <knepley(a)gmail.com> >> wrote: >> > Dear Firedrake, >> > >> > Long-time listener, first time mailer. >> > >> > I would like to build using my own repository for PETSc. I am reading >> this page: >> > >> > https://www.firedrakeproject.org/download.html >> > >> > but it is not clear to me how to tell the installer to use mine, rather >> than install its own. >> > Do I just point to it using PETSC_DIR? >> > >> > Its not going to install itself by osmosis. >> >> Aha, you're not subscribed and people don't automatically CC. You would >> normally get a bounce notification asking you to subscribe, but I think >> someone in the past (probably me) added you to a list of addresses that get >> accepted anyway. >> >> Answers from David: >> >> > Nearly: there’s a small piece of idiot-proofing to prevent the unwary >> new user from accidentally using the wrong PETSc. You need to pass >> –honour-petsc-dir (note UK spelling) to firedrake-install >> > >> > You also need to check the install script to make sure your petsc has >> our minimal set of options. I apologise that you have to RTFS for that. >> From memory, the absolute minimum is that you need –download-hdf5 and >> –download-eigen >> >> Nicolas said: >> >> > >> > You need to define PETSC_DIR and PETSC_ARCH, then run the install >> script with the --honour-petsc-dir option. >> > >> > If you call the script with --help, you may also discover a couple of >> options you might want to use (or not) such as --disable-ssh or >> --no-package-manager >> >> And Miklos pointed out: >> >> > You don’t actually need to read the script, >> > >> > firedrake-install --show-petsc-configure-options >> > >> > tells you which options the Firedrake install script passes to PETSc’s >> configure script. It is normally safe add things, but removing things may >> result in harmless test failures (e.g. some solver packages), or in broken >> Firedrake functionality. >> >> This last option doesn't exit the installer after showing them, so it's >> not quite as useful as it seems. >> >> FWIW, we by default build with: >> >> --download-chaco --download-metis --download-parmetis >> --download-scalapack --download-hypre --download-mumps --with-zlib >> --download-netcdf --download-hdf5 --download-pnetcdf --download-exodusii >> --with-debugging=0 --with-shared-libraries=1 >> >> Cheers, >> >> Lawrence >> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> >

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Re: [firedrake] local discontinuity
by Ham, David A 05 Nov '18

05 Nov '18

Dear Floriane, I think you can do this in a manner analogous to the way that Thomasz did fluid-structure interaction. We define a mixed function space with two continuous components: (V_d, V_p). We’re going to use the first component for the solution in the disk and the second component for the solution outside the disk. We further define two DG0 functions I_d and I_p such that I_d is 1 inside the disk and 0 outside, and I_p = 1 – I_d. You can now write the Laplace equation for the two parts using essentially normal Firedrake code except that you multiply the test function by the appropriate indicator function. This ensures that you only actually assemble integral contributions on the correct part of the domain. Now we just need the surface integral over the facets on the edge of the disk. Observe that this is the only place in the domain where both indicator functions are positive. You can write your jump integrals using the *dS measure. You can restrict the intervals to the relevant edges by multiplying the integrand by 4*avg(I_p)*avg(I_d). If W = V_d * V_p and u_d, u_p = TrialFunctions(W) then you can write the jump as: avg(u_d) – avg(u_p) The avg is mathematically unnecessary and does nothing, however in UFL all terminals that appear in dS integrals have to be restricted (you could just as well write u_d(‘+’) – u_p(‘+’)). Finally, when you come to the solve, you need to ensure that all the V_d nodes outside the disk are eliminated, and all the V_p nodes inside the disk too. You do this using the same DirichletBC subclassing trick which is in https://www.firedrakeproject.org/demos/linear_fluid_structure_interaction.p… I realise that is slightly involved, but it should work and the syntax will be fairly clean once you have done it. Feel free to ask for clarifications. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Floriane Gidel [RPG]" <mmfg(a)leeds.ac.uk> Reply-To: firedrake <firedrake(a)imperial.ac.uk> Date: Friday, 5 October 2018 at 15:33 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] local discontinuity Dear Firedrakers, I would like to solve equations in a domain made of two subdomains: - a disk, inside which test functions are continuous (Omega_d) - a plane around the disk, in which test functions are continuous (Omega_p) However, I would like the test functions to be discontinuous across the interface Gamma between the disk and the surrounding plane. This is to solve Laplace equation in each domain, augmented by a dynamic boundary condition on the jump between the two domains, that is Delta u = 0 in Omega_d Delta u = 0 in Omega_p partial_t [u] = ... on Gamma, where [u]= u(+)-u(-) is the jump Is there a way to define a functionspace on the full mesh, with continuous basis functions in each subdomain but discontinuous across the interface ? Or is there any better way to solve this kind of system ? Thank you for your help, Floriane

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Solving nonlinear algebraic equation
by Amireh Mousavi 01 Nov '18

01 Nov '18

Dear Firedrake team, I'm trying to solve Hamilton-Jacobi-Bellman equation. It is a fully nonlinear equation, so after linearization, in each iteration in first we need to determine a parameter which is obtained from solving nonlinear algebraic equation and after that we solve the linear PDE. How can I solve nonlinear algebraic equation in Firedrake? Consider the simple example: mesh = UnitSquareMesh(4, 4)R = FunctionSpace(mesh, "R", 0)Ralpha = Function(R)alpha = variable(Ralpha)A_alpha = as_tensor([[cos(alpha) , -sin(alpha)] , [sin(alpha) , cos(alpha)]])A = Constant([[20 ,1] , [1 , 0.1]])A_alphaA = inner(A_alpha , A) #dA_alphaA = solve(diff(A_alphaA , alpha ), alpha) How can I solve "diff(A_alphaA , alpha)=0" in Firedrake ? Thank you in advance. All the best, Amireh

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Installation with my own PETSc repository
by Matthew Knepley 31 Oct '18

31 Oct '18

Dear Firedrake, Long-time listener, first time mailer. I would like to build using my own repository for PETSc. I am reading this page: https://www.firedrakeproject.org/download.html but it is not clear to me how to tell the installer to use mine, rather than install its own. Do I just point to it using PETSC_DIR? Thanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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