June 2018 - firedrake - imperial.ac.uk

Tensor function
by Amireh Mousavi 29 Jun '18

29 Jun '18

Dear all, 1-how can I see the list of functions families which are supported by Firedrake? ( I mean "CG", "DG", "BDM",...) 2- how can I handle a tensor function? I need to define a tensor function as a coefficient, but I don't know how to do it. Thank you in advance. Best, Amireh

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Postdoc position for a new Firedrake core developer
by Ham, David A 26 Jun '18

26 Jun '18

Dear All, As we announced at Firedrake ’18 and in the Slack channel, we are looking for a postdoc to join us as a member of the Firedrake core team. In this role you would undertake scientific computing research, add to Firedrake’s capabilities, and become a key member of the Firedrake community. If that could be you, please check out the advert at http://www.imperial.ac.uk/jobs/description/NAT00209/research-associate-code… and apply! I am very happy to field any informal enquiries about the position. Regards, David

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Re: [firedrake] mixed function space
by Andrew McRae 24 Jun '18

24 Jun '18

This needs to be TrialFunctions(V) and TestFunctions(V) (notice the plural) An equivalent way of doing this is ugHp = TrialFunction(V) u, g, H, p = split(ugHp) Andrew On 24 June 2018 at 16:23, Amireh Mousavi <amireh.mousavi(a)math.iut.ac.ir> wrote: > Hi, for 4×4 system of PDEs, I considered trial and test functions mixed of > 4 function spaces as the following: > V1 = FunctionSpace(mesh, "CG", deg) > V2 = VectorFunctionSpace(mesh, "CG", deg) > V3 = TensorFunctionSpace(mesh, "CG", deg) > P = FunctionSpace(mesh, "CG", deg) > V = V1 * V2 * V3 * P > u, g, H, p = TrialFunction(V) > phi1, phi2, phi3, q = TestFunction(V) > > but I got the following error > > > > > *Traceback (most recent call last): File "test1.py", line 58, in > <module> u, g, H, p = TrialFunction(V) ValueError: too many values to > unpack (expected 4)* > > Many thanks if someone could give me some direction about that. > Best, > Amireh > > > > >

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mixed function space
by Amireh Mousavi 24 Jun '18

24 Jun '18

Hi, for 4×4 system of PDEs, I considered trial and test functions mixed of 4 function spaces as the following: V1 = FunctionSpace(mesh, "CG", deg) V2 = VectorFunctionSpace(mesh, "CG", deg) V3 = TensorFunctionSpace(mesh, "CG", deg) P = FunctionSpace(mesh, "CG", deg) V = V1 * V2 * V3 * P u, g, H, p = TrialFunction(V) phi1, phi2, phi3, q = TestFunction(V) but I got the following error Traceback (most recent call last): File "test1.py", line 58, in <module> u, g, H, p = TrialFunction(V) ValueError: too many values to unpack (expected 4) Many thanks if someone could give me some direction about that. Best, Amireh

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error in solving
by Amireh Mousavi 23 Jun '18

23 Jun '18

Hi, I intend to implement a system of PDEs (4‍‍×4) in Firedeake package, which the function spaces are mix of tensor, vector and scalar. For this reason I prefer to understand the code of mixed formulation for Poisson equation completly. In the mixed formulation code of Poisson equation, when I change the function space from "FunctionSpace(mesh, "BDM", 1)" to "VectorFunctionSpace(mesh, "CG", 1)", there is a bug in solvig the system. I implement the following code: mesh = UnitSquareMesh(10, 10) VCG = VectorFunctionSpace(mesh, "CG", 1) DG = FunctionSpace(mesh, "DG", 0) W = VCG * DG sigma, u = TrialFunctions(W) tau, v = TestFunctions(W) x, y = SpatialCoordinate(mesh) f = Function(DG).interpolate( 10*exp(-(pow(x - 0.5, 2) + pow(y - 0.5, 2)) / 0.02)) a = (dot(sigma, tau) + div(tau)*u + div(sigma)*v)*dx L = - f*v*dx bc0 = DirichletBC(W.sub(0), as_vector([0.0, -sin(5*x)]), 1) bc1 = DirichletBC(W.sub(0), as_vector([0.0, sin(5*y)]), 2) w = Function(W) solve(a == L, w, bcs=[bc0, bc1]) sigma, u = w.split() File("poisson_mixed.pvd").write(u) try: import matplotlib.pyplot as plt except: warning("Matplotlib not imported") try: plot(u) except Exception as e: warning("Cannot plot figure. Error msg '%s'" % e) try: plt.show() except Exception as e: warning("Cannot show figure. Error msg '%s'" % e) f.interpolate(cos(x*pi*2)*cos(y*pi*2)) print(sqrt(assemble(dot(u - f, u - f) * dx))) and I get the following error: Traceback (most recent call last): File "test2.py", line 156, in <module> solve(a == L, w, bcs=[bc0, bc1]) File "/home/amireh/firedrake/src/firedrake/firedrake/solving.py", line 121, in solve _solve_varproblem(*args, **kwargs) File "/home/amireh/firedrake/src/firedrake/firedrake/solving.py", line 151, in _solve_varproblem solver.solve() File "/home/amireh/firedrake/src/firedrake/firedrake/variational_solver.py", line 242, in solve solving_utils.check_snes_convergence(self.snes) File "/home/amireh/firedrake/src/firedrake/firedrake/solving_utils.py", line 231, in check_snes_convergence %s""" % (snes.getIterationNumber(), msg)) firedrake.exceptions.ConvergenceError: Nonlinear solve failed to converge after 0 nonlinear iterations. Reason: Inner linear solve failed to converge after 10000 iterations with reason: DIVERGED_MAX_IT

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edge length
by Eric M 22 Jun '18

22 Jun '18

Hello, Any way to get an edge length for an interior element edge? I want to compute integrals on interior edges, and in each integral I need the edge length often denoted h_e.

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Re: [firedrake] Fw: Runing problem
by Andrew McRae 18 Jun '18

18 Jun '18

You need to close the plot for the program to continue. Did you do that? Andrew On 18 June 2018 at 13:55, Amireh Mousavi <amireh.mousavi(a)math.iut.ac.ir> wrote: > Dear all, > > I'm beginner in Firedrake so I preferred to start with examples which > there are in the website. I copied the code of Helmholtz example and saw > the contour plot of error but the amount of error wasn't printed. After any > run, I should stop the running with ctrl+z. > The python file of code and the screenshot of my desktop have been > attached. Many thanks if someone guide me about this problem. > Best, > Amireh > >

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Fw: Runing problem
by Amireh Mousavi 18 Jun '18

18 Jun '18

Dear all, I'm beginner in Firedrake so I preferred to start with examples which there are in the website. I copied the code of Helmholtz example and saw the contour plot of error but the amount of error wasn't printed. After any run, I should stop the running with ctrl+z. The python file of code and the screenshot of my desktop have been attached. Many thanks if someone guide me about this problem. Best, Amireh

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register for PhD
by Gorman, Gerard J 04 Jun '18

04 Jun '18

Hi Stephan I checked with Amanda. What you need to do is to just fill in the online application form for a PhD as usual - it shouldn’t take you more than 30 mins. It goes to the department as usual and you have a interview with Peter Allison or someone he delegates. In your case this is only a formality. They fill in a form then to approve the registration. https://www.imperial.ac.uk/study/pg/apply/how-to-apply/ It is really trivial. I’m happy to help march this through the system. If you have any question or concerns then just ask. Gerard

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Re: [firedrake] Error on Installation
by Andrew McRae 01 Jun '18

01 Jun '18

This failed to download the NETCDF library from ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz Are you able to download that directly? If not, maybe there is something blocking the download on your network. If you want to run with NETCDF, the log file contains some instructions for a workaround. Otherwise, it's easiest to just run firedrake-install with the --minimal-petsc option. Andrew On 30 May 2018 at 02:09, Amireh Mousavi <amireh.mousavi(a)math.iut.ac.ir> wrote: > > The attachment is the new log file. > > > > ------------------------------ > -----Original Message----- > From: "Ham, David A" <david.ham(a)imperial.ac.uk> > To: firedrake <firedrake(a)imperial.ac.uk> > Date: 09/03/97 13:58 > Subject: Re: [firedrake] Error on Installation > > Ah. This log file isn't from the install attempt you posted earlier. This > log file is from a subsequent attempt which failed because the firedrake > directory already existed from the previous attempt. Please rm -rf > firedrake and then run the installer again. Please post the log file from > this new attempt. > > Regards, > > David > > Dr David Ham > Department of Mathematics > Imperial College London > > On 30 May 2018, at 14:23, Amireh Mousavi <amireh.mousavi(a)math.iut.ac.ir> > wrote: > > Yes of course. The firedrake-install.log has been attached. > > > > > > > ------------------------------ > -----Original Message----- > From: "Ham, David A" <david.ham(a)imperial.ac.uk> > To: firedrake <firedrake(a)imperial.ac.uk> > Date: 09/03/97 13:11 > Subject: Re: [firedrake] Error on Installation > > Hi Amireh, > > PETSc failed to install. In order to see why that happened, we need to > look at your firedrake-install.log could you post that please? > > Regards > > David > > Sent from my iPhone > > On 30 May 2018, at 13:22, Amireh Mousavi <amireh.mousavi(a)math.iut.ac.ir> > wrote: > > > > Dear all, > I tried to install Firedrake on Ubuntu 18.04 but I have problem on > installation. Here are the errors I get: > > > Running firedrake-install > Checking for presence of package build-essential... > installed. > Checking for presence of package autoconf... > installed. > Checking for presence of package automake... > installed. > Checking for presence of package cmake... > installed. > Checking for presence of package gfortran... > installed. > Checking for presence of package git-core... > missing. > Checking for presence of package libblas-dev... > installed. > Checking for presence of package liblapack-dev... > installed. > Checking for presence of package libopenmpi-dev... > installed. > Checking for presence of package libtool... > installed. > Checking for presence of package mercurial... > installed. > Checking for presence of package openmpi-bin... > installed. > Checking for presence of package python3-dev... > installed. > Checking for presence of package python3-pip... > installed. > Checking for presence of package python3-tk... > installed. > Checking for presence of package python3-venv... > installed. > Checking for presence of package zlib1g-dev... > installed. > Installing missing packages: git-core. > [sudo] password for amireh: > Reading package lists... Done > Building dependency tree > Reading state information... Done > Note, selecting 'git' instead of 'git-core' > git is already the newest version (1:2.17.0-1ubuntu1). > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > Creating firedrake venv in '/home/amireh/firedrake'. > Cloning firedrake > > Failed to clone firedrake using ssh, falling back to https. > Successfully cloned repository firedrake. > Checking out branch master > Successfully checked out branch master > Cloning the dependencies of firedrake > Cloning ufl > > Failed to clone ufl using ssh, falling back to https. > Successfully cloned repository ufl. > Checking out branch master > Successfully checked out branch master > Cloning fiat > > Failed to clone fiat using ssh, falling back to https. > Successfully cloned repository fiat. > Checking out branch master > Successfully checked out branch master > Cloning FInAT > > Failed to clone FInAT using ssh, falling back to https. > Successfully cloned repository FInAT. > Checking out branch master > Successfully checked out branch master > Cloning tsfc > > Failed to clone tsfc using ssh, falling back to https. > Successfully cloned repository tsfc. > Checking out branch master > Successfully checked out branch master > Cloning PyOP2 > > Failed to clone PyOP2 using ssh, falling back to https. > Successfully cloned repository PyOP2. > Checking out branch master > Successfully checked out branch master > Cloning the dependencies of PyOP2 > Cloning petsc > > Failed to clone petsc using ssh, falling back to https. > Successfully cloned repository petsc. > Checking out branch firedrake > Successfully checked out branch firedrake > Cloning petsc4py > > Failed to clone petsc4py using ssh, falling back to https. > Successfully cloned repository petsc4py. > Checking out branch firedrake > Successfully checked out branch firedrake > Cloning COFFEE > > Failed to clone COFFEE using ssh, falling back to https. > Successfully cloned repository COFFEE. > Checking out branch master > Successfully checked out branch master > 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! > Traceback (most recent call last): > File "firedrake-install", line 1074, in <module> > install("petsc/") > File "firedrake-install", line 554, in install > build_and_install_petsc() > File "firedrake-install", line 660, in build_and_install_petsc > run_pip_install(["--ignore-installed", "petsc/"]) > File "firedrake-install", line 529, in run_pip_install > check_call(pipinstall + pipargs) > File "firedrake-install", line 366, in check_call > log.debug(subprocess.check_output(arguments, > stderr=subprocess.STDOUT, env=env).decode()) > File "/usr/lib/python3.6/subprocess.py", line 336, in check_output > **kwargs).stdout > File "/usr/lib/python3.6/subprocess.py", line 418, in run > output=stdout, stderr=stderr) > *subprocess.CalledProcessError:* Command '['/home/amireh/firedrake/bin/python', > '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', > '--ignore-installed', 'petsc/']' returned non-zero exit status 1. > > > Install log saved in firedrake-install.log > > > Please guide me to install. > > Best regards, > > Amireh > > > > _______________________________________________ > 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-install.log> > > _______________________________________________ > 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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