- firedrake - imperial.ac.uk

Installation issue
by Ollie Street 01 Dec '21

01 Dec '21

Hi, I’m still attempting to get a stable version of firedrake installed on my MacBook, I have encountered an issue with PETSc. It first hit an issue with the file 'eigen-3.3.3.tgz’, so I downloaded this separately and modified the installation file to point it towards this. The installation seemingly got over this issue, but returned the following error on the command line. I’ve also attached the install log. Any help would be much appreciated! Best, Oliver Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/Users/os3918/Documents/firedrake-install", line 1650, in <module> install("petsc/") File "/Users/os3918/Documents/firedrake-install", line 882, in install build_and_install_petsc() File "/Users/os3918/Documents/firedrake-install", line 1019, in build_and_install_petsc check_call(["make", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch), "all"]) File "/Users/os3918/Documents/firedrake-install", line 539, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['make', 'PETSC_DIR=/Users/os3918/Documents/firedrake/src/petsc', 'PETSC_ARCH=default', 'all']' returned non-zero exit status 2. Install log saved in /Users/os3918/Documents/firedrake-install.log

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Updates to YouTube's Terms of Service
by YouTube 25 Nov '21

25 Nov '21

On 5 January 2022, we're updating our Terms of Service ("Terms") to help clarify and make it easier to understand what to expect as you use the service. These changes won't affect the way you use YouTube. You can review a summary of the changes and the updated Terms here <https://notifications.google.com/g/p/AD-FnEx7E-8e9EDNYMardAda7k6fZXdrkdVZW3…>. At a glance, this update covers: * More clarity on what to expect: We're providing more transparency about how we develop, improve and update our service, including more details about why we make changes and updates and the advanced notice that we provide to you. * General updates for improved readability: While our Terms remain a legal document, we've done our best to make them easier to understand. This includes reorganising some sections (such as Account Suspension and Termination) and rewording others (such as Changing this Agreement). * Inclusion of the Community Guidelines strikes process: Your use of YouTube has always been subject to the Community Guidelines and its strikes process, but we're now explicitly including the Community Guidelines strikes <https://notifications.google.com/g/p/AD-FnEymOUTDuXs4DCguqSJdL7Jiu4j3e2p2me…> information in the Terms to increase transparency. There are no changes to how Community Guidelines strikes operate, or when a channel or content might receive a strike. Please make sure that you read the updates to the Terms <https://notifications.google.com/g/p/AD-FnExS59v8KK4XmGI0__wqwbwgiQv7pewl-7…>. By continuing to use YouTube after this date, you are agreeing to the updated Terms. Note: If you allow your child to use YouTube Kids or manage your child's use of YouTube through Family Link <https://notifications.google.com/g/p/AD-FnEzFiyVfe-1xaY5FEpiW03xo41c_aZkvAO…>, take a moment to talk to them about these changes. Thank you for being part of our global community! Help Centre <https://notifications.google.com/g/p/AD-FnEy6Yoqm7h5DYkRMlrFcVcHFJX6iZXcr7j…> Email options <https://notifications.google.com/g/p/AD-FnExxCVR2QkIIgIe5z8ImrWaK5VA27sOuGb…> You have received this email to update you about important changes to YouTube's Terms of Service. (c) 2021 Google LLC, 1600 Amphitheatre Parkway, Mountain View, CA, 94043

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Logger module and MPI
by Andrew Hicks 17 Nov '21

17 Nov '21

Hi all, I have a quick question. When using the built-in logger module in Firedrake after having called MPI (e.g. mpiexec -n 4 python main.py), the default output one would expect is for each time logger is called to log something, it would be called for each process. So in the above example, every time I log a message, it would log it 4 times. Is there a way, other than simply writing something like "if COMM.rank == 0", to get it to only log once? Thanks, Andrew Hicks

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simulation of incompressible Navier-Stokes equation using Firedrake
by Kamal Sharma 17 Nov '21

17 Nov '21

Hi everyone, My name is Kamal and I am a PhD student in the University of Hamburg, Germany. My PhD project deals with the simulation of coupled atmoshpere-ocean models. I want to use Firedrake to simulate my models and therefore to get accustomed with the software I have been using it for the past couple of months to solve some test/tutorial problems. At present, I am working on the following benchmark problems for the*incompressible fluid flow**: * 1. *Driven cavity (2D) *: Consider a square cavity with sides of unit length and kinematic viscosity ν = 1/1000. No-slip boundary conditions are imposed on each edge of the square, except at the upper edge where the velocity is set to u = (1, 0). 2.*Pressure-driven channel flow (2D)* : The geometry of the channel is the unit square [0,1]^2 and the kinematic viscosity is ν = 1/8. No-slip boundary conditions are applied to the velocity at the upper and lower walls, and Neumann boundary conditions are applied at the inlet and outlet. Dirichlet boundary conditions are applied to the pressure at the inlet and outlet, with p = 1 at the inlet and p = 0 at the outlet. The initial condition is u = (0, 0) for the velocity. 3. *Taylor–Green vortex (2D)* : We consider the Taylor-Green vortex which is a periodic flow with exact solution given by u(x, y, t) =(cos(πx)* sin(πy)*exp(−2tνπ^2), cos(πy) *sin(πx)*exp(−2tνπ^2)), p(x, y, t) =− 0.25*(cos(2πx) + cos(2πy))*exp(−4tνπ^2), on the domain [-1,1]^2. The kinematic viscosity is set to ν = 1/100. Periodic boundary conditions are imposed in both the x and y directions. For discretization, I have used a pure space-time Galerkin finite element scheme (with trapezoidal time-stepping). My code works well for the first two problems and my solutions are pretty close to the exact solutions. But for the third problem (Taylor-Green vortex) somehow, my solution is completely off and I am unable to understand the reason for it. Can you please help me figure out what I maybe doing wrong ? I have attached my code for the third test problem. In case you need more information, please let me know. Any kind of help is really appreciated. Thank you. Kind regards Kamal Sharma Department of Mathematics, University of Hamburg, Germany

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Install error with MacOS
by Street, Oliver 16 Nov '21

16 Nov '21

Hi, I’m attempting to get Firedrake installed on a MacBook I’m temporarily using whilst mine is being repaired - and I’ve encountered an installation error. It seems to hit the error when attempting to install PETSc, I’ve attached the install log. I’ve updated homebrew to the latest version and it can locate gcc, but no luck. Any ideas? Best wishes, Oliver

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Writing to file in parallel
by Andrew Hicks 28 Sep '21

28 Sep '21

Hello all, The website mentions a way to print data from a function that has been computed in parallel: with u.dat.vec_ro as vu: vu.view() However, I want to write this data to a file, and I'm not sure how. Moreover, is there a way I can format this so that instead of printing everything in one row, it prints it in as many rows as there are coordinates of the function? So for instance, can I write a file with three rows of data for a three dimensional function space? Thank you, Andrew Hicks

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Quadrature elements
by Bhavesh Shrimali 02 Sep '21

02 Sep '21

Hi everyone, Are quadrature elements supported in firedrake? I couldn't find any examples/documentation nor anything in the list of supported elements: https://www.firedrakeproject.org/variational-problems.html#supported-finite… The use case is modeling of dissipative phenomena such as viscoelasticity, plasticity, viscoplasticity (all from solid mechanics) Thanks Bhavesh -- *Bhavesh Shrimali* *Ph.D. Student, **Civil and Environmental Engineering,* *University of Illinois Urbana-Champaign* *Champaign, IL, United States* *Email : bshrima2(a)illinois.edu <bshrima2(a)illinois.edu>* *Web : **https://bhaveshshrimali.github.io/ <https://bhaveshshrimali.github.io/>*

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How to get mesh diameter
by Praveen C 28 Aug '21

28 Aug '21

Dear all I am a new user of firedrake but old user of fenics. I need your help to compute the mesh diameter, i.e., max diameter of all cells in the mesh or some representative mesh size to use in a mesh convergence study. Thanks a lot praveen

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Firedrake '21 - Abstract submission and early registration deadline approaching
by Ward, Connor 25 Aug '21

25 Aug '21

Dear Firedrakers, This is a reminder that the deadline for abstract submission and early registration for the Firedrake '21 workshop is 31st August - next Tuesday. The workshop will be held online in the afternoons (UK time) of 15-17 September. It is an opportunity for users and developers of Firedrake and its related tools to present their work, and to learn from and interact with other members of the Firedrake community. We encourage everyone, no matter what you are using Firedrake for, to come and show off your work. Early registration is just £10, increasing to £20 after next week's deadline. For further details and links to abstract submission and registration, see: https://firedrakeproject.org/firedrake_21.html. Firedrake '21 — Firedrake 0.13.0+4698.gdd139d71 documentation<https://firedrakeproject.org/firedrake_21.html> Firedrake ‘21¶. We are very happy to announce that the fifth Firedrake user and developer workshop will be held online between 15-17 September 2021. firedrakeproject.org Warm regards, Connor

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Recurring memory error
by Andrew Hicks 14 Aug '21

14 Aug '21

Hello all, I am struggling because I often get this same error popping up after I have been running many (several thousand) time steps of my PDE solve in Firedrake: OSError: /scratch/ahick17/firedrake/.cache/pyop2/94/0b1edf26475b324382a572af1239dc.so: cannot change memory protections Thankfully I always save state so I can simply resume the time steps and it always resolves. However, this is a bit annoying to have to deal with and I was wondering, what is causing this, and is there any way to fix it? Andrew Hicks

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