April 2021 - firedrake - imperial.ac.uk

Solving PDE system
by Pedro Henrique da Silva Singue Cerqueira 27 Apr '21

27 Apr '21

Dear all, I am looking for an open source library to solve a set of PDEs as follow: [image: image.png] I would like to use an 1D-mesh, specifying the mass flow (m) at inlet and fixing the pressure value (p) at the outlet. Do you think that FireDrake library could help me solve this problem? If so, any particular example to suggest to me? Thank you in advance. Best regards,

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Periodic mesh question
by Andrew Hicks 26 Apr '21

26 Apr '21

Dear all, I made a periodic mesh in Gmsh with the opposite sides being identified with one another except for the top and bottom. The script I used for the .geo file is this: Box(1) = {0, 0, 0, 1, 1, 0.67}; Periodic Surface {2} = {1} Translate {1, 0, 0}; Periodic Surface {4} = {3} Translate {0, 1, 0}; But when I tried to define a vector function space over this mesh, I got the following error: File "main.py", line 59, in <module> H1_vec = VectorFunctionSpace(mesh, "CG", 1, 5) File "/home/andrewh/firedrake/src/firedrake/firedrake/functionspace.py", line 177, in VectorFunctionSpace sub_element = make_scalar_element(mesh, family, degree, vfamily, vdegree) File "/home/andrewh/firedrake/src/firedrake/firedrake/functionspace.py", line 40, in make_scalar_element mesh.init() File "/home/andrewh/firedrake/src/firedrake/firedrake/mesh.py", line 1295, in init self._callback(self) File "/home/andrewh/firedrake/src/firedrake/firedrake/mesh.py", line 1678, in callback (self.num_vertices(), geometric_dim)) File "firedrake/cython/dmcommon.pyx", line 1077, in firedrake.cython.dmcommon.reordered_coords ValueError: cannot reshape array of size 1172043 into shape (130337,3) Does anyone know what's going on here? The mesh I made seems very simple so I'm not sure what could have gone wrong. Andrew Hicks

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Firedrake installation
by Majdi Fanous 21 Apr '21

21 Apr '21

Hello, I am trying to install firedrake on Linux but not using Ubuntu distribution ( I am running using an HPC). I am getting into trouble when doing the installation since I am getting errors for apt-get. Is there any manual for installation Linux distributions without having Ubuntu one? Thanks Regards, Majdi Fanous No.1 Modern University in the Midlands Guardian University Guide 2021 1st for Overseas Student Experiences based on student trips abroad from HESA 2018/19 UK data Top 30 in the World for International Students QS World University Rankings 2021 University of the Year for Student Experience 2019 The Times and Sunday Times Good University Guide 2019 NOTICE This message and any files transmitted with it is intended for the addressee only and may contain information that is confidential or privileged. Unauthorised use is strictly prohibited. If you are not the addressee, you should not read, copy, disclose or otherwise use this message, except for the purpose of delivery to the addressee. Any views or opinions expressed within this e-mail are those of the author and do not necessarily represent those of Coventry University.

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Question about the efficiency of the Navier-Stokes solver in the Firedrake
by Zizhou Huang 13 Apr '21

13 Apr '21

To one whom it may concern, I'm a PhD student at NYU. I'm working on a project on solving the Navier-Stokes equation with FEM, so I'm really interested in the amazing demo of solving the Navier-Stokes equation on the website. ( https://www.firedrakeproject.org/demos/navier_stokes.py.html) I modified the code to solve the 3d lid-driven cavity problem with a uniform grid of size 40x40x40, and found that it takes extremely long time and large memory. I had the same issue with my code of similar sizes, which uses Pardiso to solve the linear system. I'm wondering if fem is indeed unsolvable for a large problem like this? Do you have any experience to make it faster by changing the parameters in the linear solver? Looking forward to hearing from you. Best, Zizhou

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Subscription
by Majdi Fanous 12 Apr '21

12 Apr '21

Hello again, I have subscribed to the mailing list to be able to contact you. Could you also send me an invitation to join the slack channel? Thanks again. Regards, Majdi Fanous No.1 Modern University in the Midlands Guardian University Guide 2021 1st for Overseas Student Experiences based on student trips abroad from HESA 2018/19 UK data Top 30 in the World for International Students QS World University Rankings 2021 University of the Year for Student Experience 2019 The Times and Sunday Times Good University Guide 2019 NOTICE This message and any files transmitted with it is intended for the addressee only and may contain information that is confidential or privileged. Unauthorised use is strictly prohibited. If you are not the addressee, you should not read, copy, disclose or otherwise use this message, except for the purpose of delivery to the addressee. Any views or opinions expressed within this e-mail are those of the author and do not necessarily represent those of Coventry University.

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Installing Thetis
by Majdi Fanous 12 Apr '21

12 Apr '21

Hello, My name is Majdi Fanous and I am a post-graduate researcher at Coventry University. I have installed Firedrake by following the instructions from : https://www.firedrakeproject.org/download.html. However, when I want to install Thetis from: https://zenodo.org/record/3385804#.YHRDpBLTWwE, I am facing errors. Could you please guide me on the installation of this version of Thetis, after installing Firedrake, from Zenodo as it is important from my research. If you could provide me with the necessary commands and steps to do so would be great. Thanks. Regards, Majdi Fanous No.1 Modern University in the Midlands Guardian University Guide 2021 1st for Overseas Student Experiences based on student trips abroad from HESA 2018/19 UK data Top 30 in the World for International Students QS World University Rankings 2021 University of the Year for Student Experience 2019 The Times and Sunday Times Good University Guide 2019 NOTICE This message and any files transmitted with it is intended for the addressee only and may contain information that is confidential or privileged. Unauthorised use is strictly prohibited. If you are not the addressee, you should not read, copy, disclose or otherwise use this message, except for the purpose of delivery to the addressee. Any views or opinions expressed within this e-mail are those of the author and do not necessarily represent those of Coventry University.

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Parallelism question
by Andrew Hicks 06 Apr '21

06 Apr '21

Dear all, I am testing out using parallelism with Firedrake now that I have access to a computer with multiple cores. I have successfully used parallelism on a simple Laplace problem in 3D, and have also read the tutorial on using PETSc's Sys.Print() function to print output and using the "with" statement to compute the L-infinity norm. My question is, am I using parallelism correctly when I write Paraview files? Because when I create a new File object and run the .write() method, for each time step it seems to create a number of VTU files equal to the number of cores used, as well as a PVTU file. Is this correct? My other question is, is there a way to tell Python to only use the first core when doing other tasks? For example, I have a Python script in my code which writes a simple text file. What I really don't want is for Python to write to this text file 22 times when it only needs to do it once. Thanks for the help, Andrew Hicks

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How to convert tuple of C string expressions to UFL?
by Alexei Colin 05 Apr '21

05 Apr '21

Hi, firedrake-bench/elasticity (from 'experiments' branch) uses C string expressions which are no longer supported. I read some tips for conversion here, however, the help doesn't cover the case where there is a tuple of C string expressions: https://www.firedrakeproject.org/interpolation.html#c-string-expressions How to convert this? f = Function(V) f.interpolate(Expression( ("cos(2*pi*x[0])*cos(2*pi*x[1])*cos(2*pi*x[2])", "cos(2*pi*x[0])*cos(2*pi*x[1])*cos(2*pi*x[2])", "cos(2*pi*x[0])*cos(2*pi*x[1])*cos(2*pi*x[2])"))) Please forgive if this is obvious, I have no knowledge in this domain at all, just trying to blindly run this code. Thank you.

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