December 2019 - firedrake - imperial.ac.uk

firedrake testing
by Smail Merabet 23 Dec '19

23 Dec '19

Dear firedrake users, I am trying to test the installation, but I get the following error message (base) MacBook-Pro-de-Merabet:~ merabet$ unset PETSC_DIR (base) MacBook-Pro-de-Merabet:~ merabet$ unset PETSC_ARCH (base) MacBook-Pro-de-Merabet:~ merabet$ source /Users/merabet/firedrake/bin/activate (firedrake) (base) MacBook-Pro-de-Merabet:~ merabet$ cd Desktop/Firedrake/ (firedrake) (base) MacBook-Pro-de-Merabet:Firedrake merabet$ python helmholtz.py Traceback (most recent call last): File "helmholtz.py", line 51, in <module> from firedrake import * File "/Users/merabet/firedrake/src/firedrake/firedrake/__init__.py", line 19, in <module> import firedrake.petsc as petsc File "/Users/merabet/firedrake/src/firedrake/firedrake/petsc.py", line 4, in <module> petsc4py.init(sys.argv) File "/Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 73, in Import module = import_module(pkg, name, path, arch) File "/Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 58, in import_module with f: return imp.load_module(fullname, f, fn, info) File "/Users/merabet/opt/anaconda3/lib/python3.7/imp.py", line 242, in load_module return load_dynamic(name, filename, file) File "/Users/merabet/opt/anaconda3/lib/python3.7/imp.py", line 342, in load_dynamic return _load(spec) ImportError: dlopen(/Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/lib/default/ PETSc.cpython-37m-darwin.so <http://petsc.cpython-37m-darwin.so/>, 2): Library not loaded: @rpath/libmpi.12.dylib Referenced from: /Users/merabet/firedrake/lib/python3.7/site-packages/petsc4py/lib/default/ PETSc.cpython-37m-darwin.so <http://petsc.cpython-37m-darwin.so/> Reason: image not found (firedrake) (base) MacBook-Pro-de-Merabet:Firedrake merabet$ Thanks

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Firedrake USA '20 registration is now open
by Ham, David A 20 Dec '19

20 Dec '19

Dear all, Registration is now open for Firedrake ’20 USA. Early registration runs until 15 January, which is also the abstract submission deadline, so go on: get that registration in before you leave for Christmas! The workshop promises to be a great opportunity for those Firedrakers based in the Americas, as well as those of us travelling over for SIAM PP ’20 to exchange ideas, developments, and results face to face. I look forward to seeing many of you there. Register here: https://www.firedrakeproject.org/firedrake_usa_20.html Merry Christmas, David

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Firedrake/DMPlex parallel restriction: one d.o.f. per process
by Ed Bueler 18 Dec '19

18 Dec '19

Firedrake devs -- This is substantially a matter of curiosity, but I figure I am missing something I should understand. Namely, parallel runs will generate "RuntimeError: Mesh must have at least one cell on every process" if you attempt to have less. My understanding is that this restriction is not intrinsic to PETSc DMPlex, though the restriction does apply to DMDA. I know that Firedrake uses separate DMPlex for the mesh and for the data layout. What is the basic story here? Thanks, Ed -- Ed Bueler Dept of Mathematics and Statistics University of Alaska Fairbanks Fairbanks, AK 99775-6660 306C Chapman

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Mesh coordinates for higher degree of FE
by Luca Mechelli 11 Dec '19

11 Dec '19

******************* This email from originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear all, I am wondering if it is possible to access the list of all points used by piecewise quadratic (or higher order) elements on a regular mesh. For example, let's say I use the simple example of the Poisson equation at https://www.firedrakeproject.org/demos/poisson.py.html If I print mesh.coordinates.dat.data_ro I can see the verteces of the mesh, but not the middle points used to build the quadratic elements, then if I print u.dat.data_ro the array has not the same length of mesh.coordinates.dat.data_ro because the middle points nodes are missing from the second array. Is it possible to obtain the full list of coordinates used? If yes, how? Thank you in advance, best regards, Luca Mechelli -- Dr. Luca Mechelli Wissenschaftlicher Mitarbeiter Arbeitsgruppe Numerik Fachbereich Mathematik und Statistik Universität Konstanz Fach D 198 D-78464 Konstanz Telefon: +49-(0) 7531-88-3646

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galerkin coarse grid operators
by Heldman, Max 07 Dec '19

07 Dec '19

******************* This email from originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi, I’m working on a multigrid code and I’m wondering if there’s any way to get Galerkin coarse grid operators. The context is that I’m writing a Newton-multigrid type method, so I’m linearizing my PDE around the current iterate using automatic differentiation and then building the levels. I saw a 2016 paper which uses the coarsen_form function to get the coarse grid form, but that doesn’t seem to work anymore (and I’m not sure exactly what it does). Sincerely, Max Heldman

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Firedrake USA '20, University of Washington, 10 & 11 February 2020
by Ham, David A 06 Dec '19

06 Dec '19

Dear Firedrakers, I am exceptionally happy to be able to announce that the Firedrake workshop is coming to North America. The wonderful Dan Shapero of Icepack fame will host the workshop at the University of Washington on 10 and 11 February. That’s the Monday and Tuesday before SIAM PP 20, which runs from Wednesday and is also in Seattle. The Firedrake workshop is an opportunity for Firedrake developers and users to exchange ideas in person about advances in Firedrake itself, applications of Firedrake, and future directions. The first half day of the workshop will be a Firedrake tutorial, so it’s also an opportunity to learn how to drive the Firedrake system. If you’re a Firedraker from the Western side of the pond, or if you’re heading to the US for SIAM PP, or if you just fancy a trip to the beautiful city of Seattle, please come and present your work at Firedrake USA ’20. Key Dates * Early registration deadline: 15 January 2020 * Registration deadline: 31 January 2020 * Abstract submission deadline: 15 January 2020 * Workshop: 10-11 February 2020 For more information, see the workshop web page: https://www.firedrakeproject.org/firedrake_usa_20.html Regards, David

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Re: [firedrake] Firedrake on the Isambard HPC system
by Ham, David A 05 Dec '19

05 Dec '19

Dear all, Apologies for the warning which appeared on Dave’s email. This is a new piece of overzealous ICT idiocy at Imperial. I will try to get them to switch it off for this list. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Acreman, David" <D.M.Acreman(a)exeter.ac.uk> Date: Thursday, 5 December 2019 at 12:04 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] Firedrake on the Isambard HPC system Caution - This email from D.M.Acreman(a)exeter.ac.uk originated outside Imperial Hi all, If anyone is interesting in running Firedrake on the Isambard HPC system there are now instructions available at https://github.com/firedrakeproject/isambard (the procedure is similar to setting up Firedrake on Archer). Isambard is one of the EPSRC tier-2 services and will be available to use during the changeover between Archer and Archer-2. Isambard has over 10,000 cores provided by ARM64 processors which have proven particularly effective at running memory-bound applications. If you would like to apply for an account please follow the instructions at https://gw4-isambard.github.io/docs/user-guide/requestaccount.html Regards, Dave Dr. David Acreman, Senior Research Fellow, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4QL

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Firedrake on the Isambard HPC system
by Acreman, David 05 Dec '19

05 Dec '19

******************* This email from D.M.Acreman(a)exeter.ac.uk originated outside Imperial. ******************* Hi all, If anyone is interesting in running Firedrake on the Isambard HPC system there are now instructions available at https://github.com/firedrakeproject/isambard (the procedure is similar to setting up Firedrake on Archer). Isambard is one of the EPSRC tier-2 services and will be available to use during the changeover between Archer and Archer-2. Isambard has over 10,000 cores provided by ARM64 processors which have proven particularly effective at running memory-bound applications. If you would like to apply for an account please follow the instructions at https://gw4-isambard.github.io/docs/user-guide/requestaccount.html Regards, Dave Dr. David Acreman, Senior Research Fellow, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4QL

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