- firedrake - imperial.ac.uk

Difficulty installing firedrake
by Rajdip Nayek 18 Jan '21

18 Jan '21

Hi there, I am a Windows 10 user trying to install firedrake using WSL (Windows Subsystem for Linux) but have been unsuccessful. Could someone guide me on the installation? I keep getting this error message. [image: image.png] Or even better if someone can help me get it installed on google colab; I will share a google colab notebook for that purpose if you like. Thanks in advance. Rajdip -- Rajdip Nayek, PhD Research Associate The Department of Mechanical Engineering The University of Sheffield

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21 Dec '20

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Important policy changes for Google Account storage
by Google 16 Dec '20

16 Dec '20

Dear Google User, We are writing to let you know that we recently announced new storage policies for Google accounts using Gmail<https://www.google.com/appserve/mkt/p/AD-FnEzCXJeXc8gkk3sf4v1O-npVhh_whYbwM…>, Google Drive<https://www.google.com/appserve/mkt/p/AD-FnEyGnoRV4IItcOcgb50qsilVjF6CXywit…> (including Google Docs, Sheets, Slides, Drawings, Forms and Jamboard files) and/or Google Photos<https://www.google.com/appserve/mkt/p/AD-FnEzmHavVV4jP_G42T-R_ewh5mb4PQKFZj…> that bring us in line with industry practices. Since you have previously used one or more of these products in your Google account storage<https://www.google.com/appserve/mkt/p/AD-FnEwrwNe9p4Qm02lktCuNFizZh69-QcxMh…>, we wanted to tell you about the new policies well before they go into effect on 1 June 2021. Below is a summary of the new policies. Please reference our Help Centre article<https://www.google.com/appserve/mkt/p/AD-FnExGO3hjG-hjJXmMFPdAz9mwkqZBoV1yn…> for a complete list of what's changing. Summary of the new policies (effective 1 June 2021): - If you're inactive<https://www.google.com/appserve/mkt/p/AD-FnEwm6x9puP3HHcOQHCH3mIK2au09Clmz6…> for two years (24 months) in Gmail, Drive or Photos, we may delete the content in the product(s) in which you're inactive. Google One<https://www.google.com/appserve/mkt/p/AD-FnExIVFETC7vRR74_7E46f9Pu9axCs12_E…> members who are within their storage quota and in good-standing<https://www.google.com/appserve/mkt/p/AD-FnEzdCZtQOziEOeErOxuCiXksjkFHfPBk0…> will not be impacted by this new inactive policy. - If you exceed your storage limit for two years, we may delete your content across Gmail, Drive and Photos. What this means for you: - You won't be impacted by these changes unless you've been inactive or over your storage limit for two years. As this policy goes into effect 1 June 2021, the earliest it would be enforced is 1 June 2023. - After 1 June 2021, if you are either inactive or over your storage limit, we will send you email reminders and notifications in advance and prior to deleting any content. - Even if you are either inactive or over your storage limit for one or more of these services and content is deleted, you will still be able to sign in. - Note: The inactivity and over-quota storage policies will apply only to consumer users of Google services. Google Workspace, G Suite for Education and G Suite for Nonprofits policies are not changing at this time, and admins should look to the Admin Help Centre<https://www.google.com/appserve/mkt/p/AD-FnExAxEjEjq3Ny32tXMAetCl6_3ve6DhXG…> for storage policies related to their subscriptions. Learn more about how to keep your account active - To learn more about how to remain active with these products, visit this Help Centre page<https://www.google.com/appserve/mkt/p/AD-FnEyjpkHt5O1Bdjv6PZDC1UXG9J9Zjx6mL…>. - The Inactive Account Manager<https://www.google.com/appserve/mkt/p/AD-FnEyrpInLkIy5i7pIMxfu5jZ9gdmCyM7ZM…> can help you to manage specific content and notify a trusted contact if you stop using your Google account for a certain period of time (between 3–18 months). Note: The new two-year inactive policy will apply regardless of your Inactive Account Manager settings. You can learn more about these changes and ways to manage your or a loved one's account in our Help Centre<https://www.google.com/appserve/mkt/p/AD-FnExmhhr8LDjPVxMfgmm9vBqxwrWxFMYna…>. Learn how to manage your storage - Learn more about the over-quota policy<https://www.google.com/appserve/mkt/p/AD-FnEz9hYvGeM7VY2YkLC3PKO_iGFko881Mp…> and what counts against storage quota<https://www.google.com/appserve/mkt/p/AD-FnEw8eKPk1HTcr7yZK-Q3-P5RXNvCluurD…>. - You can use the free storage manager in the Google One app<https://www.google.com/appserve/mkt/p/AD-FnExyddioi8S39eFbS7nR37x6hXge8M516…> and on the web<https://www.google.com/appserve/mkt/p/AD-FnExrG-tnbuxllLFC_qB0SleSjEpRLuWcC…> to see how you're using your Google account storage, and free up space across Gmail, Google Drive and Google Photos. Thank you for using our services. Your Google Team © 2020 Google LLC 1600 Amphitheatre Parkway, Mountain View, CA 94043 You have received this mandatory email announcement to update you about important information related to your Google account.

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log_view
by Karin&NiKo 02 Dec '20

02 Dec '20

Dear Firedrakers, I frequently use the option -log_view with PETSc scripts in order to get flops and timing information. How can I get firedrake to ask PETSc to print this information for me? Using the key/value {'log_view':None} is no use in the solver parameters. Thanks, Nicolas

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by BTC System 30 Nov '20

30 Nov '20

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Problem updating firedrake
by Andrew Hicks 16 Nov '20

16 Nov '20

Dear Firedrakers, I'm having trouble updating Firedrake. The error I get is this: Running /home/andrewh/firedrake/firedrake/bin/firedrake-update Configuration saved to /home/andrewh/firedrake/firedrake/.configuration.json Updating the git repository for firedrake Traceback (most recent call last): File "/home/andrewh/firedrake/firedrake/bin/firedrake-update", line 1394, in <module> git_update("firedrake") File "/home/andrewh/firedrake/firedrake/bin/firedrake-update", line 670, in git_update check_call(["git", "pull", "--recurse-submodules"]) File "/home/andrewh/firedrake/firedrake/bin/firedrake-update", line 526, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.6/subprocess.py", line 356, in check_output **kwargs).stdout File "/usr/lib/python3.6/subprocess.py", line 438, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['git', 'pull', '--recurse-submodules']' returned non-zero exit status 1. And then, when I try to rebuild firedrake-update, I get this error when I try 'git pull': error: cannot lock ref 'refs/remotes/origin/wence/test/petsc-debugging': 'refs/remotes/origin/wence/test' exists; cannot create 'refs/remotes/origin/wence/test/petsc-debugging' >From https://github.com/firedrakeproject/firedrake ! [new branch] wence/test/petsc-debugging -> origin/wence/test/petsc-debugging (unable to update local ref) Anyone know why this is happening? Because of this my Firedrake is outdated. Andrew Hicks

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Interpolating with FacetNormal giving AssertionError
by Andrew Hicks 09 Nov '20

09 Nov '20

Dear Firedrakers, I've encountered an issue in my code where it won't allow me to interpolate anything containing a reference to a defined FacetNormal onto a Function. Here is a snippet of code where I purposefully tried to put the bare minimum required to get the error: H1 = VectorFunctionSpace(mesh,'CG',1,5) x0,x1,x2 = SpatialCoordinate(mesh) nu = FacetNormal(mesh) h = interpolate(as_vector([nu[0],0,0,0,0]),H1) If I try to run this, I get the following traceback: File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/function.py", line 353, in interpolate return interpolation.interpolate(expression, self, subset=subset) File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/interpolation.py", line 36, in interpolate return Interpolator(expr, V, subset=subset, access=access).interpolate() File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/interpolation.py", line 58, in __init__ self.callable, arguments = make_interpolator(expr, V, subset, access) File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/interpolation.py", line 163, in make_interpolator loops.extend(_interpolator(V, tensor, expr, subset, arguments, access)) File "</home/andrewh/firedrake/firedrake/lib/python3.6/site-packages/decorator.py:decorator-gen-22>", line 2, in _interpolator File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/utils.py", line 64, in wrapper return f(*args, **kwargs) File "/home/andrewh/firedrake/firedrake/src/firedrake/firedrake/interpolation.py", line 214, in _interpolator ast, oriented, needs_cell_sizes, coefficients, _ = compile_ufl_kernel(expr, to_pts, coords, coffee=False) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/driver.py", line 338, in compile_expression_at_points ir, = fem.compile_ufl(expression, point_sum=False, **config) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/fem.py", line 645, in compile_ufl result = map_expr_dags(context.translator, expressions) File "/home/andrewh/firedrake/firedrake/src/ufl/ufl/corealg/map_dag.py", line 73, in map_expr_dags r = handlers[v._ufl_typecode_](v) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/ufl_utils.py", line 144, in _modified_terminal return self.modified_terminal(o) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/fem.py", line 303, in modified_terminal return translate(mt.terminal, mt, self.context) File "/usr/lib/python3.6/functools.py", line 807, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/fem.py", line 379, in translate_reference_normal return ctx.entity_selector(callback, mt.restriction) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/fem.py", line 98, in entity_selector return callback(self.entity_ids[0]) File "/home/andrewh/firedrake/firedrake/src/tsfc/tsfc/fem.py", line 377, in callback n = ctx.fiat_cell.compute_reference_normal(ctx.integration_dim, facet_i) File "/home/andrewh/firedrake/firedrake/src/fiat/FIAT/reference_element.py", line 387, in compute_reference_normal assert facet_dim == self.get_spatial_dimension() - 1 AssertionError Anyone know what could be the problem here? Any help would be much appreciated. -AH

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Hybridization and postprocessing in FEEC
by Cotter, Colin J 02 Nov '20

02 Nov '20

Dear Firedrakers, We are hosting Ari Stern (WUSTL) for a talk on Zoom about his work on hybridization of finite element exterior calculus, with Firedrake implementation. This talk is open to all members of the Firedrake community, and the title, abstract and Zoom link (thanks for hosting, Lawrence) is below. The talk is on Tuesday 3rd November, 3pm GMT. all the best --cjc === TITLE Hybridization and postprocessing in finite element exterior calculus ABSTRACT Finite element exterior calculus (FEEC) unifies several families of conforming finite element methods for Laplace-type problems, including the scalar and vector Poisson equations. This talk presents a framework for hybridization of FEEC, which recovers known hybrid methods for the scalar Poisson equation and gives new hybrid methods for the vector Poisson equation. We also generalize Stenberg postprocessing, proving new superconvergence estimates. Based on joint work with Gerard Awanou, Maurice Fabien, and Johnny Guzman (arXiv:2008.00149). === https://durhamuniversity.zoom.us/j/94677202864?pwd=NGFkZ2QyUkRBREU3NTlnUjhi… Join our Cloud HD Video Meeting<https://durhamuniversity.zoom.us/j/94677202864?pwd=NGFkZ2QyUkRBREU3NTlnUjhi…> Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom Rooms is the original software-based conference room solution used around the world in board, conference, huddle, and training rooms, as well as executive offices and classrooms. Founded in 2011, Zoom helps businesses and organizations bring their teams together in a frictionless environment to get more done. Zoom is a publicly traded company headquartered in San Jose, CA. durhamuniversity.zoom.us Meeting ID: 946 7720 2864 Passcode: 870478

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Re: [firedrake] Troubles when trying to update firedrake
by Karin&NiKo 16 Oct '20

16 Oct '20

I found a workaround. The problem seems to be known in the preCICE community https://github.com/precice/precice/pull/299 ; importing MPI from mpi4py seems to fix the problem. Does this inspire you for a more generic solution ? Python 3.7.0 (default, Oct 15 2020, 11:45:50) [GCC 6.3.0 20170516] on linux Type "help", "copyright", "credits" or "license" for more information. >>> from mpi4py import MPI >>> import firedrake >>> Le jeu. 15 oct. 2020 à 13:39, Karin&NiKo <niko.karin(a)gmail.com> a écrit : > unfortunately not... > > Le jeu. 15 oct. 2020 à 13:17, Lawrence Mitchell <wence(a)gmx.li> a écrit : > >> >> >> > On 15 Oct 2020, at 12:15, Karin&NiKo <niko.karin(a)gmail.com> wrote: >> > >> > Dear David, >> > I installed python 3.7.0 using the Archer script (slightly modified) >> and the installation procedure did succeed. >> > Nevertheless, when trying to import firedrake, I get the following >> error : >> > >> > Python 3.7.0 (default, Oct 15 2020, 11:45:50) >> > [GCC 6.3.0 20170516] on linux >> > Type "help", "copyright", "credits" or "license" for more information. >> > >>> import firedrake >> > >> -------------------------------------------------------------------------- >> > It looks like orte_init failed for some reason; your parallel process is >> > likely to abort. There are many reasons that a parallel process can >> > fail during orte_init; some of which are due to configuration or >> > environment problems. This failure appears to be an internal failure; >> > here's some additional information (which may only be relevant to an >> > Open MPI developer): >> > >> > setting topology failed >> > --> Returned value Error (-1) instead of ORTE_SUCCESS >> > >> -------------------------------------------------------------------------- >> > >> -------------------------------------------------------------------------- >> > It looks like orte_init failed for some reason; your parallel process is >> > likely to abort. There are many reasons that a parallel process can >> > fail during orte_init; some of which are due to configuration or >> > environment problems. This failure appears to be an internal failure; >> > here's some additional information (which may only be relevant to an >> > Open MPI developer): >> > >> > orte_ess_init failed >> > --> Returned value Error (-1) instead of ORTE_SUCCESS >> > >> -------------------------------------------------------------------------- >> > >> -------------------------------------------------------------------------- >> > It looks like MPI_INIT failed for some reason; your parallel process is >> > likely to abort. There are many reasons that a parallel process can >> > fail during MPI_INIT; some of which are due to configuration or >> environment >> > problems. This failure appears to be an internal failure; here's some >> > additional information (which may only be relevant to an Open MPI >> > developer): >> > >> > ompi_mpi_init: ompi_rte_init failed >> > --> Returned "Error" (-1) instead of "Success" (0) >> > >> -------------------------------------------------------------------------- >> > *** An error occurred in MPI_Init_thread >> > *** on a NULL communicator >> > *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, >> > *** and potentially your MPI job) >> > [machineName:31007] Local abort before MPI_INIT completed completed >> successfully, but am not able to aggregate error messages, and not able to >> guarantee that all other processes were killed! >> > >> > >> > It clearly comes from openMPI but I do not see why it happens since I >> can run other mpi processes (like "mpirun -n2 ls"). >> >> >> Does >> >> mpirun -n 2 python -c "import firedrake" >> >> work? >> >> On some supercomputers you always have to run MPI-enabled programs via >> the mpirun system. >> >> Lawrence > >

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Fw: Workshop on pre- and post-processing at the exascale.
by Cotter, Colin J 15 Oct '20

15 Oct '20

Dear Firedrakers, If you are interested in meshing please check out the workshop below. all the best -cjc ________________________________ From: Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> Sent: 14 October 2020 13:37 Subject: Workshop on pre- and post-processing at the exascale. Hi All, We are hosting a workshop next week which may be of interest to you or your researchers. The workshop will present the current state-of-the-art in meshing and discuss the challenges going forward towards the Exascale - it is free and open to attend for anyone with an interest in the topic. Details can be found under: https://epcced.github.io/ELEMENT/workshops.html Many thanks, Spencer. Spencer Sherwin FREng, FRAeS Head of Aerodynamics Section, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, South Kensington Campus, Imperial College London, SW7 2AZ, UK Phone: +44 (0)20 7594 5052 http://www.imperial.ac.uk/people/s.sherwin/

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