October 2020 - firedrake - imperial.ac.uk

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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Troubles when trying to update firedrake
by Karin&NiKo 15 Oct '20

15 Oct '20

Dear Firedrakers, I installed firedrake with the following options few months ago : python3 firedrake-install --disable-ssh --mpiexec mpirun.openmpi --mpicc mpicc.openmpi --mpicxx mpicxx.openmpi --mpif90 mpif90.openmpi I am now trying to update the code. So I am activating the virtualenv and I run : firedrake-update I then get the error : Running firedrake-update --verbose Traceback (most recent call last): File "firedrake-update", line 1254, in <module> mpiexec_loc = shutil.which(args.mpiexec) AttributeError: 'Namespace' object has no attribute 'mpiexec' But if I run the following in a python script, everything seems OK : >>> import shutil >>> shutil.which('mpiexec') '/home/mylogin/dev/Firedrake/firedrake/bin/mpiexec' What is going wrong? Nicolas

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Continuing informal reading group
by Lawrence Mitchell 06 Oct '20

06 Oct '20

Dear firedrakers, after our (I think) reasonable success running an online reading group over the summer, I propose continuing it as the Autumn kicks in. Over the summer we read through Joachim Schoeberl's thesis on parameter robust multigrid methods (see https://github.com/firedrakeproject/firedrake/wiki/schoeberl-thesis) I propose that we switch to going through papers, rather than complete theses. These sessions are reasonably informal, and I (at least) learned some things this time round. Given that we've just closed out one topic, I'm soliciting both timeslots for interested parties, and potential papers (and volunteers to lead on the reading!). If you're interested in participating, please fill in this doodle selecting times that work for you: https://doodle.com/poll/vt8smu76c9m66hbv (ignore the dates, we'll try and make it a weekly thing) I'll then try and find a time that suits most people, and we can decide on a paper to start with. Thanks, Lawrence

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Using Paraview
by Mathieu Dutour 02 Oct '20

02 Oct '20

Dear all, I know it is more a paraview question than firedrake, but the question is about how to visualize the data using paraview. The documentation on the firedrake website is quite succinct and does not tell anything about the User Interface of Paraview, which is fine. But I do not know how to get pictures and I wonder where the error lies. If I run some example, like say, Camassa-Holm I obtain a sequence of .vtu files. When opening with paraview 5.8.1 the files u.pvd or u_0.pvd I obtain the image in attachment. The image points out to several errors: "Number of cells: 0" "Number of points: 0" "X range: not available" "Y range: not available" "Z range: not available" So clearly some grid is missing somewhere but I do not know how to provide it. Would it be possible to provide some basic information on how to use paraview on the vtu files? Alternatively, since Paraview is scriptable, I would very much appreciate having a python script for creating output from paraview (such as the double-slit youtube video) in one of the tutorial test cases. Thank you very much in advance for any help, Mathieu

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