- firedrake - imperial.ac.uk

Fw: Second PRISM workshop on applications: Beyond CFD that will be held on Wed, 30 September 2020 at 14:00 – 16:00
by Cotter, Colin J 08 Sep '20

08 Sep '20

Dear Firedrakers, You may be interested in the PRISM workshop below. It has an odd title but it is really about composability, coupling and the outer loop. all the best --cjc ________________________________ From: Radomska, Anna <a.radomska(a)imperial.ac.uk> Sent: 08 September 2020 16:00 To: patrick.farrell <patrick.farrell(a)maths.ox.ac.uk>; Cotter, Colin J <colin.cotter(a)imperial.ac.uk>; Ham, David A <david.ham(a)imperial.ac.uk>; Kelly, Paul H J <p.kelly(a)imperial.ac.uk>; Cohen, Jeremy <jeremy.cohen(a)imperial.ac.uk>; Moxey, David <D.Moxey(a)exeter.ac.uk>; Gorman, Gerard J <g.gorman(a)imperial.ac.uk>; Piggott, Matthew D <m.d.piggott(a)imperial.ac.uk> Cc: Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> Subject: Second PRISM workshop on applications: Beyond CFD that will be held on Wed, 30 September 2020 at 14:00 – 16:00 Dear All, Please join us for the second PRISM workshop on applications: Beyond CFD that will be held on Wed, 30 September 2020 at 14:00 – 16:00. In this workshop we wish to share experiences on application of PDE solvers which go beyond CFD tools, for example composable solvers, stability analysis, inverse problems, data assimilation and uncertainty quantification. The format of the on-line workshop will involve a series of 3 short 10-minutes talks followed by small group discussions and a summary session. The event's programme includes: 2.00pm-2.10pm Matt Knepley (University at Buffalo) 2.10pm-2.20pm Patrick Farrell (University of Oxford) 2.20pm-2.30pm Koki Sagiyama (Imperial College London) on "Firedrake: Solving equations on subspaces" 2.30pm-3.30pm Small group discussions 3.30pm-3.45pm Summary session If you could kindly share this announcement through your network it would be greatly appreciated. To register please sign-up here<https://www.eventbrite.co.uk/e/beyond-cfd-tickets-117983109657> so you can receive a Microsoft Teams calendar invite which will be distributed closer to the date of the event. With best regards, Anna

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Is there a way to calculate a flux on the edges of each cell in Firedrake
by Mohammad Sarraf Joshaghani 07 Sep '20

07 Sep '20

Hello, I am trying to implement a postprocessing flux-limiting scheme for a DG advection problem to eliminate the under/overshoots that appears in the vicinity of the front. In order to achieve this, I need to iterate over each mesh element and then on each facet of the element calculate the value of numerical flux. Based on the sign of this Flux value, a constant edge-specific alpha is calculated and the new corrected solutions are then reconstructed for the cell. In firedrake, Is there any way to iterate over facets of each cell, and calculate an integral of an expression (e.g, avg(inner(grad(sol,n))) ) on that facet? This is how I achieved it in fenics: ----------------------------------------------------- facet_domains = MeshFunction('size_t',mesh,mesh.topology().dim()-1) dS = Measure('dS', subdomain_data = facet_domains) elnum = 0 for cell in cells(mesh): flux=np.zeros(3) for fct in facets(cell): flux[fct.index] = assemble( (avg(inner(grad(sol) , n) ) )*dS(fct.index()) print(flux) . . do some operations based on flux[fct.index] values . . elnum += 1 -------------------------------------------------------- Thank you, Sarraf

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Calculate a flux on the edges of each cell
by Mohammad Sarraf Joshaghani 31 Aug '20

31 Aug '20

Hello, I am trying to implement a postprocessing flux-limiting scheme for a DG advection problem to eliminate the under/overshoots that appears in the vicinity of the front. In order to achieve this, I need to iterate over each mesh element and then on each facet of the element calculate the value of numerical flux. Based on the sign of this Flux value, a constant edge-specific alpha is calculated and the new corrected solutions are then reconstructed for the cell. In firedrake, Is there any way to iterate over facets of each cell, and calculate an integral of an expression (e.g, avg(inner(grad(sol,n))) ) on that facet? This is how I achieved it in fenics: ----------------------------------------------------- facet_domains = MeshFunction('size_t',mesh,mesh.topology().dim()-1) dS = Measure('dS', subdomain_data = facet_domains) elnum = 0 for cell in cells(mesh): flux=np.zeros(3) for fct in facets(cell): flux[fct.index] = assemble( (avg(inner(grad(sol) , n) ) )*dS(fct.index()) print(flux) . . do some operations based on flux[fct.index] values . . elnum += 1 -------------------------------------------------------- Regards, Sarraf

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retrieve dof and entities of assembled matrix entries
by Karin&NiKo 28 Aug '20

28 Aug '20

Dear Firedrakers, I wonder how to retrieve the dof and support entities of the entries of an assembled matrix. To make it clearer, let's say I consider a simple elasticity problem that I discretize with P2 elements. I would like to know which nodes and degrees of freedom the values of the assembly matrix refer to. Best regards, Nicolas

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Questions about Firedrake PETSc.
by Junho Choi 13 Aug '20

13 Aug '20

Dear the development team, I am Junho, a researcher at University of Leeds. Using Firedrake PETSc, I am trying to solving a linear system. To do this, I refer to your instruction about Interfacing directly with PETSc(https://www.firedrakeproject.org/petsc-interface.html), but it is hard to follow the instruction for me because of no example. So would you let me know how to apply the instruction if simply setting a system Bx=b where B=[1, 2, 3; 3, 4,5; 4, 5,6], b=[2; 3; 5]? In addition, if I solve a linear system with PETSc like your instruction, can I use parallel computing to shorten computing time? If yes, how can I use the parallel computing? Thank you. Junho

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SIAM CSE21 Code Generation Minisymposterium
by Hill, Reuben 12 Aug '20

12 Aug '20

Dear Firedrake users, We are proposing a minisymposterium (a poster session) at SIAM CSE21<https://www.siam.org/conferences/cm/conference/cse21> due to be held March 1-5 2021. The proposed title and abstract are Automatic simulation code generation tools and their applications. Automatic code generation provides a mechanism for creating high performance simulations using sophisticated numerical methods at minimal development cost. Tools such as Firedrake, FEniCS, FreeFEM++, Devito and many others enable developers to work in a highly productive way at a high level of mathematical abstraction, while still creating optimised low-level code which is frequently faster than would have been written by hand. Code generation approaches also facilitate a separation of concerns in which new numerical methods or performance improvements become directly available to application developers without the need for repeated recoding. This minisymposterium provides the opportunity for developers and users of code generation frameworks to present recent developments in both the capabilities and applications of these frameworks. The poster session will also provide the opportunity for informal exchanges of ideas in this community, and to support dialog between developers, and existing and potential users of these frameworks. We need to collect poster titles and authors for inclusion in the proposal so they can be exhibited together (note, though, that they still need to be submitted to the conference directly). I have made a survey for this purpose, which is accessible via the below link https://imperial.eu.qualtrics.com/jfe/form/SV_efEu8ddYj1nicdv Please share this with anyone in the code generation community who may wish to participate in the minisymposterium - it should be a great opportunity to present and share ideas. See also SIAM's COVID-19 contingency plans for CSE21 here<https://sinews.siam.org/Details-Page/faq-on-covid-19-contingency-plans-for-…>. Best wishes, Reuben Hill

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Re: [firedrake] trying to install Firedrake on the LSU HPC cluster
by Ham, David A 24 Jul '20

24 Jul '20

Dear Shawn, The install instructions on the website are more directed at workstation/laptop users than supercomputers. Automation of dependency installation on supercomputers isn’t really possible because we need to use the compiler toolchains and MPI that the system specifies. I would, however, note that the comments that the sysadmin made about Firedrake being specifically geared towards Ubuntu and MacOS are not correct. Rather, we provide automatic upstream dependency installation on those platforms for the benefit of novice users. Running ./firedrake-install --show-dependencies will list the core external dependencies. All of these are probably already available, possibly by loading the correct set of modules. This is the output: ************************************************ The following dependencies need to be installed: ************************************************ * A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * Blas and Lapack * Boost * Git * Python version >=3.6 * The Python headers * autoconf, automake, libtool * CMake You’re also likely to need to tell the installer something about your toolchain, and in particular what the MPI compilers and launch command are. Another frequent source of issues on supercomputers are less than fully functional Python installs – either because missing pip or lacking ssl certificates. Sometimes users end up building Python from source in order to get a fully working Python. A couple of recent examples of scripts which people have written to install Firedrake on supercomputers are at: https://github.com/firedrakeproject/firedrake-archer/blob/master/install_fi… https://github.com/firedrakeproject/isambard/blob/master/install_firedrake_… Finally, if you have issues, then posting an issue on GitHub including the firedrake-install.log is usually the best thing to do. Regards, David -- Dr David Ham Department of Mathematics Imperial College London https://www.imperial.ac.uk/people/david.ham From: <firedrake-bounces(a)imperial.ac.uk> on behalf of Shawn W Walker <walker(a)lsu.edu> Date: Thursday, 23 July 2020 at 19:23 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] trying to install Firedrake on the LSU HPC cluster Hello Firedrake people. The IT staff here at LSU are having some trouble installing firedrake on our clusters. I’m forwarding the email below detailing those difficulties for your information. If you have any suggestions, please let me know. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Thursday, July 23, 2020 11:58 AM To: Shawn W Walker <walker(a)lsu.edu> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Another update: 1. Native installation wasn't successful, yet. The installation script states "Any required system packages are installed using brew (MacOS) or apt (Ubuntu and similar Linux systems). On a Linux system without apt, the installation will fail if a dependency is not found." Since we run Redhat, taking care of all dependencies will take some time. 2. I was able to build a working container image on a box running Fedora, but the same image fails on the cluster with the issue reported here: https://github.com/firedrakeproject/firedrake/issues/1712<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> It's supposed to be fixed last month, but I'm still getting it on the cluster. 3. Overall it's not very friendly with clusters. For one, it's specifically geared towards Ubuntu, but I don't think there are many clusters running Ubuntu. The difficulties are summarized in the issue report here: https://github.com/firedrakeproject/firedrake/issues/1779<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/20/2020 18:35 - Shawn W Walker wrote: Thanks Le. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Monday, July 20, 2020 4:50 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Just a quick update: I was able to build a container for it, but ran into errors running the example on their website, most likely due to permission issues in the container as well as how MPI is set up. I may need to install it from source. I'll get back to you as soon as possible. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:42 - LONI Systems Support wrote: Hi Shawn, Let me take a look and get back to you. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:37 - Shawn W Walker wrote: Hello. I would like to get Firedrake up and running on the HPC system. Can you help? -Shawn From: Le Yan Sent: Thursday, July 16, 2020 3:28 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: firedrake on LSU HPC? Hi Shawn, I just took a look at it and it seems to have Docker images available, so we could try to create a Singularity container image. I'll get back to you. Could you please forward the email to sys-help(a)loni.org<mailto:sys-help@loni.org> so we will have a record? And I assume either SuperMIC or Super Mike 2 should be fine, right? Cheers, Le ----------------------------------------- Le Yan, PhD Assistant Director High Performance Computing Information Technology Services Louisiana State University 343 Frey Computing Services Building, Baton Rouge, LA 70808 office 225-578-7524 | fax 225-578-6400 lsu.edu<http://www.lsu.edu/> | hpc.lsu.edu<http://hpc.lsu.edu/> ________________________________ From: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Sent: Thursday, July 16, 2020 3:16 PM To: Le Yan <lyan1(a)lsu.edu<mailto:lyan1@lsu.edu>> Subject: firedrake on LSU HPC? Hello Le. Do you know if this software can be “easily” installed on the HPC system: https://www.firedrakeproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fired…> It is similar to FEniCS. The main issue is whether PETSC is configured properly for Firedrake. -Shawn

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trying to install Firedrake on the LSU HPC cluster
by Shawn W Walker 23 Jul '20

23 Jul '20

Hello Firedrake people. The IT staff here at LSU are having some trouble installing firedrake on our clusters. I’m forwarding the email below detailing those difficulties for your information. If you have any suggestions, please let me know. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Thursday, July 23, 2020 11:58 AM To: Shawn W Walker <walker(a)lsu.edu> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Another update: 1. Native installation wasn't successful, yet. The installation script states "Any required system packages are installed using brew (MacOS) or apt (Ubuntu and similar Linux systems). On a Linux system without apt, the installation will fail if a dependency is not found." Since we run Redhat, taking care of all dependencies will take some time. 2. I was able to build a working container image on a box running Fedora, but the same image fails on the cluster with the issue reported here: https://github.com/firedrakeproject/firedrake/issues/1712<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> It's supposed to be fixed last month, but I'm still getting it on the cluster. 3. Overall it's not very friendly with clusters. For one, it's specifically geared towards Ubuntu, but I don't think there are many clusters running Ubuntu. The difficulties are summarized in the issue report here: https://github.com/firedrakeproject/firedrake/issues/1779<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/20/2020 18:35 - Shawn W Walker wrote: Thanks Le. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Monday, July 20, 2020 4:50 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Just a quick update: I was able to build a container for it, but ran into errors running the example on their website, most likely due to permission issues in the container as well as how MPI is set up. I may need to install it from source. I'll get back to you as soon as possible. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:42 - LONI Systems Support wrote: Hi Shawn, Let me take a look and get back to you. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:37 - Shawn W Walker wrote: Hello. I would like to get Firedrake up and running on the HPC system. Can you help? -Shawn From: Le Yan Sent: Thursday, July 16, 2020 3:28 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: firedrake on LSU HPC? Hi Shawn, I just took a look at it and it seems to have Docker images available, so we could try to create a Singularity container image. I'll get back to you. Could you please forward the email to sys-help(a)loni.org<mailto:sys-help@loni.org> so we will have a record? And I assume either SuperMIC or Super Mike 2 should be fine, right? Cheers, Le ----------------------------------------- Le Yan, PhD Assistant Director High Performance Computing Information Technology Services Louisiana State University 343 Frey Computing Services Building, Baton Rouge, LA 70808 office 225-578-7524 | fax 225-578-6400 lsu.edu<http://www.lsu.edu/> | hpc.lsu.edu<http://hpc.lsu.edu/> ________________________________ From: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Sent: Thursday, July 16, 2020 3:16 PM To: Le Yan <lyan1(a)lsu.edu<mailto:lyan1@lsu.edu>> Subject: firedrake on LSU HPC? Hello Le. Do you know if this software can be “easily” installed on the HPC system: https://www.firedrakeproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fired…> It is similar to FEniCS. The main issue is whether PETSC is configured properly for Firedrake. -Shawn

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MatNest and blockSize
by Karin&NiKo 12 Jul '20

12 Jul '20

Dear Firedrakers, I am solving a 3 fields coupled problem with Firedrake. I would like to use a multiplicative block-preconditioner but PETSc complains about a local size not being correct. [0] Arguments are incompatible [0] Local size 9 not compatible with block size 2 I have noticed that the use of a MatAij solves the problem (see comment in line 132) but I am afraid this is just a side effect. Am I missing something? Thanks in advance, Nicolas

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plea for images
by Cotter, Colin J 07 Jul '20

07 Jul '20

Dear Firedrakers, Firedrake is partially supported by the Platform for Research in Simulation Methods (an EPSRC grant at Imperial College) [yes I know PRISM is an unfortunate acronym!]. We are looking for some new images for the PRISM website prism.ac.uk. If you have a flashy image from your Firedrake-based work that you don't mind being used to promote Firedrake through the prism.ac.uk website please can you send it to me offlist and I will pass it on. all the best --cjc Professor Colin Cotter (he/him) Department of Mathematics 755, Huxley Building Imperial College London South Kensington Campus United Kingdom of Great Britain and Northern Ireland +44 2075943468

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