- firedrake - imperial.ac.uk

Firedrake '22 workshop, 4-6 January 2023
by Ham, David A 10 Oct '22

10 Oct '22

Dear Firedrakers, The only-slightly-inaccurately-named Firedrake ’22 workshop will be held at Dartington Hall from 4-6 January 2023. This is an opportunity to present your work on or using Firedrake and to interact with and collaborate with the rest of the Firedrake community face to face at long last. Abstracts are due by 18 November and there is more information about the workshop at: https://firedrakeproject.org/firedrake_22.html I look forward to seeing many of you there! Yours, David -- Dr David A. Ham Reader in Computational Mathematics Department of Mathematics Imperial College London https://firedrakeproject.org https://www.imperial.ac.uk/people/david.ham [signature_506698884]<https://object-oriented-python.github.io/>

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Research Software Study
by rsstudy 05 Sep '22

05 Sep '22

Apologies if you have already answered our survey, we greatly appreciate your response. If you have not answered our survey and would like to please read this email and follow the link. This is the last time we will invite you to take part in this survey. You have not been added to a mailing list. Hi, We are investigating the roles involved with software development in research and the types of activities researchers perform while developing code. Our goal is to recognise contributor roles in software to bring more value to research effort. We are contacting you because we believe you develop code to support your research. If this is incorrect, we apologize; if you know of someone who is then we'd be grateful if you could forward this invitation to them. If you'd like to help in our investigation, we'd appreciate 5 minutes of your time to answer our questionnaire. The answers are mostly tick boxes and some short text box answers (one or two words required). Please follow this link if you'd like to participate: https://forms.office.com/r/b1MrNg9w77<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.off…> Participant information can be found here: https://sotonac-my.sharepoint.com/:w:/g/personal/hsp2m10_soton_ac_uk/EWs8Ob… Any questions please respond to this email. Ergo number: 75892 Kind regards, Heather – Dr Heather Packer New Frontier Fellow Web and Internet Science Group University of Southampton

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2 Postdoc positions working on Firedrake at Imperial
by Ham, David A 17 Aug '22

17 Aug '22

Dear Firedrakers, I’m really happy to announce that we have two research associate positions available to work on Firedrake at Imperial. Please consider applying yourself and please also pass the advert on to anyone you know who might be in the market for a postdoc position: https://www.imperial.ac.uk/jobs/description/NAT01233/research-associate-com… Yours, David -- Dr David A. Ham Reader in Computational Mathematics Department of Mathematics Imperial College London https://firedrakeproject.org https://www.imperial.ac.uk/people/david.ham [signature_213336399]<https://object-oriented-python.github.io/>

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Research Software Study
by rsstudy 11 Aug '22

11 Aug '22

Hi, We are investigating the roles involved with software development in research and the types of activities researchers perform while developing code. Our goal is to recognise contributor roles in software to bring more value to research effort. We are contacting you because we believe you develop code to support your research. If this is incorrect, we apologize; if you know of someone who is then we'd be grateful if you could forward this invitation to them. If you'd like to help in our investigation, we'd appreciate 5-10 minutes of your time to answer our questionnaire. The answers are mostly tick boxes and some short text box answers (one or two words required). Please follow this link if you'd like to participate: https://forms.office.com/r/b1MrNg9w77<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.off…> Participant information can be found here: https://sotonac-my.sharepoint.com/:w:/g/personal/hsp2m10_soton_ac_uk/EWs8Ob… Any questions please respond to this email. We may send another invite in two weeks if you don't respond, but you will not be added to a mail listing. Ergo number: 75892 Kind regards, Heather – Dr Heather Packer New Frontier Fellow Web and Internet Science Group University of Southampton

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Do you need project support and CNC machining?
by Lucie Cai 29 Jul '22

29 Jul '22

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solver optimisations for ASMVankaPC
by Cotter, Colin J 16 Jun '22

16 Jun '22

Hi folks, I'm doing some stuff with ASMVankaPC applied to an extruded mesh (so I'm working on a patch of columns) and a mixed system, so the matrices are getting relatively big. Does anyone have any tips on how to use different algorithms with the solver to use less memory? One idea I had is that I think that it would be possible to eliminate down to one single variable, solve that and back substitute. It looks like MUMPS has some Schur complement options, for example, but I don't know how to pipe the DOFs I want to eliminate down to MUMPS - is it possible? 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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Re: [firedrake] [petsc-maint] Firedrake - PETSC CONFIGURATION CRASH
by Matthew Knepley 16 May '22

16 May '22

On Fri, Apr 22, 2022 at 10:58 AM John Snyder via petsc-maint < petsc-maint(a)mcs.anl.gov> wrote: > Satish, > I must be an idiot. I tried using your potential fix, > But I cannot find the branch? > I looked in fired rack and PETSc GitHub but searching I was unable to > locate the repo. > I tried: > Notice that this is cloning the FIredrake fork of PETSc, which probably does not have this branch. I have added them to this thread. Thanks, Matt > ... > 2022-04-22 09:28:47,265 DEBUG Running command 'git clone -q --recursive > https://github.com/firedrakeproject/petsc.git' > 2022-04-22 09:30:37,982 DEBUG > 2022-04-22 09:30:37,991 INFO Successfully cloned repository petsc. > 2022-04-22 09:30:38,001 DEBUG Old path > '/data/gpfs/Users/l1057678/firedrake-new/build/src' > 2022-04-22 09:30:38,001 DEBUG Pushing path > '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' > 2022-04-22 09:30:38,001 INFO Checking out branch > balay/fix-executables-search-path > 2022-04-22 09:30:38,001 DEBUG Running command 'git checkout -q > balay/fix-executables-search-path' > 2022-04-22 09:30:38,031 DEBUG error: pathspec > 'balay/fix-executables-search-path' did not match any file(s) known to git. > > 2022-04-22 09:30:38,031 ERROR Failed to check out branch > balay/fix-executables-search-path > 2022-04-22 09:30:38,031 DEBUG Popping path > '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' > 2022-04-22 09:30:38,031 DEBUG New path > '/data/gpfs/Users/l1057678/firedrake-new/build/src’ > > > I used the following: > */hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 > ./firedrake-install --no-package-manager --venv-name build --tinyasm > --disable-ssh --minimal-petsc --slepc --documentation-dependencies > --install thetis --install gusto --install icepack --install irksome > --install femlium --package-branch petsc balay/fix-executables-search-path > --package-branch slepc balay/fix-executables-search-path* > > > What am I doing wrong? > > > Best Regards, > John > P.S. Thank you for all you assistance. > > > On Apr 21, 2022, at 1:24 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > I pushed a potential fix [off release] in branch > balay/fix-executables-search-path - can you try it? > > [if you need this fix on main branch - you can merge it over locally - and > test] > > Satish > > On Thu, 21 Apr 2022, Satish Balay via petsc-maint wrote: > > > --with-executables-search-path=/hrtc/apps/devtools/cmake/x86_64/3.8.2/bin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/sbin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin:/hrtc/apps/mpi/openmpi/4.0.1/RDHPC/gcc/8.2.0/bin:/apps/gcc/8.2.0/x86_64/libexec/gcc/x86_64-pc-linux-gnu/8.2.0:/apps/gcc/8.2.0/x86_64/bin:.:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/apps/slurm/x86/20.02.0/bin:/apps/slurm/x86/20.02.0/sbin:/usr/bin > > Hm - did this option ever work? [I don't remember seeing this in a very > long time > > I suspect its expecting a list - in python notation [and not in PATH > notation]. So probably needs fixing. But do you need this option? > > Satish > > On Thu, 21 Apr 2022, John Snyder via petsc-maint wrote: > > Team, > Please note, firedrake installation fails !!! > > Configuring PETSc to compile on your system > > ============================================================================================= > TESTING: configureExternalPackagesDir from > config.framework(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/framework.py:1030) > TESTING: configureDebuggers from > config.utilities.debuggers(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/utilities/debuggers.py:20) > TESTING: configureDirectories from > PETSc.options.petscdir(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/PETSc/options/petscdir.py:22) > > ******************************************************************************* > CONFIGURATION CRASH (Please send configure.log to > petsc-maint(a)mcs.anl.gov<mailto:petsc-maint@mcs.anl.gov > <petsc-maint(a)mcs.anl.gov>>) > > > > ===================================================================================================================== > This failure during install is from: > export PETSC_CONFIGURE_OPTIONS="--with-cc=mpicc --CC=mpicc --CXX=mpic++ > --FC=mpifort --download-openblas --with-executables-search-path=${PATH}" > --download-ml --download-mpich --download-pastix --download-ptscotch > --with-cxx-dialect=C++11 > --download-eigen=/data/gpfs/Users/l1057678/firedrake-spack/firedrake/src/eigen-3.3.3.tgz > --with-fortran-bindings=0 --download-cmake --with-debugging=0 > --download-hdf5 --download-superlu_dist --download-netcdf --with-c2html=0 > --download-suitesparse --download-scalapack --download-hypre > --download-pnetcdf --with-shared-libraries=1 --download-hwloc > --with-bison-exec=/usr/bin/bison > > > /hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 > ./firedrake-install --no-package-manager --venv-name build --tinyasm > --disable-ssh --minimal-petsc --slepc --documentation-dependencies > --install thetis --install gusto --install icepack --install irksome > --install femlium --package-branch petsc connorjward/merge-upstream > --package-branch slepc connorjward/merge-upstream > > > Please see attached firedrake-install.log and petsc configure.log > > > > Best Regard, > John > > P.S. Any and all assistance is greatly appreciated. > > > > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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calledprocesserror in firedrake installation
by Zhou, Shuchan 14 May '22

14 May '22

Dear Sir or Madam, I'm trying to install firedrake on my Mac and met an "calledprocesserror" when installing PETSc. I have attached the firedrake-install.log. Can anyone help me with it? Best wishes, Shuchan

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postdoc position
by Cotter, Colin J 07 Mar '22

07 Mar '22

Dear Firedrakers, I have a postdoc position open, which is Firedrake-adjacent - please share it with anyone who might be interested. I'm particularly looking for people with some form of UQ/inverse problems/data assimilation interests. https://www.imperial.ac.uk/jobs/description/NAT01106/research-associate-com… 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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Error with Point Evaluation and VertexOnlyMesh
by Venketeswaran, Abhishek (FN) 01 Mar '22

01 Mar '22

Dear Koki and Lawrence, I am having trouble extracting my results at certain points on my mesh. I understand that there are 2 methods to do this (i) at() function and (ii) VertexOnlyMesh. Both dont work for me. While the former raises Point Not in Domain Error, the latter raises TypeError: an integer is required. Here is a minimal example of trying both methods out: from firedrake import * from firedrake.petsc import PETSc from firedrake.mesh import VertexOnlyMesh from collections import OrderedDict import numpy as np mesh = UnitSquareMesh(10, 10) V = FunctionSpace(mesh, "CG", 1) v = TestFunction(V) u = TrialFunction(V) a = inner(grad(u), grad(v)) * dx L = Constant(0) * v * dx bc1 = DirichletBC(V, 0.0, 1) bc2 = DirichletBC(V, 1.0, 2) sol = Function(V) problem1 = LinearVariationalProblem(a, L, sol, bcs=[bc1, bc2], constant_jacobian=True) solver1 = LinearVariationalSolver(problem1, solver_parameters={"ksp_type": "cg", "pc_type": "jacobi"}) solver1.solve() print(sol.dat.data_ro) crd=[0.5256,0.5051] num_points = 25 δs = np.linspace(0.0, 1.0, num_points + 1) X, Y = np.meshgrid(δs, δs) xs = np.vstack((X.flatten(), Y.flatten())).T vm=1 pe=1 #Test VertexOnlyMesh Generation if vm: point_cloud = VertexOnlyMesh(mesh, xs) #Test Point Evaluation of Function if pe: print(sol.at(crd)) Kindly let me know where I should start looking to fix this problem. -- Abhishek Venketeswaran NETL Research Associate - ORISE National Energy Technology Laboratory Department of Energy abhishek.venketeswaran(a)netl.doe.gov Work: 412-386-4833 Mobile: 716-507-7890 www.netl.doe.gov<http://www.netl.doe.gov> [cid:b3222045-e3c2-4f40-9a6f-b6c662401b72]

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