- firedrake - imperial.ac.uk

FEniCS'18 Conference 21-23 March, University of Oxford
by Patrick Farrell 15 Feb '18

15 Feb '18

Dear Firedrake community, Due to several requests, we have decided to extend the abstract submission deadline for FEniCS'18 by a week. Abstract submission will close on 21 February. For further details please see https://fenicsproject.org/fenics18/ . We are very much looking forward to seeing you in Oxford! Best regards, Patrick

1 0

.at() PETSC error
by Floriane Gidel [RPG] 08 Feb '18

08 Feb '18

Dear all, I try to extract the values of a function h, at some specific positions with the function .at() . I define a coarse mesh with Nx_fine = int(Lx/0.4) + 1 Ny_fine = int(Ly/0.4) + 1 coarse_mesh = RectangleMesh(Nx_coarse,Ny_coarse,Lx,Ly,quadrilateral=True) coarse_V = FunctionSpace(coarse_mesh, "CG", 1) coarse_h = Function(coarse_V, name="h") V_vec_c = VectorFunctionSpace(coarse_mesh, "CG", 1) coarse_points = Function(V_vec_c , name="coarse_points") coarse_points.interpolate(SpatialCoordinate(coarse_mesh)) Then I define a finer mesh with Nx_fine = int(Lx/0.1) + 1 Ny_fine = int(Ly/0.1) + 1 fine_mesh = RectangleMesh(Nx_fine,Ny_fine,Lx,Ly,quadrilateral=True) fine_V = FunctionSpace(fine_mesh, "CG", 1) fine_h = Function(fine_V, name="h") Then I load an h5 function into fine_h (defined on the same function space) with dumb_file_fine = DumbCheckpoint(save_path+"fine/h_0", mode=FILE_READ) dumb_file_fine.load(fine_h) dumb_file_fine.close() But then, when I try to extract the values of fine_h at the coordinates of coarse_mesh with coarse_data_fine = fine_h.at(coarse_points.dat.data_ro) I get this error: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Is someone familiar with this error ? Thanks, Floriane

2 10

FEniCS'18 Conference 21-23 March, University of Oxford
by Patrick Farrell 06 Feb '18

06 Feb '18

Dear Firedrake community, You are warmly invited to the FEniCS 2018 meeting, on 21-23 March, at the University of Oxford. Registration and abstract submission are now open. Abstract submission closes on 14 February. For further details please see https://fenicsproject.org/fenics18/ . We are very much looking forward to seeing you in Oxford! Best regards, Patrick

1 0

PDESoft 2018 submission deadline
by Lawrence Mitchell 05 Feb '18

05 Feb '18

Dear Firedrakers, if you are interested in the development of PDE software more broadly than just Firedrake itself (!), you may be interested in PDESoft in Norway this summer (the week before the Firedrake workshop). The abstract submission deadline has been extended until 19th February. A brief one-paragraph description: The PDE Software Frameworks 2018 conference takes place May 28-30 in Bergen, Norway. This conference provides a forum for the developers and users of software solving the diverse stages of the numerical PDE process, and for discussing future directions of research and development. http://www.iris.no/pdesoft18/pde-software-homepage Cheers, Lawrence

1 0

firedrake install failing
by William Booker [RPG] 05 Feb '18

05 Feb '18

Dear Firedrakers, Attached the log file. How do I fix this? Regards Will

2 1

Firedrake user and developer workshop: 7-8 June 2018
by Lawrence Mitchell 01 Feb '18

01 Feb '18

Dear all, the second Firedrake users and developers meeting will be held this summer at Imperial College on the 7th and 8th June. It will once again provide an opportunity for users and developers of Firedrake to get together, exchange ideas, application challenges, and future development directions. The workshop will start with a half-day introductory tutorial for interested new users. The call for contributions, and registration is now open. Please see https://www.firedrakeproject.org/firedrake_18.html for more details. Important dates: - Early registration and abstract closes 10th April - Registration closes 25th May (but book early, it's cheaper!) - Workshop: 7-8th June We hope to see many of you in June! Cheers, Lawrence (and the Firedrake team)

1 0

publications
by Tomasz Salwa [RPG] 29 Jan '18

29 Jan '18

Dear Firedrakers, Could you add the entires below to the list of publications using Firedrake? Thank you, Tomasz @Article{Salwa:2017, author = {Salwa, Tomasz and Bokhove, Onno and Kelmanson, Mark A.}, title = {Variational modelling of wave--structure interactions with an offshore wind-turbine mast}, journal = {Journal of Engineering Mathematics}, year = {2017}, month = {Sep}, day = {15}, issn = {1573-2703}, doi = {10.1007/s10665-017-9936-4} } @Article{Salwa:2016, author = {Salwa, Tomasz and Bokhove, Onno and Kelmanson, Mark A.}, title = {Variational modelling of wave-structure interactions for offshore wind turbines}, journal = {Extended paper for Int. Conf. on Ocean, Offshore and Arctic Eng., OMAE2016, Busan, South-Korea}, month = {June}, year = 2016, url = "http://proceedings.asmedigitalcollection.asme.org/proceeding.aspx?articleID…" }

1 0

PDE Software Frameworks 2018 -- May 28-30, Hotel Zander K, Bergen, Norway.
by Robert Kloefkorn 16 Dec '17

16 Dec '17

Dear friends and colleagues, It is a great pleasure to announce the PDE Software Frameworks (PDESoft) 2018 Conference, which will be held at the hotel Zander K (https://www.zanderk.no/en/) Bergen, Norway, May 28 - 30, 2018. The scientific committee of the conference consists of the following people: - Donna Calhoun (Boise State University) - Lois Curfman McInnes (Argonne National Laboratory) - Guido Kanschat (Heidelberg University) - Eirik Keilegavlen (University of Bergen) - Robert Klöfkorn (International Research Institute of Stavanger) - Lawrence Mitchell (Imperial College London) - Christophe Prud'homme (University of Strasbourg) - Garth Wells (University of Cambridge) - Barbara Wohlmuth (Technical University of Munich) We welcome abstracts on topics related to software for - meshing and adaptive mesh refinement, - solvers for large systems of equations, - numerical PDE solvers, - data visualization systems, - user interfaces to scientific software, and - reproducible science. The accepted abstracts will be scheduled for either oral or poster presentations. This workshop does not publish full papers, so submission of a full paper is not required. The deadline for abstract submission is Feb. 1, 2018. For more information, please see the PDESoft18 web page: http://www.iris.no/pdesoft18/. We are looking forward to meeting you in Bergen. With best regards, Robert Klöfkorn, on behalf of the organizing committee -- Dr. Robert Kloefkorn Senior Research Scientist | http://www.iris.no International Research Institute of Stavanger (Bergen office) Thormoehlensgt. 55 | 5006 Bergen Phone: +47 482 93 024

1 0

Firedrake in the Classroom
by Francis Poulin 14 Dec '17

14 Dec '17

Hello everyone, In January I start teaching an introductory course in PDEs. I have taught this many times but this time I plan to have a weekly computer lab where the students can learn to run software (based on firedrake) and then write a lab report. I have a bunch of notebooks that I will give to them one at a time and get them to solve a variety of problems. Before I do I have a few questions. * I presume no one has a problem with this? * There are 40 some students registered in the class. I don't plan to get them to change the code except for parameters and maybe functions. But if students have questions they can go through the usual channels to ask questions, i.e. email and slack? * I know that it is good practice for each firedraker to install their own code but I am going to install it on a server and let them use it, since it will be so much easier for them. If you have any warning as to what might go wrong please let me know. * If it would be helpful to advertise somewhere that I am using firedrake in a course, please let me know how. Cheers, Francis ------------------ Francis Poulin Associate Dean, Undergraduate Studies Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637

2 1

problems installing slepc
by Francis Poulin 14 Dec '17

14 Dec '17

Hello, I recently had to reinstall firedrake, which went well, but then when I tried installing slepc using "firedrake-update --slepc" I got the following error. I am including the log file. Any idea what might be the problem? Cheers, Francis Failed to clone slepc using ssh, falling back to https. Successfully cloned repository slepc. Checking out branch firedrake Successfully checked out branch firedrake Installing slepc/ Traceback (most recent call last): File "../bin/firedrake-update", line 1161, in <module> build_and_install_slepc() File "../bin/firedrake-update", line 757, in build_and_install_slepc install("slepc/") File "../bin/firedrake-update", line 543, in install run_pip_install(["--ignore-installed", package]) File "../bin/firedrake-update", line 513, in run_pip_install check_call(pipinstall + pipargs) File "../bin/firedrake-update", line 350, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/usr/lib/python3.5/subprocess.py", line 626, in check_output **kwargs).stdout File "/usr/lib/python3.5/subprocess.py", line 708, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '--ignore-installed', 'slepc/']' returned non-zero exit status 1 ------------------ Francis Poulin Associate Dean, Undergraduate Studies Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637

2 3