March 2017 - firedrake - imperial.ac.uk

Re: [firedrake] Integro-Differential Equations
by Colin Cotter 17 Mar '17

17 Mar '17

You could also take a look at how we initialise hydrostatic balance in Gusto (in gusto/initialisation_tools.py) which uses the same idea (although not coupled with a timestepping scheme). all the best -cjc On 17 March 2017 at 12:56, Chris Eldred <chris.eldred(a)gmail.com> wrote: > Thanks for the help Colin, I will see if I can work something out based on > this idea. > > -Chris > > On Fri, Mar 17, 2017 at 11:04 AM, Colin Cotter < > colin.cotter(a)imperial.ac.uk> wrote: > >> Well if you have an integral I(s) = \int_0^t f(s) ds then it satisfies >> I_s(s) = f(s). >> >> -cjc >> >> On 17 March 2017 at 09:36, Chris Eldred <chris.eldred(a)gmail.com> wrote: >> >>> Hey Colin, >>> >>> What would that look like? Do you have a reference that describes how >>> this works? >>> >>> Regards, >>> -Chris >>> >>> On Fri, Mar 17, 2017 at 10:32 AM, Colin Cotter < >>> colin.cotter(a)imperial.ac.uk> wrote: >>> >>>> Hi Chris, >>>> Not really, that requires rather specialist tools. What you can do is >>>> introduce an auxiliary variable to write your integro-differential equation >>>> as a system of PDEs, and solve the resulting mixed system. >>>> >>>> all the best >>>> --cjc >>>> >>>> On 17 March 2017 at 09:30, Chris Eldred <chris.eldred(a)gmail.com> wrote: >>>> >>>>> Hey Firedrakers, >>>>> >>>>> I am interested in solving an integro-differential equation, with the >>>>> integral occurring in only one direction, and differentiation in the >>>>> other directions. Has anyone done something like this using Firedrake? >>>>> I would be using an extruded mesh, with extrusion occurring in the >>>>> direction of integration. >>>>> >>>>> If so, is a there a reference or tutorial available? I have attached a >>>>> description of the problem. Any help would be greatly appreciated! >>>>> >>>>> Regards, >>>>> Chris Eldred >>>>> >>>>> -- >>>>> Chris Eldred >>>>> https://www.math.univ-paris13.fr/~eldred/ >>>>> Postdoctoral Fellow, LAGA, University of Paris 13 >>>>> PhD, Atmospheric Science, Colorado State University, 2015 >>>>> DOE Computational Science Graduate Fellow (Alumni) >>>>> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >>>>> chris.eldred(a)gmail.com >>>>> >>>> >>>> >>>> >>>> -- >>>> http://www.imperial.ac.uk/people/colin.cotter >>>> >>>> www.cambridge.org/9781107663916 >>>> >>>> >>>> >>>> _______________________________________________ >>>> firedrake mailing list >>>> firedrake(a)imperial.ac.uk >>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>> >>>> >>> >>> >>> -- >>> Chris Eldred >>> https://www.math.univ-paris13.fr/~eldred/ >>> Postdoctoral Fellow, LAGA, University of Paris 13 >>> PhD, Atmospheric Science, Colorado State University, 2015 >>> DOE Computational Science Graduate Fellow (Alumni) >>> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >>> chris.eldred(a)gmail.com >>> >> >> >> >> -- >> http://www.imperial.ac.uk/people/colin.cotter >> >> www.cambridge.org/9781107663916 >> >> >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> > > > -- > Chris Eldred > https://www.math.univ-paris13.fr/~eldred/ > Postdoctoral Fellow, LAGA, University of Paris 13 > PhD, Atmospheric Science, Colorado State University, 2015 > DOE Computational Science Graduate Fellow (Alumni) > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Problems with SLEPc
by Andrew McRae 17 Mar '17

17 Mar '17

"Adding expressions with non-matching form arguments {0} vs {1}." It looks like you declared one of the forms incorrectly, e.g. used a trial function instead of a test function, or tried to add a form with a test function to a form with no test function, etc. On 12 March 2017 at 12:49, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > I am trying to build on the QG SLEPc demo that I put together a while ago > to solve for the linear instability of a 1D Shallow Water Jet. I've done > this in the past using spectral methods and have had much success, but I > often get spurious modes, which requires very high resolution to remove. > I have been told by a reliable source that the FEM should be less prone to > these spurious modes, which would be great. > > I have a notebook and a python script at the following links: > > https://github.com/francispoulin/firedrakeQG/blob/master/Linear% > 20Stability%20Analysis%20SW%20Jet%20(Firedrake).ipynb > > https://github.com/francispoulin/firedrakeQG/blob/master/LSA_SW_Jet_ > Firedrake.py > > The error comes from the assemble part. I have done this previously with > QG and SW in 2D and managed to get it working. This is only a 1D problem, > so a little bit different, but should be easier. Unfortunately, when I do > try it I get the following error, see below. I have tried different > combinations but am not having any success. > > One issue is that there are three variables: u, v, eta (height). I define > the solution space to be V*V*V where V is a CG space. This is the major > difference compared to what I tried before. > > I am pretty sure that I am getting the syntax wrong here. Can anyone offer > any advice? > > Cheers, Francis > > > (firedrake) fpoulin@fpoulin-Gazelle:~/Research/2015-Ben_Storer/Firedrake$ > python LSA_SW_Jet_Firedrake.py > ('Ro = ', 0.25) > ('Bu = ', 0.0004) > ('profile = ', 'bickley') > Traceback (most recent call last): > File "LSA_SW_Jet_Firedrake.py", line 103, in <module> > petsc_a = assemble(a, mat_type='aij', bcs=bc).M.handle > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/assemble.py", > line 102, in assemble > allocate_only=allocate_only) > File "<decorator-gen-279>", line 2, in _assemble > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/utils.py", > line 62, in wrapper > return f(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/assemble.py", > line 192, in _assemble > kernels = tsfc_interface.compile_form(f, "form", > parameters=form_compiler_parameters, inverse=inverse) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/tsfc_interface.py", > line 193, in compile_form > number_map).kernels > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/caching.py", > line 200, in __new__ > obj = make_obj() > File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/caching.py", > line 190, in make_obj > obj.__init__(*args, **kwargs) > File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/tsfc_interface.py", > line 112, in __init__ > tree = tsfc_compile_form(form, prefix=name, parameters=parameters) > File "/home/fpoulin/software/firedrake/src/tsfc/tsfc/driver.py", line > 44, in compile_form > fd = ufl_utils.compute_form_data(form) > File "/home/fpoulin/software/firedrake/src/tsfc/tsfc/ufl_utils.py", > line 56, in compute_form_data > do_estimate_degrees=do_estimate_degrees, > File "/home/fpoulin/software/firedrake/src/ufl/ufl/ > algorithms/compute_form_data.py", line 387, in compute_form_data > check_form_arity(preprocessed_form, self.original_form.arguments()) > # Currently testing how fast this is > File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", > line 152, in check_form_arity > check_integrand_arity(itg.integrand(), arguments) > File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", > line 145, in check_integrand_arity > args = map_expr_dag(rules, expr, compress=False) > File "/home/fpoulin/software/firedrake/src/ufl/ufl/corealg/map_dag.py", > line 37, in map_expr_dag > result, = map_expr_dags(function, [expression], compress=compress) > File "/home/fpoulin/software/firedrake/src/ufl/ufl/corealg/map_dag.py", > line 86, in map_expr_dags > r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands]) > File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", > line 42, in sum > raise ArityMismatch("Adding expressions with non-matching form > arguments {0} vs {1}.".format(a, b)) > ufl.algorithms.check_arities.ArityMismatch: Adding expressions with > non-matching form arguments (Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, > FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > interval, 1), dim=1), 1)), 0, None), Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, > FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > interval, 1), dim=1), 1)), 1, None)) vs (Argument(WithGeometry( > FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, > FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', > interval, 1), dim=1), 1)), 0, None),). > > > ------------------ > Francis Poulin > 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 <(519)%20888-4567> > >

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Re: [firedrake] Integro-Differential Equations
by Colin Cotter 17 Mar '17

17 Mar '17

Well if you have an integral I(s) = \int_0^t f(s) ds then it satisfies I_s(s) = f(s). -cjc On 17 March 2017 at 09:36, Chris Eldred <chris.eldred(a)gmail.com> wrote: > Hey Colin, > > What would that look like? Do you have a reference that describes how this > works? > > Regards, > -Chris > > On Fri, Mar 17, 2017 at 10:32 AM, Colin Cotter < > colin.cotter(a)imperial.ac.uk> wrote: > >> Hi Chris, >> Not really, that requires rather specialist tools. What you can do is >> introduce an auxiliary variable to write your integro-differential equation >> as a system of PDEs, and solve the resulting mixed system. >> >> all the best >> --cjc >> >> On 17 March 2017 at 09:30, Chris Eldred <chris.eldred(a)gmail.com> wrote: >> >>> Hey Firedrakers, >>> >>> I am interested in solving an integro-differential equation, with the >>> integral occurring in only one direction, and differentiation in the >>> other directions. Has anyone done something like this using Firedrake? >>> I would be using an extruded mesh, with extrusion occurring in the >>> direction of integration. >>> >>> If so, is a there a reference or tutorial available? I have attached a >>> description of the problem. Any help would be greatly appreciated! >>> >>> Regards, >>> Chris Eldred >>> >>> -- >>> Chris Eldred >>> https://www.math.univ-paris13.fr/~eldred/ >>> Postdoctoral Fellow, LAGA, University of Paris 13 >>> PhD, Atmospheric Science, Colorado State University, 2015 >>> DOE Computational Science Graduate Fellow (Alumni) >>> B.S. Applied Computational Physics, Carnegie Mellon University, 2009 >>> chris.eldred(a)gmail.com >>> >> >> >> >> -- >> http://www.imperial.ac.uk/people/colin.cotter >> >> www.cambridge.org/9781107663916 >> >> >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> > > > -- > Chris Eldred > https://www.math.univ-paris13.fr/~eldred/ > Postdoctoral Fellow, LAGA, University of Paris 13 > PhD, Atmospheric Science, Colorado State University, 2015 > DOE Computational Science Graduate Fellow (Alumni) > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Integro-Differential Equations
by Colin Cotter 17 Mar '17

17 Mar '17

Hi Chris, Not really, that requires rather specialist tools. What you can do is introduce an auxiliary variable to write your integro-differential equation as a system of PDEs, and solve the resulting mixed system. all the best --cjc On 17 March 2017 at 09:30, Chris Eldred <chris.eldred(a)gmail.com> wrote: > Hey Firedrakers, > > I am interested in solving an integro-differential equation, with the > integral occurring in only one direction, and differentiation in the > other directions. Has anyone done something like this using Firedrake? > I would be using an extruded mesh, with extrusion occurring in the > direction of integration. > > If so, is a there a reference or tutorial available? I have attached a > description of the problem. Any help would be greatly appreciated! > > Regards, > Chris Eldred > > -- > Chris Eldred > https://www.math.univ-paris13.fr/~eldred/ > Postdoctoral Fellow, LAGA, University of Paris 13 > PhD, Atmospheric Science, Colorado State University, 2015 > DOE Computational Science Graduate Fellow (Alumni) > B.S. Applied Computational Physics, Carnegie Mellon University, 2009 > chris.eldred(a)gmail.com > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Integro-Differential Equations
by Chris Eldred 17 Mar '17

17 Mar '17

Hey Firedrakers, I am interested in solving an integro-differential equation, with the integral occurring in only one direction, and differentiation in the other directions. Has anyone done something like this using Firedrake? I would be using an extruded mesh, with extrusion occurring in the direction of integration. If so, is a there a reference or tutorial available? I have attached a description of the problem. Any help would be greatly appreciated! Regards, Chris Eldred -- Chris Eldred https://www.math.univ-paris13.fr/~eldred/ Postdoctoral Fellow, LAGA, University of Paris 13 PhD, Atmospheric Science, Colorado State University, 2015 DOE Computational Science Graduate Fellow (Alumni) B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com

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Re: [firedrake] Installing firedrake issues
by David Ham 15 Mar '17

15 Mar '17

Hi Will, The error you got was from the PETSc installer, so you need to pass those options to PETSc, not directly to firedrake-install. export PETSC_CONFIGURE_OPTIONS="--download-fblaslapack=1" python firedrake-install --no-package-manager --disable-ssh Also note that you probably don't want --honour-pythonpath set. Unless you have a very special reason why the firedrake virtualenv needs to see external python packages, it is much safer to unset PYTHONPATH. Regards, David On Wed, 15 Mar 2017 at 11:12 William Booker <scwb(a)leeds.ac.uk> wrote: Dear Firedrakers, Running the install script $ python firedrake-install --no-package-manager --disable-ssh --honour-pythonpath gave me the following error: Could not find a functional BLAS. Run with --with-blas-lib=<lib> to indicate the library containing BLAS. Or --download-fblaslapack=1 to have one automatically downloaded and installed But the download option does not seem to be a recognised command for the install script $ python firedrake-install --no-package-manager --disable-ssh --honour-pythonpath --download-fblaslapack=1 firedrake-install: error: unrecognized arguments: --download-fblaslapack=1 Thanks Will -- Dr David Ham Department of Mathematics Imperial College London

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Installing firedrake issues
by William Booker 15 Mar '17

15 Mar '17

Dear Firedrakers, Running the install script $ python firedrake-install --no-package-manager --disable-ssh --honour-pythonpath gave me the following error: Could not find a functional BLAS. Run with --with-blas-lib=<lib> to indicate the library containing BLAS. Or --download-fblaslapack=1 to have one automatically downloaded and installed But the download option does not seem to be a recognised command for the install script $ python firedrake-install --no-package-manager --disable-ssh --honour-pythonpath --download-fblaslapack=1 firedrake-install: error: unrecognized arguments: --download-fblaslapack=1 Thanks Will

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Problems with SLEPc
by Francis Poulin 12 Mar '17

12 Mar '17

Hello, I am trying to build on the QG SLEPc demo that I put together a while ago to solve for the linear instability of a 1D Shallow Water Jet. I've done this in the past using spectral methods and have had much success, but I often get spurious modes, which requires very high resolution to remove. I have been told by a reliable source that the FEM should be less prone to these spurious modes, which would be great. I have a notebook and a python script at the following links: https://github.com/francispoulin/firedrakeQG/blob/master/Linear%20Stability… https://github.com/francispoulin/firedrakeQG/blob/master/LSA_SW_Jet_Firedra… The error comes from the assemble part. I have done this previously with QG and SW in 2D and managed to get it working. This is only a 1D problem, so a little bit different, but should be easier. Unfortunately, when I do try it I get the following error, see below. I have tried different combinations but am not having any success. One issue is that there are three variables: u, v, eta (height). I define the solution space to be V*V*V where V is a CG space. This is the major difference compared to what I tried before. I am pretty sure that I am getting the syntax wrong here. Can anyone offer any advice? Cheers, Francis (firedrake) fpoulin@fpoulin-Gazelle:~/Research/2015-Ben_Storer/Firedrake$ python LSA_SW_Jet_Firedrake.py ('Ro = ', 0.25) ('Bu = ', 0.0004) ('profile = ', 'bickley') Traceback (most recent call last): File "LSA_SW_Jet_Firedrake.py", line 103, in <module> petsc_a = assemble(a, mat_type='aij', bcs=bc).M.handle File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/assemble.py", line 102, in assemble allocate_only=allocate_only) File "<decorator-gen-279>", line 2, in _assemble File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/assemble.py", line 192, in _assemble kernels = tsfc_interface.compile_form(f, "form", parameters=form_compiler_parameters, inverse=inverse) File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 193, in compile_form number_map).kernels File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/caching.py", line 200, in __new__ obj = make_obj() File "/home/fpoulin/software/firedrake/src/PyOP2/pyop2/caching.py", line 190, in make_obj obj.__init__(*args, **kwargs) File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 112, in __init__ tree = tsfc_compile_form(form, prefix=name, parameters=parameters) File "/home/fpoulin/software/firedrake/src/tsfc/tsfc/driver.py", line 44, in compile_form fd = ufl_utils.compute_form_data(form) File "/home/fpoulin/software/firedrake/src/tsfc/tsfc/ufl_utils.py", line 56, in compute_form_data do_estimate_degrees=do_estimate_degrees, File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/compute_form_data.py", line 387, in compute_form_data check_form_arity(preprocessed_form, self.original_form.arguments()) # Currently testing how fast this is File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 152, in check_form_arity check_integrand_arity(itg.integrand(), arguments) File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 145, in check_integrand_arity args = map_expr_dag(rules, expr, compress=False) File "/home/fpoulin/software/firedrake/src/ufl/ufl/corealg/map_dag.py", line 37, in map_expr_dag result, = map_expr_dags(function, [expression], compress=compress) File "/home/fpoulin/software/firedrake/src/ufl/ufl/corealg/map_dag.py", line 86, in map_expr_dags r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands]) File "/home/fpoulin/software/firedrake/src/ufl/ufl/algorithms/check_arities.py", line 42, in sum raise ArityMismatch("Adding expressions with non-matching form arguments {0} vs {1}.".format(a, b)) ufl.algorithms.check_arities.ArityMismatch: Adding expressions with non-matching form arguments (Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 1)), 0, None), Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 1)), 1, None)) vs (Argument(WithGeometry(FunctionSpace(<firedrake.mesh.MeshTopology object at 0x7f2a458c5290>, FiniteElement('Lagrange', interval, 2), name=None), Mesh(VectorElement(FiniteElement('Lagrange', interval, 1), dim=1), 1)), 0, None),). ------------------ Francis Poulin 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

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Interfacing directly with PETSc
by Florian Bruckner 10 Mar '17

10 Mar '17

hi, i am wondering if the method to interace PETSc ( http://www.firedrakeproject.org/petsc-interface.html) would also work in parallel? i tried a slightly modified code (since i am using dolfin at the moment), which works on one processor but fails in parallel. Is there an easy way to pack a sequence of dolfin / firedrake operators into one parallel petsc opterator (matshell) thanks a lot best wishes Florian Bruckner

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firedrake-install script fails using wrong C++ compiler
by Buesing, Henrik 10 Mar '17

10 Mar '17

Dear Firedrake developers, I'm trying to install Firedrake with the install script on CentOS Linux release 7.3.1611. I'm doing a "firedrake-install --no_package_manager --disable-ssh". The script fails when building pyop2/sparsity.cpp, because it did not find mpi.h. I notice that he uses gcc for compiling while he should use the appropriate MPI Wrapper function mpicxx. There are environment variables available in my system ($MPICC, $MPICXX, $MPIFC) pointing to the appropriate MPI Wrappers (mpicc, mpicxx, mpif90). How do I tell the install script to use these? I notice the option "--mpicc" for the C compiler, but how do I set the C++ (and Fortran) compiler? Thank you! Henrik -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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