- firedrake - imperial.ac.uk

Compile error
by William Booker 18 Mar '16

18 Mar '16

Dear all, I've been trying to compile the attached code for a compressible acoustic wave, but I've been getting the following error. How do I fix this? Traceback (most recent call last): File "compressible_acoustic.py", line 118, in <module> solve(a == L, out) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", line 120, in solve _solve_varproblem(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", line 147, in _solve_varproblem solver.solve() File "<decorator-gen-277>", line 2, in solve File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/profiling.py", line 203, in wrapper return f(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/variational_solver.py", line 173, in solve self.snes.solve(None, v) File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve (src/petsc4py.PETSc.c:169677) File "PETSc/petscsnes.pxi", line 253, in petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33478) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving_utils.py", line 187, in form_function nest=problem._nest) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 68, in assemble inverse=inverse, nest=nest) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/assemble.py", line 101, in _assemble inverse=inverse) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/ffc_interface.py", line 279, in compile_form ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/PyOP2-0.11.0_397_g9860f8d-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/ffc_interface.py", line 188, in __init__ ffc_tree = ffc_compile_form(form, prefix=name, parameters=parameters) File "build/bdist.linux-x86_64/egg/ffc/compiler.py", line 159, in compile_form File "build/bdist.linux-x86_64/egg/ffc/representation.py", line 108, in compute_ir File "build/bdist.linux-x86_64/egg/ffc/representation.py", line 351, in _compute_integral_ir File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", line 95, in compute_integral_ir File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", line 191, in _transform_integrals_by_type File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturerepresentation.py", line 223, in _transform_integrals File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 772, in generate_terms File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 548, in index_sum File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 511, in indexed File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 724, in component_tensor File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 103, in visit r = h(o, *[self.visit(op) for op in o.ufl_operands]) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 511, in indexed File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 668, in negative_restricted File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/ufl/algorithms/transformer.py", line 107, in visit r = h(o) File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 474, in coefficient File "build/bdist.linux-x86_64/egg/ffc/quadrature/optimisedquadraturetransformer.py", line 558, in create_function File "build/bdist.linux-x86_64/egg/ffc/quadrature/quadraturetransformerbase.py", line 1290, in _create_function_name UnboundLocalError: local variable 'loop_index' referenced before assignment

1 0

TSFC talk at Imperial this Thursday
by Miklós Homolya 18 Mar '16

18 Mar '16

Dear Firedrakers, especially those based in London. I will give a talk at Imperial College, titled: "TSFC: a structure-preserving form compiler" this Thursday (17 March 2016), starting at 3pm in the Grantham Boardroom. Abstract: Since early February 2016 Firedrake comes with TSFC, a new compiler which replaced a modified version of FFC. TSFC provides good compile-time performance for complicated forms, which was crucial to support non-affine elements in our master branches. It was designed with some anticipated future needs (e.g. of FInAT) in mind as well. In this talk I will give an overview of why TSFC was born, explain the core ideas behind it, and walk through a simple example to show how TSFC works. Kind regards, Miklós

2 3

Debug and Optimised mode
by Floriane Gidel [RPG] 17 Mar '16

17 Mar '16

Dear all, Is there a debug and/or optimised mode in Firedrake, to speed up the simulations? How can I access it? Thanks a lot, Floriane

3 13

Instant and petsc4py issues with DMDA?
by Chris Eldred 10 Mar '16

10 Mar '16

Hey All, I am not sure if this is the correct mailing list for this, but I am using instant and petsc4py from a Firedrake install so I figured I would start here. I am trying to get instant to compile a (minimal) example of a C function that takes in a DM (actually a DMDA), a Vec and a Mat, and then call this compiled function from a python script. Here is the code: ****************************** import sys, petsc4py petsc4py.init(sys.argv) from petsc4py import PETSc import instant import os include_dirs = [os.path.join(os.getenv('PETSC_DIR'), 'include'), petsc4py.get_include(), '/usr/lib/openmpi/include', '/usr/lib/openmpi/include/openmpi', ] swig_include_dirs = [petsc4py.get_include()] library_dirs = [os.path.join(os.getenv('PETSC_DIR'),'lib')] libraries = ['petsc'] test_routine = r""" #ifdef SWIG #%include "petsc4py/petsc4py.i" #endif #include <petsc.h> PetscErrorCode testfunction(DM da, Mat A, Vec v) { } """ testfunction = instant.build_module(code=test_routine, include_dirs=include_dirs, library_dirs=library_dirs, libraries=libraries, swig_include_dirs=swig_include_dirs).testfunction da = PETSc.DMDA().create([10,],stencil_width=1,comm=PETSc.COMM_WORLD) mat = PETSc.Mat().create(comm=PETSc.COMM_WORLD) vec = PETSc.Vec().create(comm=PETSc.COMM_WORLD) testfunction(da,mat,vec) ******************************************** This fails with: File "minimal_instant_fail_example.py", line 37, in <module> testfunction(da,mat,vec) TypeError: in method 'testfunction', argument 1 of type 'DM' It looks like DMDA is not being properly recognized as a subclass of DM? Is there something else that I am missing? Any help is greatly appreciated! Regards, -Chris Eldred -- Chris 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

2 4

(no subject)
by William Booker 10 Mar '16

10 Mar '16

Dear all, I've implemented my boundary conditions weakly in my compressible stratified problem, but I get the following error now: How should I proceed to fix this? Will Traceback (most recent call last): File "compressible.py", line 181, in <module> solve(a == L, out) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", line 120, in solve _solve_varproblem(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving.py", line 145, in _solve_varproblem options_prefix=options_prefix) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/variational_solver.py", line 232, in __init__ super(LinearVariationalSolver, self).__init__(*args, **kwargs) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/variational_solver.py", line 118, in __init__ if ctx.is_mixed: File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/solving_utils.py", line 152, in is_mixed return self._jacs[-1]._M.sparsity.shape != (1, 1) File "/home/cserv1_a/apps/install/firedrake/0.12.0/lib64/python2.7/site-packages/firedrake/function.py", line 248, in __getattr__ return getattr(self._data, name) AttributeError: 'CoordinatelessFunction' object has no attribute '_M' Exception AttributeError: "'LinearVariationalSolver' object has no attribute '_parameters'" in <bound method LinearVariationalSolver.__del__ of <firedrake.variational_solver.LinearVariationalSolver object at 0x7fcc08180090>> ignored

2 5

Deadline extended: Student travel grants for Workshop on “DG methods FEM software”, Bath Jun 2016
by Eike Mueller 03 Mar '16

03 Mar '16

Dear all, we still have a small number of travel grants for students to attend our workshop in Bath this summer. We therefore decided to extend the deadline until Friday, 18th Mar. We would be very grateful if you could bring this to the attention of any suitable candidates and encourage them to apply. Please see the original announcement below. Thank you very much, Eike > Title: Student Travel grants for Workshop on “Higher-order DG > methods and finite element software on modern architectures”, Bath > 31 May - 2nd Jun 2016 > > > We are organising a 3-day workshop on finite element software and > applications in Bath this summer, > see https://sites.google.com/site/bathdgworkshop/ for details. > > > Confirmed plenary speakers are: Markus Geveler (Dortmund), Frank > Giraldo (Monterey), David Ham (Imperial), Rob Kirby (Baylor), Martin > Kronbichler (TUM), Tom Melvin (Met Office), Steffen > Müthing (Heidelberg), Marie Rognes (Simula). In addition there will > be representatives from major chip manufacturers and HPC vendors. > > > Although participation is by invitation-only, we are offering a > small number of grants for students to attend the meeting. The exact > amount available depends on the number of successful applications, > but is likely in the range of £100-£200 per person. > > > To apply, please send us a brief statement (not more than 2 pages) > with the following information by 18th Mar 2016: > > > (1) Description of your research interests > (2) Motivation for attending the workshop > (3) List of publications > (4) Short supporting statement from your supervisor > > > In addition, please state whether you are interested in giving a > presentation at the workshop.

1 0

Re: [firedrake] Feeding extra args into Kernels
by Colin Cotter 02 Mar '16

02 Mar '16

Just to translate this more meaningfully, I think Lawrence at some point implemented an optional argument to pass a path to a C library to link against when compiling a kernel - maybe on a branch, it would be good if this could make it into the trunk version (Ali reports that it isn't). all the best --cjc On 2 March 2016 at 12:28, Gregory, Alastair <a.gregory14(a)imperial.ac.uk> wrote: > Hi, > > > I need to feed arguments (a C library) into a kernel that goes into a > parallel loop. I have tried using the kernel function in > https://github.com/OP2/PyOP2/pull/476 to do, > > > Kernel(str,args*), > > > but when I put this into par_loop, I get the error, 'Kernel' object > doesn't have 'replace', as Kernel isn't a string, it's as above. > > > Does anyone know how I go about placing the Kernel with the extra > arguments into par_loop? > > > Many Thanks, > > > > > *Alastair Gregory* > > ------------------------------------------------------------------------------------------ > > *Numerical Analysis Research Postgraduate Imperial College London -** > Grantham Institute of Climate Change * > Room 759 Huxley Building, South Kensington > *(Tel: 07794 243913) | (Email: a.gregory14(a)imperial.ac.uk > <a.gregory14(a)imperial.ac.uk>)* > > ------------------------------------------------------------------------------------------- > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

2 1

Feeding extra args into Kernels
by Gregory, Alastair 02 Mar '16

02 Mar '16

Hi, I need to feed arguments (a C library) into a kernel that goes into a parallel loop. I have tried using the kernel function in https://github.com/OP2/PyOP2/pull/476 to do, Kernel(str,args*), but when I put this into par_loop, I get the error, 'Kernel' object doesn't have 'replace', as Kernel isn't a string, it's as above. Does anyone know how I go about placing the Kernel with the extra arguments into par_loop? Many Thanks, Alastair Gregory ------------------------------------------------------------------------------------------ Numerical Analysis Research Postgraduate Imperial College London - Grantham Institute of Climate Change Room 759 Huxley Building, South Kensington (Tel: 07794 243913) | (Email: a.gregory14(a)imperial.ac.uk) -------------------------------------------------------------------------------------------

1 0

Python Modules Not Installed in Virtual Environment
by Gregory, Alastair 29 Feb '16

29 Feb '16

Hi Firedrakers, After updating Firedrake for the new form compiler, scipy and matplotlib don't exist according to python and ipython in the virtual environment. 'No module named scipy' Does anyone know what's happening? Many Thanks, Alastair Gregory ------------------------------------------------------------------------------------------ Numerical Analysis Research Postgraduate Imperial College London - Grantham Institute of Climate Change Room 759 Huxley Building, South Kensington (Tel: 07794 243913) | (Email: a.gregory14(a)imperial.ac.uk) -------------------------------------------------------------------------------------------

2 1

Firedrake Zenodo integration and Github move
by David Ham 24 Feb '16

24 Feb '16

Dear Firedrakers, As of today, Firedrake integrates with Zenodo. What this means for you is that there is a streamlined mechanism for generating a set of DOIs which record the precise version of Firedrake and its dependencies which you used in a publication. We think this is a big step towards best practice reproducible computational science. The instructions on how to use this are documented at: http://firedrakeproject.org/zenodo.html One side effect of this is that Firedrake's forks of FIAT, UFL, PETSc and PETSc4py are now on GitHub rather than Bitbucket. Your Firedrake install should automatically pick up the new repositories next time you run firedrake-update. If you are using your own branches of any component, these will also automatically repoint at the GitHub repo rather than Bitbucket, so future changes and pull requests will happen on GitHub. Regards, David

1 0