February 2016 - firedrake - imperial.ac.uk

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) -------------------------------------------------------------------------------------------

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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

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Facetnormal compile error
by William Booker 23 Feb '16

23 Feb '16

Dear all, I've been trying a shallow water dam break problem, but currently have a compile error Discontinuous type FacetNormal must be restricted. Would this be because of how I've defined my roe averages or is there something further wrong in my definition of the residual? Regards, Will

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Re: [firedrake] Restricting a test function space
by David Ham 22 Feb '16

22 Feb '16

Hi Will, Can you provide a bit more context as to what you are attempting to do? It is indeed the case that Dirichlet boundary conditions restrict the test space in that sense (this is often referred to as "lifting" the boundary conditions). However it's not generally possible to lift the component of a vector field normal to the boundary (because this does not directly correspond to a particular set of degrees of freedom), so if you can provide a little more context about the problem, we may be able to provide a suitable alternative. Regards, David On Wed, 17 Feb 2016 at 19:50 William Booker <scwb(a)leeds.ac.uk> wrote: > > > Dear all, > > If I wanted to restrict a test function space, say $\underline{\Phi} . > \underline{n}$ = 0 , would that be covered by including a dirichlet > boundary condition for the test function in the solver options? > > Regards > Will >

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Re: [firedrake] Time loop
by Andrew McRae 19 Feb '16

19 Feb '16

What is in the .err file and the corresponding .c file? On 19 Feb 2016 13:15, "Angwenyi David" <kipkoej(a)gmail.com> wrote: > Hi all, > > I still have a problem with the time loop. I get the following error. > > Traceback (most recent call last): > > File "<stdin>", line 3, in <module> > > File > "/Users/master/firedrake/lib/python2.7/site-packages/firedrake/constant.py", > line 116, in assign > > self.dat.data = value > > File "<decorator-gen-21>", line 2, in data > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", > line 115, in modifies > > retval = method(self, *args, **kwargs) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line > 2761, in data > > _trace.evaluate(set(), set([self])) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line > 170, in evaluate > > comp._run() > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line > 4070, in _run > > return self.compute() > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line > 4111, in compute > > fun = self._jitmodule > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line > 64, in __get__ > > obj.__dict__[self.__name__] = result = self.fget(obj) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/sequential.py", > line 151, in _jitmodule > > direct=self.is_direct, iterate=self.iteration_region) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/caching.py", > line 203, in __new__ > > obj = make_obj() > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/caching.py", > line 193, in make_obj > > obj.__init__(*args, **kwargs) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/host.py", line > 700, in __init__ > > self.compile() > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/host.py", line > 801, in compile > > compiler=compiler.get('name')) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/compilation.py", > line 292, in load > > dll = compiler.get_so(src, extension) > > File > "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/compilation.py", > line 146, in get_so > > Compile errors in %s""" % (e.cmd, e.returncode, logfile, errfile)) > > pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', > '-Wall', '-framework', 'Accelerate', '-march=native', '-O3', > '-I/Users/master/firedrake/lib/python2.7/site-packages/petsc/include', > '-I/Users/master/firedrake/lib/python2.7/site-packages/pyop2', '-msse', > '-o', > '/var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.so.tmp', > '/var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.c', > '-dynamiclib', > '-L/Users/master/firedrake/lib/python2.7/site-packages/petsc/lib', > '-Wl,-rpath,/Users/master/firedrake/lib/python2.7/site-packages/petsc/lib', > '-lpetsc', '-lm']" return error status 1. > > Unable to compile code > > Compile log in > /var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.log > > Compile errors in > /var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.err > > > How can I fix it? > > Angwenyi >

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Time loop
by Angwenyi David 19 Feb '16

19 Feb '16

Hi all, I still have a problem with the time loop. I get the following error. Traceback (most recent call last): File "<stdin>", line 3, in <module> File "/Users/master/firedrake/lib/python2.7/site-packages/firedrake/constant.py", line 116, in assign self.dat.data = value File "<decorator-gen-21>", line 2, in data File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", line 115, in modifies retval = method(self, *args, **kwargs) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 2761, in data _trace.evaluate(set(), set([self])) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 170, in evaluate comp._run() File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 4070, in _run return self.compute() File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/base.py", line 4111, in compute fun = self._jitmodule File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/sequential.py", line 151, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/host.py", line 700, in __init__ self.compile() File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/host.py", line 801, in compile compiler=compiler.get('name')) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/compilation.py", line 292, in load dll = compiler.get_so(src, extension) File "/Users/master/firedrake/lib/python2.7/site-packages/pyop2/compilation.py", line 146, in get_so Compile errors in %s""" % (e.cmd, e.returncode, logfile, errfile)) pyop2.exceptions.CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-framework', 'Accelerate', '-march=native', '-O3', '-I/Users/master/firedrake/lib/python2.7/site-packages/petsc/include', '-I/Users/master/firedrake/lib/python2.7/site-packages/pyop2', '-msse', '-o', '/var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.so.tmp', '/var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.c', '-dynamiclib', '-L/Users/master/firedrake/lib/python2.7/site-packages/petsc/lib', '-Wl,-rpath,/Users/master/firedrake/lib/python2.7/site-packages/petsc/lib', '-lpetsc', '-lm']" return error status 1. Unable to compile code Compile log in /var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.log Compile errors in /var/folders/8q/tv2c50fj0n3_27j_3yjmyv7c0000gp/T/pyop2-cache-uid502/59ddbd69d6d404a58876bfb1da21738a_p675.err How can I fix it? Angwenyi

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Restricting a test function space
by William Booker 17 Feb '16

17 Feb '16

Dear all, If I wanted to restrict a test function space, say $\underline{\Phi} . \underline{n}$ = 0 , would that be covered by including a dirichlet boundary condition for the test function in the solver options? Regards Will

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dimension with external mesh
by Tomasz Salwa [RPG] 17 Feb '16

17 Feb '16

Dear All, How do I instruct Firedrake about the dimension of the problem when using external mesh from gmsh? I had a working code with utility mesh. I changed: mesh = RectangleMesh(nx, nz, Lx, Lz) V = VectorFunctionSpace(mesh, "CG", 1) to: mesh = Mesh("mesh.msh") V = VectorFunctionSpace(mesh, "CG", 1, dim=2) yet I get the error at further expressions that worked previously: ... File "/home/mmtjs/work/programs/lin_coupled_fd_2d/lib/beam.py", line 73, in initialize_solvers + self.mu * ( fd.inner( delX, delv_B + fd.transpose(delv_B) ) ) File "/opt/firedrake/1510/lib/python2.7/site-packages/ufl/exproperators.py", line 177, in _add return Sum(self, o) File "/opt/firedrake/1510/lib/python2.7/site-packages/ufl/algebra.py", line 55, in __new__ error("Can't add expressions with different shapes.") File "/opt/firedrake/1510/lib/python2.7/site-packages/ufl/log.py", line 151, in error raise self._exception_type(self._format_raw(*message)) ufl.log.UFLException: Can't add expressions with different shapes. Thank you, Tomasz

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Par Loop Issues
by Gregory, Alastair 17 Feb '16

17 Feb '16

Hi firedrakers, Is there a limit to the number of Dictionary inputs you can put into parloop(kernel,dx,Dictionary)? I have to input an arbitrary amount of functions (N) into a kernel, via appending them to a dictionary, and then carry out a simple linear expression using all functions for each cell. As for the linear combination, it is simply, a(1)*function(1) + ..... + a(N)*function(N) where a's are constants. I do some string appending etc to get the above as a string that I can put directly into a kernel. However, when I input over ~50 functions (which is a lot but theoretically C should be able to do this) the linear expression returns NaNs for each of the cells. The kernel seems to be correctly implemented, however it looks like the C under the hood is breaking down. Could anyone help? 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) -------------------------------------------------------------------------------------------

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Re: [firedrake] Periodic rectangle mesh in x-direction
by Colin Cotter 11 Feb '16

11 Feb '16

Hi Tuomas, This is easy with quads, as we just extrude a periodic interval. For triangles I suggest to mesh a cylinder embedded in 3D, and then prune it, like we do for the other periodic meshes. all the best --cjc On 10 February 2016 at 20:24, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > Hi all, > > Is there an easy way to create a rectangular mesh with two periodic > boundaries? PeriodicRectangleMesh is a torus so all 4 sides are > connected. I'd need a triangular RectangleMesh where only sides x=0 and > x=Lx are connected. > > - Tuomas > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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