November 2015 - firedrake - imperial.ac.uk

Re: [firedrake] help (firedrake)
by David Ham 25 Nov '15

25 Nov '15

Dear David, Thanks for downloading Firedrake. Firedrake is a python package, not an executable, so one would not expect to type "firedrake" on the Python command line. First, you need to ensure that python will see your installed Firedrake. If you installed using the install script, then you have to source the activate script for the Python virtualenv in which the script lives. If your shell is in the top directory of your firedrake install, the command to do this is: . ./bin/activate note the first . which is important. Once you have done this, then from the python (preferably ipython) shell, you can "from firedrake import *" and you are good to go. You probably want to start by trying some of the tutorials at http://firedrakeproject.org/documentation.html For future support requests, please use the firedrake mailing list, to which I have copied this answer. You'll need to subscribe at https://mailman.ic.ac.uk/mailman/listinfo/firedrake Regards, David On Tue, 24 Nov 2015 at 13:52 Angwenyi David <kipkoej(a)gmail.com> wrote: > Dear sir, > > I am doctoral student of Prof. Dr. Sebastian Reich, Universität Potsdam. > We have been trying to install and run firedrake. It has been installed > successfully but I seemingly cannot start it off by typing ‘firedrake’ at > the Python command line; or rather, when I do try it this way, I get a > feedback: command not found. Could you please advise. > > Thanks in advance. > > Angwenyi David

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Re: [firedrake] weirdness on bendy branch
by Fabio Luporini 23 Nov '15

23 Nov '15

Hi Stephan. Thanks, I will look into this first thing next week and will get back to you. Cheers -- Fabio 2015-11-19 14:59 GMT+00:00 Kramer, Stephan <s.kramer(a)imperial.ac.uk>: > Hey guys > > More weirdness related to facet integrals from IP viscosity that only > appears with COFFEE optimisations. This time both on the bendy branches > and on master (of last week). In the code below, the matrices M, Ms and > M1+M2 should all be the same. > > For DG1 they are not equal on a recent (last week, before any sprint > merges) install of firedrake/ffc/ufl/coffee on master. It is also > incorrect on an older install I had, so it's not a recent thing. DG1 > does however produce the right answer on the bendy branches: firedrake > (bendy_changes) + ffc/ufl (fd_bendy) + coffee (master). > > For RT1 on the other hand it's the opposite: the matrices are correct > and equal on master, but with bendy some of them are different from the > correct answer. > > All of this only if use COFFEE optimisation, i.e. with > parameters['coffee']={} the matrices are correct and all equal. > > I realize at this point the best thing to do is probably to wait if this > all gets magically fixed when the sprint is over - will report back if > not - but just thought to let you guys know already > > Cheers > Stephan > > from firedrake import * > mesh2d = UnitSquareMesh(1,1) > U = VectorFunctionSpace(mesh2d, "DG", 1) > v = TestFunction(U) > u = Function(U) > > #parameters['coffee']={} > n = FacetNormal(mesh2d) > > def outer_jump(v, n): > return outer(v('+'), n('+'))+outer(v('-'), n('-')) > > F1 = inner(outer_jump(v, n), outer_jump(u,n))*dS > F2 = inner(outer_jump(v, n), outer_jump(n,u))*dS > F = inner(outer_jump(v, n), outer_jump(u,n)+outer_jump(n,u))*dS > > M1 = assemble(derivative(F1, u)).M.values > M2 = assemble(derivative(F2, u)).M.values > Ms = assemble(derivative(F1+F2, u)).M.values > M = assemble(derivative(F, u)).M.values > print abs(M-(M1+M2)).max() > print abs(M-Ms).max() > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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matrix entries
by Tomasz Salwa [RPG] 23 Nov '15

23 Nov '15

Dear Firedrakers, I have a problem similar to Anna's previous one. How can and I access and modify matrices assembled for a given form, so that they can be used later in solvers? For reference, my code is in: https://github.com/mmtjs/lin_coupled_fd_2d_oop with description of the scheme that I would like to implement in "FSI_scheme.pdf" (black terms clear - no coupling; blue - UFL suffices to define; red - I need to build the matrices directly). e.g. I have the following code: ... def initialize_solvers(self): .... a_phi = fd.dot( self.n_vec, fd.grad(self.trial) ) * self.v * fd.ds_t - fd.dot( fd.grad(self.trial), fd.grad(self.v) ) * fd.dx L_phi = self.Pw * self.v * fd.ds_v(2) a_eta = self.trial * self.v * fd.ds_t L_eta = ( self.eta + self.dt * fd.dot( self.n_vec, fd.grad(self.phi) ) ) * self.v * fd.ds_t ... I would like to access the PETSc matices corresponding to the forms, modify the entries and solve the system with the updated matrices. How can I find out to which nodes the given entries correspond? I need to map between two domains, which I did for functions, but in case of matrices it may be different. Thank you, Tomasz

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Jacobian wrong with -snes_fd_color
by Buesing, Henrik 23 Nov '15

23 Nov '15

Dear all, I have a lot of coefficients in my form, e.g. 1) Calculate density rhow pointwise from temperature and pressure via interpolation of a table rhow = Function(DG1) rhow.dat.data[:]=calc_rhow(temp,Tsat,pw) 2) Averaging rhow_avg = (rhow('+') + rhow('-')) / 2.0 3) Use rhow_avg in my form. This works all right for calulcating F(u), but fails when computing the Jacobian. Since I calculate things pointwise and providing all the derivatives is not so easy I use -snes_fd_color. What I would want to happen is that the function calc_rhow is called every time rhow_avg is needed. This seems not to be the case. Rather the coefficient is assumed constant and thus the derivative is zero. How can I make sure that the function calc_rhow is called every time I need rhow_avg? 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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Errors
by Justin Chang 20 Nov '15

20 Nov '15

Hi all, Just the latest update, and got these errors when trying to output a solution that is in CG1 space: Traceback (most recent call last): File "2D_OS_point_ex1.py", line 309, in <module> outFile_psiA << u0_A File "/Users/justin/Software/firedrake/src/firedrake/firedrake/io.py", line 110, in __lshift__ self._file << data File "/Users/justin/Software/firedrake/src/firedrake/firedrake/io.py", line 524, in __lshift__ self._update_PVD(data) File "/Users/justin/Software/firedrake/src/firedrake/firedrake/io.py", line 542, in _update_PVD new_vtk << function File "/Users/justin/Software/firedrake/src/firedrake/firedrake/io.py", line 188, in __lshift__ coords_p1 = is_family1(ce, 'Lagrange') or is_family1(ce, 'Q') File "/Users/justin/Software/firedrake/src/firedrake/firedrake/io.py", line 157, in is_family1 if isinstance(e, (hc.HDiv, hc.HCurl)): AttributeError: 'module' object has no attribute 'HDiv' I noticed that there have been many updates/changes regarding UFL, so could this have something to do with it? On a side note, I also got these warnings: *Mesh.cell() is deprecated, please use .ufl_cell() instead.* Thanks, Justin

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absolute value of gradient
by George Ovchinnikov 20 Nov '15

20 Nov '15

Hello folks, I have a scalar field in 2D, $w$, say: V = FunctionSpace(mesh, "CG", 1) w = Function(V) w.interpolate(Expression("1")) and I need too find an norm of grad(w) in every point of the given area, i.e. get a scalar field back. I've found no way to iterate through individual elements of grad(w) to be able to do in manually, neither abs(grad(w)) or something similar works. Any ideas? Do I need to solve some variational problem for this, too? Sincerely, George

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weirdness on bendy branch
by Stephan Kramer 19 Nov '15

19 Nov '15

Hey guys I've been trying to implement a simple IP viscosity scheme for DG, but was getting weird results, which I think I've tracked down to a bug related to fd_bendy. If I run the following: from firedrake import * mesh2d = UnitSquareMesh(1,1) V = VectorFunctionSpace(mesh2d, "DG", 1) uv = Function(V) U_test = TestFunction(V) n = FacetNormal(mesh2d) F1 = dot(jump(U_test[0], n), jump(uv[0], n))*dS F2 = -dot(avg(grad(U_test[0])), jump(uv[0], n))*dS F=F1+F2 F0 = dot(jump(U_test[0],n)-avg(grad(U_test[0])), jump(uv[0], n))*dS M=assemble(derivative(F, uv)).M.values M1=assemble(derivative(F1, uv)).M.values M2=assemble(derivative(F2, uv)).M.values M0=assemble(derivative(F0, uv)).M.values I really expect M, M1+M2 and M0 to be all the same. On firedrake master (and in fact Dolfin) these are all the same indeed. But in my fd_bendy enviroment (fd_bendy for ffc and ufl, bendy_changes for firedrake) the values for M are different. Final piece of information is that if I use parameters['coffee']={}, everything is fine again. Other than that I'm stuck though, so I'd much appreciate any pointers into what I could check next Cheers Stephan

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Multi-grid preconditioning
by Justin Chang 16 Nov '15

16 Nov '15

Hi everyone, Is there support for Multi-grid preconditioning? I think I saw somewhere where this was not supported yet. Because applying -pc_type gamg for my mixed forms returns me errors. Thanks, Justin

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path issue? maybe?
by Wingate, Beth 15 Nov '15

15 Nov '15

All, Between the Gung Ho conference and this evening, I’ve managed to change something enough so that I can’t get the firedrake demos to work. Then, I finally just imported firedrake at the python command prompt and that didn’t work either. Any ideas? Thanks! Beth Wingate b.wingate(a)exeter.ac.uk<mailto:b.wingate@exeter.ac.uk> The world is but a canvas to the imagination - Thoreau [firedrake] (Windowsill)> python Python 2.7.10 (default, Sep 23 2015, 04:34:21) [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.72)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from firedrake import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/wingate/firedrake/lib/python2.7/site-packages/firedrake/__init__.py", line 3, in <module> import firedrake.petsc as petsc File "/Users/wingate/firedrake/lib/python2.7/site-packages/firedrake/petsc.py", line 5, in <module> petsc4py.init(sys.argv) File "/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: dlopen(/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so, 2): Library not loaded: /opt/local/lib/libhwloc.5.dylib Referenced from: /Users/wingate/firedrake/lib/python2.7/site-packages/petsc/lib/libpetsc.3.06.2.dylib Reason: image not found >>>

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Installing Firedrake on an HPC machine
by Justin Chang 14 Nov '15

14 Nov '15

Hi everyone, I have installed firedrake on my university's HPC machine, and whenever i attempt to run any Firedrake program, I get this error: -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: compute-0-0 (PID 28214) MPI_COMM_WORLD rank: 0 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- Why is this happening? Program seems fine when I only use a few processes but when I use two or more compute nodes, my program hangs. I'll do my best to explain how I built firedrake: 1) Our system has openmpi-1.8.3 and gcc-4.9.2 available. so those are the only modules I have loaded, everything else was downloaded. 2) I built Python 2.7.10 from source and installed it in ${HOME}/.local 3) pip was obtained via python get-pip.py 4) PETSc was installed --with-cc=mpmicc, --with-cxx=mpicxx, and has all the necessary external packages 5) petsc4py was installed via git clone ... and set up with python setup.py build/install 6) PyOP2 was built with python setup.py build_ext --inplace 7) Firedrake was built via make and everything else was installed via 'pip install <package>'. I had to manually install swig and pcre. Any ideas what this may be? And/or how I can circumvent this issue? Thanks, Justin

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