- firedrake - imperial.ac.uk

DG for advection-diffusion
by Justin Chang 29 Sep '16

29 Sep '16

Hi all, I have written here the Discontinuous Galerkin method for 1D advection-diffusion equations using backward euler time discretization: mesh = UnitIntervalMesh(100) V = FunctionSpace(mesh, 'DG', 1) u = TrialFunction(V) v = TestFunction(V) u0 = Function(V, name="initial") sol = Function(V, name="solution") # Diffusivity D = Constant(0.005) # Velocity vel = as_vector((Constant(1.0),)) # Forcing function f = interpolate(Expression(....),V) # Penalty k = 1 d = 1 gamma = Constant((k+1)*(k+d)/d)*FacetArea(mesh)/avg(CellVolume(mesh)) # based on the formula in http://webpages.sdsmt.edu/~kshahbaz/shahbazi_05.pdf # Other parameters n = FacetNormal(mesh) h = CellSize(mesh) vn = 0.5*(dot(vel,n) + abs(dot(vel,n))) # Weak form a = v*u/dt*dx - dot(grad(v),vel*u)*dx + dot(jump(v),vn('+')*u('+')-vn('-')*u('-'))*dS + dot(v, vn*u)*ds \ + dot(grad(v),D*grad(u))*dx - dot(jump(v,n),avg(D*grad(u)))*dS - dot(avg(D*grad(v)),jump(u,n))*dS \ + gamma*dot(jump(v,n),jump(u,n))*dS L = v*f*dx + v*u0/dt*dx ... I have a couple questions: 1) If say I am solving for the transport of 4 chemical species, Normally I would create a mixed function space like V_mixed = V*V*V*V, split u into u1, u2, u3, and u4, write bilinear and linear forms for each of these individual components and add them up. That is, a = a1 + a2 + a3 + a4, L = L1 + L2 + L3 + L4. This can become quite a lot of code if I end up having to solve ~20 chemical species eventually. The catch is that the velocity and diffusivity will be the same for all species but the forcing function and boundary conditions are going to be different. Is there a more efficient of writing the bilinear and linear form instead of having to copy and paste the a = ... and L = ... multiple times and changing the trial/test functions? 2) I see that in FEniCS's undocumented dg-advection-diffusion example, they enforce the DirichletBC's strongly. Is it possible to enforce them weakly like the SIPG or DG upwinding techniques for the pure diffusion or advection equations? Thanks, Justin

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kernel of operator
by Colin Cotter 27 Sep '16

27 Sep '16

Dear Firedrakers, I have a (non-symmetric) system that I would like to extract a kernel from, probably using QR factorisation or similar. What is the best way to do this at scale? all the best --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] Strange MPI error/warning after upgrading homebrew
by David Ham 22 Sep '16

22 Sep '16

Hmm. FWIW I can't reproduce this. I've updated everything from homebrew and in particular have open-mpi 2.0.1 and mpi4py 2.0.0 installed as above. If I run: python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank" then I just get the expected output of "0" Regards, David On Wed, 21 Sep 2016 at 04:37 Justin Chang <jychang48(a)gmail.com> wrote: > It has come back. I tried the steps Lawrence suggested but the messages > won't go away: > > (firedrake)*➜ **~* python -c "from firedrake import *" > > [Justins-MacBook-Pro-2.local:00492] [[25811,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00492] [[25811,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > (firedrake)*➜ **~* python -c "from mpi4py import MPI; print > MPI.COMM_WORLD.rank" > > [Justins-MacBook-Pro-2.local:00563] [[26380,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00563] [[26380,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > 0 > > (firedrake)*➜ **~* pip uninstall mpi4py > > > Uninstalling mpi4py-2.0.0: > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py-2.0.0-py2.7.egg-info > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.so > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.py > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.pyc > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.py > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.pyc > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/dl.so > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pyx > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/libmpi.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi.pxi > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.h > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.i > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libmpe.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-hyb.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-mpi.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt.dylib > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/libmpi.pxd > > > /Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/mpi.cfg > > Proceed (y/n)? y > > Successfully uninstalled mpi4py-2.0.0 > > (firedrake)*➜ **~* pip install --no-binary :all: mpi4py > > > Collecting mpi4py > > Using cached mpi4py-2.0.0.tar.gz > > Skipping bdist_wheel for mpi4py, due to binaries being disabled for it. > > Installing collected packages: mpi4py > > Running setup.py install for mpi4py ... done > > Successfully installed mpi4py-2.0.0 > > (firedrake)*➜ **~* python -c "from mpi4py import MPI; print > MPI.COMM_WORLD.rank" > > [Justins-MacBook-Pro-2.local:00849] [[26222,0],0] bind() failed on error > Address already in use (48) > > [Justins-MacBook-Pro-2.local:00849] [[26222,0],0] ORTE_ERROR_LOG: Error in > file oob_usock_component.c at line 228 > > 0 > > Any ideas here? > > Thanks, > Justin > > On Tue, Sep 20, 2016 at 4:47 AM, Justin Chang <jychang48(a)gmail.com> wrote: > >> Wait, sorry, my MPI error/warning messages disappeared without a trace. I >> am not sure how I "fixed" it. >> >> I'll holler again if I see something else. >> >> On Tue, Sep 20, 2016 at 4:39 AM, Lawrence Mitchell < >> lawrence.mitchell(a)imperial.ac.uk> wrote: >> >>> >>> >>> On 20/09/16 09:30, Justin Chang wrote: >>> > Hi all, >>> > >>> > I upgraded homebrew on my macbook and had to remove firedrake because >>> > the compiled libraries were pointing to old/nonexistent brew packages. >>> > So when I tried to install a fresh copy of firedrake, i get this >>> message: >>> > >>> > $ python firedrake-install --developer --disable_ssh --log >>> > >>> > Installing command line tools... >>> > >>> > Installing required packages via homebrew. You can safely ignore >>> > warnings that packages are already installed >>> > >>> > Creating firedrake virtualenv in 'firedrake'. >>> > >>> > /Users/justin/Software/firedrake/bin/pip install -vvv -U pip >>> > >>> > >>> > Traceback (most recent call last): >>> > >>> > File "firedrake-install", line 1016, in <module> >>> > >>> > framework = fix_osx_virtualenv_python() >>> > >>> > File "firedrake-install", line 973, in fix_osx_virtualenv_python >>> > >>> > shutil.copytree(appsrc, appdest) >>> > >>> > File >>> > >>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", >>> > line 208, in copytree >>> > >>> > raise Error, errors >>> > >>> > shutil.Error: >>> > >>> [('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS', "[Errno >>> > 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/MacOS'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Resources', >>> > "[Errno 1] Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents/Resources'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', >>> > '/Users/justin/Software/firedrake/Python.app/Contents/version.plist', >>> > "[Errno 1] Operation not permitted: >>> > >>> '/Users/justin/Software/firedrake/Python.app/Contents/version.plist'"), >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', >>> > '/Users/justin/Software/firedrake/Python.app/Contents', "[Errno 1] >>> > Operation not permitted: >>> > '/Users/justin/Software/firedrake/Python.app/Contents'"), >>> > >>> ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', >>> > '/Users/justin/Software/firedrake/Python.app', "[Errno 1] Operation >>> > not permitted: '/Users/justin/Software/firedrake/Python.app'")] >>> > >>> > >>> > And when I run the script again, it installs correctly. I guess this >>> > meant the virtualenv was "successfully" installed the first time. >>> > >>> > However, I get this strange MPI warning/error that I have never before >>> > seen: >>> > >>> > $ python -c "from firedrake import *" >>> > >>> > [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] bind() failed on >>> > error Address already in use (48) >>> > >>> > [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] ORTE_ERROR_LOG: >>> > Error in file oob_usock_component.c at line 228 >>> > >>> > >>> > My firedrake programs appear to run without any error, but these >>> > messages still seem very suspicious. Any ideas what this could be? My >>> > homebrew upgrade/update has now given me Open MPI 2.0.1, and I am >>> > wondering if anyone else is having this issue. >>> >>> Can you run an mpi4py program? >>> >>> In the virtualenv: >>> >>> $ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank" >>> >>> If that fails, try uninstalling mpi4py >>> >>> $ pip uninstall mpi4py >>> >>> And then reinstalling, but crucially without using the pip cache: >>> >>> $ pip install --no-binary :all: mpi4py >>> >>> >>> Cheers, >>> >>> Lawrence >>> >>> >>> _______________________________________________ >>> firedrake mailing list >>> firedrake(a)imperial.ac.uk >>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>> >> >

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Re: [firedrake] (no subject)
by Colin Cotter 22 Sep '16

22 Sep '16

On the other hand, extra memory is very cheap... On 22 September 2016 at 17:09, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > Hi Floriane, > > I'm afraid that you're not going to be able to run very large problems on > a machine with only 6G of RAM. You could attempt to shut down running > processes to free more memory, but in reality you're really just asking too > much of your hardware. Similarly, tweaking preconditioners to reduce memory > usage might help a bit, but you're still going to be very close to the line. > > Regards, > > David > > On Thu, 22 Sep 2016 at 16:55 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> Indeed, I have less than 5G memory available: >> >> MemTotal: 5941348 kB >> MemFree: 1429500 kB >> MemAvailable: 2994648 kB >> >> Is there a way for me to free some memory? >> >> Thank you, >> Floriane >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* jeudi 22 septembre 2016 16:30:14 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Dear Floriane, >> >> I've run your code and it runs without error on current master for me. >> Looking at your last error message, it appears that you have run out of >> memory. How much memory does your machine have? For me, that problem peaks >> at a bit over 5G of memory. >> >> If that is the problem, there may be solver options we can set which >> might use less memory, or perhaps you need a larger machine. >> >> As an aside, running that problem in parallel is effective. On 8 >> processors I get about a 3x speedup. >> >> Regards, >> >> David >> >> >> >> On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear David, >>> >>> >>> Sorry about that. You should be able to access my code on that link: >>> https://bitbucket.org/Floriane_Gidel/test_bl . >>> >>> >>> Thank you, >>> Floriane >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>> ac.uk> de la part de David Ham <David.Ham(a)imperial.ac.uk> >>> *Envoyé :* jeudi 22 septembre 2016 10:32:07 >>> >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> Hi Floriane, >>> >>> Sorry for taking a couple of days to get on to this. Unfortunately those >>> files are not attached, they are on a University of Leeds sharepoint which >>> my Imperial microsoft account cannot access. Could you please provide the >>> files via an open route. >>> >>> Thanks, >>> >>> David >>> >>> On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> wrote: >>> >>>> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >>>> vous. Pour les afficher, cliquez sur les liens ci-dessous. >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> horizontal.msh >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> BL.py >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>>> >>>> Dear David, >>>> >>>> >>>> Attached is the "short" piece of code (BL.py), together with the mesh >>>> file (horizontal.msh). When running it, I get the error below. However, if >>>> I remove the weak formulations for eta(n+1) and phi(n+1) and solve >>>> only phi_solver_half and q_solver_half, then the error is for the line >>>> q_solver_half.solve(). If I also remove the solver for q_half and keeps >>>> only phi_solver_half, then it works. >>>> >>>> Thank you, >>>> >>>> Floriane >>>> >>>> >>>> Traceback (most recent call last): >>>> File "BL.py", line 69, in <module> >>>> phi_solver_half.solve() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/ >>>> firedrake/variational_solver.py", line 198, in solve >>>> >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:170168) >>>> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >>>> (src/petsc4py.PETSc.c:33847) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 261, in form_jacobian >>>> ctx._jacs[lvl].force_evaluation() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>>> line 248, in force_evaluation >>>> self.assemble() >>>> File "<decorator-gen-283>", line 2, in assemble >>>> >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>>> line 191, in assemble >>>> self._assembly_callback(self.bcs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>> line 357, in inner >>>> r = thunk(bcs) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 279, in thunk >>>> zero_tensor() >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 219, in <lambda> >>>> zero_tensor = lambda: tensor.zero() >>>> File "<decorator-gen-300>", line 2, in zero >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 126, in zeroes >>>> _force_copies(self) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 104, in _force_copies >>>> c._cow_actual_copy(obj) >>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >>>> line 687, in _cow_actual_copy >>>> self.handle = src.handle.duplicate(copy=True) >>>> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >>>> (src/petsc4py.PETSc.c:119330) >>>> petsc4py.PETSc.Error: error code 1 >>>> [0] SNESSolve() line 4060 in /tmp/pip-xbPEGV-build/src/ >>>> snes/interface/snes.c >>>> [0] SNESSolve_NEWTONLS() line 228 in /tmp/pip-xbPEGV-build/src/ >>>> snes/impls/ls/ls.c >>>> [0] SNESComputeJacobian() line 2365 in /tmp/pip-xbPEGV-build/src/ >>>> snes/interface/snes.c >>>> [0] MatDuplicate() line 4389 in /tmp/pip-xbPEGV-build/src/mat/ >>>> interface/matrix.c >>>> [0] MatDuplicate_SeqAIJ() line 4126 in /tmp/pip-xbPEGV-build/src/mat/ >>>> impls/aij/seq/aij.c >>>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>>> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >>>> [0] Memory requested 422967946 >>>> >>>> >>>> ------------------------------ >>>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>>> ac.uk> de la part de David Ham <David.Ham(a)imperial.ac.uk> >>>> *Envoyé :* mardi 20 septembre 2016 10:13:20 >>>> >>>> *À :* firedrake >>>> *Objet :* Re: [firedrake] (no subject) >>>> Dear Floriane, >>>> >>>> Please provide a minimal failing example so we can see what is going >>>> on. By a minimal failing example, we mean that you remove everything from >>>> the example that is not related to the failure. Often this requires some >>>> trial and error. The objective is to produce a very short piece of code >>>> which illustrates the problem so that we can (a) check if we can reproduce >>>> it and if so (b) find the problem easily. >>>> >>>> Regards, >>>> >>>> David >>>> >>>> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>>> wrote: >>>> >>>>> Dear all, >>>>> >>>>> >>>>> Some of my codes do not work either since I updated firedrake. I have >>>>> run firedrake-clean but still have the same error when calling the >>>>> nonlinear solvers. The error is pasted below. >>>>> >>>>> Any idea of what I could do ? >>>>> >>>>> Thanks, >>>>> >>>>> Floriane >>>>> >>>>> >>>>> >>>>> Traceback (most recent call last): >>>>> File "3D_NL.py", line 232, in <module> >>>>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/ >>>>> firedrake/variational_solver.py", line 137, in __init__ >>>>> appctx=appctx) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 138, in __init__ >>>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 138, in <genexpr> >>>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 81, in assemble >>>>> >>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>>> line 62, in wrapper >>>>> return f(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 120, in _assemble >>>>> inverse=inverse) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>>> line 189, in compile_form >>>>> number_map).kernels >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 198, in __new__ >>>>> obj = make_obj() >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 188, in make_obj >>>>> obj.__init__(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>>> line 119, in __init__ >>>>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>>> line 118, in __call__ >>>>> return t(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 198, in __new__ >>>>> obj = make_obj() >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", >>>>> line 188, in make_obj >>>>> obj.__init__(*args, **kwargs) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 3778, in __init__ >>>>> self._code = self._ast_to_c(self._ast, opts) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", >>>>> line 60, in _ast_to_c >>>>> ast_handler.plan_cpu(self._opts) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", >>>>> line 119, in plan_cpu >>>>> loop_opt.rewrite(rewrite) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>>>> line 142, in rewrite >>>>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>>> line 181, in merge >>>>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>>>> File "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>>> line 74, in _merge_loops >>>>> while isinstance(loop_b.children[0], (Block, For)): >>>>> IndexError: list index out of range >>>>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>>>> attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ >>>>> of <firedrake.variational_solver.NonlinearVariationalSolver object at >>>>> 0x595a250>> ignored >>>>> >>>>> ------------------------------ >>>>> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces@imperial. >>>>> ac.uk> de la part de Fabio Luporini <f.luporini12(a)imperial.ac.uk> >>>>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>>>> *À :* firedrake >>>>> *Objet :* Re: [firedrake] (no subject) >>>>> >>>>> Hi Will, >>>>> >>>>> Could you just try a firedrake-clean and run it again ? it should then >>>>> work >>>>> >>>>> Thanks >>>>> >>>>> -- Fabio >>>>> >>>>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>>>> >>>>>> Hi firedrakers, >>>>>> >>>>>> I had this script working on an older version of firedrake (24th >>>>>> Aug), but when I updated today I now get the following error when I try to >>>>>> run it: >>>>>> >>>>>> Traceback (most recent call last): >>>>>> File "compressible_stratified.py", line 77, in <module> >>>>>> solve ( a_u_project == L_u_project , dHdu0 , >>>>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving.py", line 119, in solve >>>>>> _solve_varproblem(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving.py", line 147, in >>>>>> _solve_varproblem >>>>>> solver.solve() >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/variational_solver.py", line 198, >>>>>> in solve >>>>>> self.snes.solve(None, v) >>>>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>>>> (src/petsc4py.PETSc.c:170168) >>>>>> File "PETSc/petscsnes.pxi", line 261, in >>>>>> petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33322) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/solving_utils.py", line 216, in >>>>>> form_function >>>>>> form_compiler_parameters=problem.form_compiler_parameters) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 81, in assemble >>>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/utils.py", line 62, in wrapper >>>>>> return f(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 444, in >>>>>> _assemble >>>>>> return thunk(bcs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assembly_cache.py", line 357, in >>>>>> inner >>>>>> r = thunk(bcs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/firedrake/assemble.py", line 394, in thunk >>>>>> op2.par_loop(*args, **kwargs) >>>>>> File "<decorator-gen-269>", line 2, in par_loop >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/versioning.py", line 154, in >>>>>> modifies_arguments >>>>>> retval = func(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/op2.py", line 269, in par_loop >>>>>> return backends._BackendSelector._backend.par_loop(kernel, >>>>>> iterset, *args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/base.py", line 4369, in par_loop >>>>>> return _make_object('ParLoop', kernel, it_space, *args, >>>>>> **kwargs).enqueue() >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/backends.py", line 72, in _make_object >>>>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>>>> File "<decorator-gen-262>", line 2, in __init__ >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/utils.py", line 130, in wrapper >>>>>> return f(*args, **kwargs) >>>>>> File "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/ >>>>>> python2.7/site-packages/pyop2/base.py", line 3999, in __init__ >>>>>> fundecl = kernel._attached_info['fundecl'] >>>>>> TypeError: 'bool' object has no attribute '__getitem__' >>>>>> >>>>>> >>>>>> What needs to be changed to get it to compile again? >>>>>> >>>>>> Thanks >>>>>> Will >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

2 1

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Hi Floriane, I'm afraid that you're not going to be able to run very large problems on a machine with only 6G of RAM. You could attempt to shut down running processes to free more memory, but in reality you're really just asking too much of your hardware. Similarly, tweaking preconditioners to reduce memory usage might help a bit, but you're still going to be very close to the line. Regards, David On Thu, 22 Sep 2016 at 16:55 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > Indeed, I have less than 5G memory available: > > MemTotal: 5941348 kB > MemFree: 1429500 kB > MemAvailable: 2994648 kB > > Is there a way for me to free some memory? > > Thank you, > Floriane > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* jeudi 22 septembre 2016 16:30:14 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Dear Floriane, > > I've run your code and it runs without error on current master for me. > Looking at your last error message, it appears that you have run out of > memory. How much memory does your machine have? For me, that problem peaks > at a bit over 5G of memory. > > If that is the problem, there may be solver options we can set which might > use less memory, or perhaps you need a larger machine. > > As an aside, running that problem in parallel is effective. On 8 > processors I get about a 3x speedup. > > Regards, > > David > > > > On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> Sorry about that. You should be able to access my code on that link: >> https://bitbucket.org/Floriane_Gidel/test_bl . >> >> >> Thank you, >> Floriane >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* jeudi 22 septembre 2016 10:32:07 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Hi Floriane, >> >> Sorry for taking a couple of days to get on to this. Unfortunately those >> files are not attached, they are on a University of Leeds sharepoint which >> my Imperial microsoft account cannot access. Could you please provide the >> files via an open route. >> >> Thanks, >> >> David >> >> On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >>> vous. Pour les afficher, cliquez sur les liens ci-dessous. >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> horizontal.msh >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> BL.py >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >>> >>> Dear David, >>> >>> >>> Attached is the "short" piece of code (BL.py), together with the mesh >>> file (horizontal.msh). When running it, I get the error below. However, if >>> I remove the weak formulations for eta(n+1) and phi(n+1) and solve only >>> phi_solver_half and q_solver_half, then the error is for the line >>> q_solver_half.solve(). If I also remove the solver for q_half and keeps >>> only phi_solver_half, then it works. >>> >>> Thank you, >>> >>> Floriane >>> >>> >>> Traceback (most recent call last): >>> File "BL.py", line 69, in <module> >>> phi_solver_half.solve() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 198, in solve >>> >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:170168) >>> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >>> (src/petsc4py.PETSc.c:33847) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 261, in form_jacobian >>> ctx._jacs[lvl].force_evaluation() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>> line 248, in force_evaluation >>> self.assemble() >>> File "<decorator-gen-283>", line 2, in assemble >>> >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >>> line 191, in assemble >>> self._assembly_callback(self.bcs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>> line 357, in inner >>> r = thunk(bcs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 279, in thunk >>> zero_tensor() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 219, in <lambda> >>> zero_tensor = lambda: tensor.zero() >>> File "<decorator-gen-300>", line 2, in zero >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 126, in zeroes >>> _force_copies(self) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 104, in _force_copies >>> c._cow_actual_copy(obj) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >>> line 687, in _cow_actual_copy >>> self.handle = src.handle.duplicate(copy=True) >>> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >>> (src/petsc4py.PETSc.c:119330) >>> petsc4py.PETSc.Error: error code 1 >>> [0] SNESSolve() line 4060 in >>> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >>> [0] SNESSolve_NEWTONLS() line 228 in >>> /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c >>> [0] SNESComputeJacobian() line 2365 in >>> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >>> [0] MatDuplicate() line 4389 in >>> /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c >>> [0] MatDuplicate_SeqAIJ() line 4126 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >>> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >>> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >>> [0] Memory requested 422967946 >>> >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> de la part de David Ham < >>> David.Ham(a)imperial.ac.uk> >>> *Envoyé :* mardi 20 septembre 2016 10:13:20 >>> >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> Dear Floriane, >>> >>> Please provide a minimal failing example so we can see what is going on. >>> By a minimal failing example, we mean that you remove everything from the >>> example that is not related to the failure. Often this requires some trial >>> and error. The objective is to produce a very short piece of code which >>> illustrates the problem so that we can (a) check if we can reproduce it and >>> if so (b) find the problem easily. >>> >>> Regards, >>> >>> David >>> >>> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> wrote: >>> >>>> Dear all, >>>> >>>> >>>> Some of my codes do not work either since I updated firedrake. I have >>>> run firedrake-clean but still have the same error when calling the >>>> nonlinear solvers. The error is pasted below. >>>> >>>> Any idea of what I could do ? >>>> >>>> Thanks, >>>> >>>> Floriane >>>> >>>> >>>> >>>> Traceback (most recent call last): >>>> File "3D_NL.py", line 232, in <module> >>>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 137, in __init__ >>>> appctx=appctx) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 138, in __init__ >>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 138, in <genexpr> >>>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 81, in assemble >>>> >>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>> File "<decorator-gen-295>", line 2, in _assemble >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 120, in _assemble >>>> inverse=inverse) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>> line 189, in compile_form >>>> number_map).kernels >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 198, in __new__ >>>> obj = make_obj() >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 188, in make_obj >>>> obj.__init__(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>>> line 119, in __init__ >>>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>> line 118, in __call__ >>>> return t(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 198, in __new__ >>>> obj = make_obj() >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>>> 188, in make_obj >>>> obj.__init__(*args, **kwargs) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >>>> 3778, in __init__ >>>> self._code = self._ast_to_c(self._ast, opts) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >>>> 60, in _ast_to_c >>>> ast_handler.plan_cpu(self._opts) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >>>> 119, in plan_cpu >>>> loop_opt.rewrite(rewrite) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>>> line 142, in rewrite >>>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>> line 181, in merge >>>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>>> File >>>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>>> line 74, in _merge_loops >>>> while isinstance(loop_b.children[0], (Block, For)): >>>> IndexError: list index out of range >>>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>>> attribute '_parameters'" in <bound method >>>> NonlinearVariationalSolver.__del__ of >>>> <firedrake.variational_solver.NonlinearVariationalSolver object at >>>> 0x595a250>> ignored >>>> >>>> ------------------------------ >>>> *De :* firedrake-bounces(a)imperial.ac.uk < >>>> firedrake-bounces(a)imperial.ac.uk> de la part de Fabio Luporini < >>>> f.luporini12(a)imperial.ac.uk> >>>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>>> *À :* firedrake >>>> *Objet :* Re: [firedrake] (no subject) >>>> >>>> Hi Will, >>>> >>>> Could you just try a firedrake-clean and run it again ? it should then >>>> work >>>> >>>> Thanks >>>> >>>> -- Fabio >>>> >>>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>>> >>>>> Hi firedrakers, >>>>> >>>>> I had this script working on an older version of firedrake (24th Aug), >>>>> but when I updated today I now get the following error when I try to run it: >>>>> >>>>> Traceback (most recent call last): >>>>> File "compressible_stratified.py", line 77, in <module> >>>>> solve ( a_u_project == L_u_project , dHdu0 , >>>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>>> line 119, in solve >>>>> _solve_varproblem(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>>> line 147, in _solve_varproblem >>>>> solver.solve() >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>>> line 198, in solve >>>>> self.snes.solve(None, v) >>>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>>> (src/petsc4py.PETSc.c:170168) >>>>> File "PETSc/petscsnes.pxi", line 261, in >>>>> petsc4py.PETSc.SNES_Function (src/petsc4py.PETSc.c:33322) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>>> line 216, in form_function >>>>> form_compiler_parameters=problem.form_compiler_parameters) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 81, in assemble >>>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>>> File "<decorator-gen-295>", line 2, in _assemble >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>>> line 62, in wrapper >>>>> return f(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 444, in _assemble >>>>> return thunk(bcs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>>> line 357, in inner >>>>> r = thunk(bcs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>>> line 394, in thunk >>>>> op2.par_loop(*args, **kwargs) >>>>> File "<decorator-gen-269>", line 2, in par_loop >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>>> line 154, in modifies_arguments >>>>> retval = func(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>>>> line 269, in par_loop >>>>> return backends._BackendSelector._backend.par_loop(kernel, >>>>> iterset, *args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 4369, in par_loop >>>>> return _make_object('ParLoop', kernel, it_space, *args, >>>>> **kwargs).enqueue() >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>>> line 72, in _make_object >>>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>>> File "<decorator-gen-262>", line 2, in __init__ >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>>>> line 130, in wrapper >>>>> return f(*args, **kwargs) >>>>> File >>>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>>> line 3999, in __init__ >>>>> fundecl = kernel._attached_info['fundecl'] >>>>> TypeError: 'bool' object has no attribute '__getitem__' >>>>> >>>>> >>>>> What needs to be changed to get it to compile again? >>>>> >>>>> Thanks >>>>> Will >>>>> >>>>> >>>>> >>>>> >>>>> >>>>

1 0

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Dear Floriane, I've run your code and it runs without error on current master for me. Looking at your last error message, it appears that you have run out of memory. How much memory does your machine have? For me, that problem peaks at a bit over 5G of memory. If that is the problem, there may be solver options we can set which might use less memory, or perhaps you need a larger machine. As an aside, running that problem in parallel is effective. On 8 processors I get about a 3x speedup. Regards, David On Thu, 22 Sep 2016 at 14:56 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > Sorry about that. You should be able to access my code on that link: > https://bitbucket.org/Floriane_Gidel/test_bl . > > > Thank you, > Floriane > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* jeudi 22 septembre 2016 10:32:07 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Hi Floriane, > > Sorry for taking a couple of days to get on to this. Unfortunately those > files are not attached, they are on a University of Leeds sharepoint which > my Imperial microsoft account cannot access. Could you please provide the > files via an open route. > > Thanks, > > David > > On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec >> vous. Pour les afficher, cliquez sur les liens ci-dessous. >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> horizontal.msh >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> BL.py >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> >> >> Dear David, >> >> >> Attached is the "short" piece of code (BL.py), together with the mesh >> file (horizontal.msh). When running it, I get the error below. However, if >> I remove the weak formulations for eta(n+1) and phi(n+1) and solve only >> phi_solver_half and q_solver_half, then the error is for the line >> q_solver_half.solve(). If I also remove the solver for q_half and keeps >> only phi_solver_half, then it works. >> >> Thank you, >> >> Floriane >> >> >> Traceback (most recent call last): >> File "BL.py", line 69, in <module> >> phi_solver_half.solve() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >> line 198, in solve >> >> self.snes.solve(None, v) >> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >> (src/petsc4py.PETSc.c:170168) >> File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian >> (src/petsc4py.PETSc.c:33847) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 261, in form_jacobian >> ctx._jacs[lvl].force_evaluation() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >> line 248, in force_evaluation >> self.assemble() >> File "<decorator-gen-283>", line 2, in assemble >> >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >> line 62, in wrapper >> return f(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", >> line 191, in assemble >> self._assembly_callback(self.bcs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >> line 357, in inner >> r = thunk(bcs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 279, in thunk >> zero_tensor() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 219, in <lambda> >> zero_tensor = lambda: tensor.zero() >> File "<decorator-gen-300>", line 2, in zero >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >> line 126, in zeroes >> _force_copies(self) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >> line 104, in _force_copies >> c._cow_actual_copy(obj) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", >> line 687, in _cow_actual_copy >> self.handle = src.handle.duplicate(copy=True) >> File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate >> (src/petsc4py.PETSc.c:119330) >> petsc4py.PETSc.Error: error code 1 >> [0] SNESSolve() line 4060 in >> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >> [0] SNESSolve_NEWTONLS() line 228 in >> /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c >> [0] SNESComputeJacobian() line 2365 in >> /tmp/pip-xbPEGV-build/src/snes/interface/snes.c >> [0] MatDuplicate() line 4389 in >> /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c >> [0] MatDuplicate_SeqAIJ() line 4126 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in >> /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c >> [0] Out of memory. Allocated: 0, Used by process: 3556626432 >> [0] Memory requested 422967946 >> >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* mardi 20 septembre 2016 10:13:20 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> Dear Floriane, >> >> Please provide a minimal failing example so we can see what is going on. >> By a minimal failing example, we mean that you remove everything from the >> example that is not related to the failure. Often this requires some trial >> and error. The objective is to produce a very short piece of code which >> illustrates the problem so that we can (a) check if we can reproduce it and >> if so (b) find the problem easily. >> >> Regards, >> >> David >> >> On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear all, >>> >>> >>> Some of my codes do not work either since I updated firedrake. I have >>> run firedrake-clean but still have the same error when calling the >>> nonlinear solvers. The error is pasted below. >>> >>> Any idea of what I could do ? >>> >>> Thanks, >>> >>> Floriane >>> >>> >>> >>> Traceback (most recent call last): >>> File "3D_NL.py", line 232, in <module> >>> wf1_solver = NonlinearVariationalSolver(wf1_problem) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 137, in __init__ >>> appctx=appctx) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 138, in __init__ >>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 138, in <genexpr> >>> for J, problem, ctx in zip(self.Js, problems, appctxs)) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 81, in assemble >>> >>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>> File "<decorator-gen-295>", line 2, in _assemble >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 120, in _assemble >>> inverse=inverse) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>> line 189, in compile_form >>> number_map).kernels >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 198, in __new__ >>> obj = make_obj() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 188, in make_obj >>> obj.__init__(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >>> line 119, in __init__ >>> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>> line 118, in __call__ >>> return t(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 198, in __new__ >>> obj = make_obj() >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >>> 188, in make_obj >>> obj.__init__(*args, **kwargs) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >>> 3778, in __init__ >>> self._code = self._ast_to_c(self._ast, opts) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >>> 60, in _ast_to_c >>> ast_handler.plan_cpu(self._opts) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >>> 119, in plan_cpu >>> loop_opt.rewrite(rewrite) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >>> line 142, in rewrite >>> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>> line 181, in merge >>> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >>> File >>> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >>> line 74, in _merge_loops >>> while isinstance(loop_b.children[0], (Block, For)): >>> IndexError: list index out of range >>> Exception AttributeError: "'NonlinearVariationalSolver' object has no >>> attribute '_parameters'" in <bound method >>> NonlinearVariationalSolver.__del__ of >>> <firedrake.variational_solver.NonlinearVariationalSolver object at >>> 0x595a250>> ignored >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> de la part de Fabio Luporini < >>> f.luporini12(a)imperial.ac.uk> >>> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >>> *À :* firedrake >>> *Objet :* Re: [firedrake] (no subject) >>> >>> Hi Will, >>> >>> Could you just try a firedrake-clean and run it again ? it should then >>> work >>> >>> Thanks >>> >>> -- Fabio >>> >>> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >>> >>>> Hi firedrakers, >>>> >>>> I had this script working on an older version of firedrake (24th Aug), >>>> but when I updated today I now get the following error when I try to run it: >>>> >>>> Traceback (most recent call last): >>>> File "compressible_stratified.py", line 77, in <module> >>>> solve ( a_u_project == L_u_project , dHdu0 , >>>> solver_parameters={'ksp_rtol': 1e-14} ) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 119, in solve >>>> _solve_varproblem(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 147, in _solve_varproblem >>>> solver.solve() >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 198, in solve >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:170168) >>>> File "PETSc/petscsnes.pxi", line 261, in petsc4py.PETSc.SNES_Function >>>> (src/petsc4py.PETSc.c:33322) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>>> line 216, in form_function >>>> form_compiler_parameters=problem.form_compiler_parameters) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 81, in assemble >>>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>>> File "<decorator-gen-295>", line 2, in _assemble >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>>> line 62, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 444, in _assemble >>>> return thunk(bcs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>>> line 357, in inner >>>> r = thunk(bcs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>>> line 394, in thunk >>>> op2.par_loop(*args, **kwargs) >>>> File "<decorator-gen-269>", line 2, in par_loop >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>>> line 154, in modifies_arguments >>>> retval = func(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>>> line 269, in par_loop >>>> return backends._BackendSelector._backend.par_loop(kernel, iterset, >>>> *args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>> line 4369, in par_loop >>>> return _make_object('ParLoop', kernel, it_space, *args, >>>> **kwargs).enqueue() >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>>> line 72, in _make_object >>>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>>> File "<decorator-gen-262>", line 2, in __init__ >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>>> line 130, in wrapper >>>> return f(*args, **kwargs) >>>> File >>>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>>> line 3999, in __init__ >>>> fundecl = kernel._attached_info['fundecl'] >>>> TypeError: 'bool' object has no attribute '__getitem__' >>>> >>>> >>>> What needs to be changed to get it to compile again? >>>> >>>> Thanks >>>> Will >>>> >>>> >>>> >>>> >>>> >>>

2 1

Re: [firedrake] (no subject)
by David Ham 22 Sep '16

22 Sep '16

Hi Floriane, Sorry for taking a couple of days to get on to this. Unfortunately those files are not attached, they are on a University of Leeds sharepoint which my Imperial microsoft account cannot access. Could you please provide the files via an open route. Thanks, David On Tue, 20 Sep 2016 at 11:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Floriane Gidel [RPG] a partagé des fichiers OneDrive Entreprise avec vous. > Pour les afficher, cliquez sur les liens ci-dessous. > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > horizontal.msh > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > BL.py > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > <https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/Documents/Pi%C…> > > Dear David, > > > Attached is the "short" piece of code (BL.py), together with the mesh file > (horizontal.msh). When running it, I get the error below. However, if I > remove the weak formulations for eta(n+1) and phi(n+1) and solve only > phi_solver_half and q_solver_half, then the error is for the line > q_solver_half.solve(). If I also remove the solver for q_half and keeps > only phi_solver_half, then it works. > > Thank you, > > Floriane > > > Traceback (most recent call last): > File "BL.py", line 69, in <module> > phi_solver_half.solve() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 198, in solve > > self.snes.solve(None, v) > File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve > (src/petsc4py.PETSc.c:170168) > File "PETSc/petscsnes.pxi", line 294, in petsc4py.PETSc.SNES_Jacobian > (src/petsc4py.PETSc.c:33847) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 261, in form_jacobian > ctx._jacs[lvl].force_evaluation() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", > line 248, in force_evaluation > self.assemble() > File "<decorator-gen-283>", line 2, in assemble > > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", > line 62, in wrapper > return f(*args, **kwargs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/matrix.py", > line 191, in assemble > self._assembly_callback(self.bcs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", > line 357, in inner > r = thunk(bcs) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", > line 279, in thunk > zero_tensor() > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", > line 219, in <lambda> > zero_tensor = lambda: tensor.zero() > File "<decorator-gen-300>", line 2, in zero > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", > line 126, in zeroes > _force_copies(self) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", > line 104, in _force_copies > c._cow_actual_copy(obj) > File > "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/petsc_base.py", > line 687, in _cow_actual_copy > self.handle = src.handle.duplicate(copy=True) > File "PETSc/Mat.pyx", line 617, in petsc4py.PETSc.Mat.duplicate > (src/petsc4py.PETSc.c:119330) > petsc4py.PETSc.Error: error code 1 > [0] SNESSolve() line 4060 in > /tmp/pip-xbPEGV-build/src/snes/interface/snes.c > [0] SNESSolve_NEWTONLS() line 228 in > /tmp/pip-xbPEGV-build/src/snes/impls/ls/ls.c > [0] SNESComputeJacobian() line 2365 in > /tmp/pip-xbPEGV-build/src/snes/interface/snes.c > [0] MatDuplicate() line 4389 in > /tmp/pip-xbPEGV-build/src/mat/interface/matrix.c > [0] MatDuplicate_SeqAIJ() line 4126 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] MatDuplicateNoCreate_SeqAIJ() line 4053 in > /tmp/pip-xbPEGV-build/src/mat/impls/aij/seq/aij.c > [0] Out of memory. Allocated: 0, Used by process: 3556626432 > [0] Memory requested 422967946 > > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* mardi 20 septembre 2016 10:13:20 > > *À :* firedrake > *Objet :* Re: [firedrake] (no subject) > Dear Floriane, > > Please provide a minimal failing example so we can see what is going on. > By a minimal failing example, we mean that you remove everything from the > example that is not related to the failure. Often this requires some trial > and error. The objective is to produce a very short piece of code which > illustrates the problem so that we can (a) check if we can reproduce it and > if so (b) find the problem easily. > > Regards, > > David > > On Tue, 20 Sep 2016 at 09:46 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear all, >> >> >> Some of my codes do not work either since I updated firedrake. I have run >> firedrake-clean but still have the same error when calling the nonlinear >> solvers. The error is pasted below. >> >> Any idea of what I could do ? >> >> Thanks, >> >> Floriane >> >> >> >> Traceback (most recent call last): >> File "3D_NL.py", line 232, in <module> >> wf1_solver = NonlinearVariationalSolver(wf1_problem) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >> line 137, in __init__ >> appctx=appctx) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 138, in __init__ >> for J, problem, ctx in zip(self.Js, problems, appctxs)) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >> line 138, in <genexpr> >> for J, problem, ctx in zip(self.Js, problems, appctxs)) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 81, in assemble >> >> inverse=inverse, mat_type=mat_type, appctx=appctx) >> File "<decorator-gen-295>", line 2, in _assemble >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >> line 62, in wrapper >> return f(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >> line 120, in _assemble >> inverse=inverse) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >> line 189, in compile_form >> number_map).kernels >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 198, in __new__ >> obj = make_obj() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 188, in make_obj >> obj.__init__(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/firedrake/tsfc_interface.py", >> line 119, in __init__ >> kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >> line 118, in __call__ >> return t(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 198, in __new__ >> obj = make_obj() >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/caching.py", line >> 188, in make_obj >> obj.__init__(*args, **kwargs) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/base.py", line >> 3778, in __init__ >> self._code = self._ast_to_c(self._ast, opts) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/pyop2/host.py", line >> 60, in _ast_to_c >> ast_handler.plan_cpu(self._opts) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/plan.py", line >> 119, in plan_cpu >> loop_opt.rewrite(rewrite) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/optimizer.py", >> line 142, in rewrite >> merged_loops = SSALoopMerger(self.expr_graph).merge(self.header) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >> line 181, in merge >> merged, l_dims, m_dims = self._merge_loops(parent, l, merging_in) >> File >> "/home/fgidel/firedrake/lib/python2.7/site-packages/coffee/scheduler.py", >> line 74, in _merge_loops >> while isinstance(loop_b.children[0], (Block, For)): >> IndexError: list index out of range >> Exception AttributeError: "'NonlinearVariationalSolver' object has no >> attribute '_parameters'" in <bound method >> NonlinearVariationalSolver.__del__ of >> <firedrake.variational_solver.NonlinearVariationalSolver object at >> 0x595a250>> ignored >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de Fabio Luporini <f.luporini12(a)imperial.ac.uk> >> *Envoyé :* jeudi 15 septembre 2016 14:14:44 >> *À :* firedrake >> *Objet :* Re: [firedrake] (no subject) >> >> Hi Will, >> >> Could you just try a firedrake-clean and run it again ? it should then >> work >> >> Thanks >> >> -- Fabio >> >> 2016-09-15 14:07 GMT+02:00 William Booker <scwb(a)leeds.ac.uk>: >> >>> Hi firedrakers, >>> >>> I had this script working on an older version of firedrake (24th Aug), >>> but when I updated today I now get the following error when I try to run it: >>> >>> Traceback (most recent call last): >>> File "compressible_stratified.py", line 77, in <module> >>> solve ( a_u_project == L_u_project , dHdu0 , >>> solver_parameters={'ksp_rtol': 1e-14} ) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>> line 119, in solve >>> _solve_varproblem(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving.py", >>> line 147, in _solve_varproblem >>> solver.solve() >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 198, in solve >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 537, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:170168) >>> File "PETSc/petscsnes.pxi", line 261, in petsc4py.PETSc.SNES_Function >>> (src/petsc4py.PETSc.c:33322) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/solving_utils.py", >>> line 216, in form_function >>> form_compiler_parameters=problem.form_compiler_parameters) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 81, in assemble >>> inverse=inverse, mat_type=mat_type, appctx=appctx) >>> File "<decorator-gen-295>", line 2, in _assemble >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/utils.py", >>> line 62, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 444, in _assemble >>> return thunk(bcs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py", >>> line 357, in inner >>> r = thunk(bcs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/firedrake/assemble.py", >>> line 394, in thunk >>> op2.par_loop(*args, **kwargs) >>> File "<decorator-gen-269>", line 2, in par_loop >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/versioning.py", >>> line 154, in modifies_arguments >>> retval = func(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/op2.py", >>> line 269, in par_loop >>> return backends._BackendSelector._backend.par_loop(kernel, iterset, >>> *args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>> line 4369, in par_loop >>> return _make_object('ParLoop', kernel, it_space, *args, >>> **kwargs).enqueue() >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/backends.py", >>> line 72, in _make_object >>> return _BackendSelector._backend.__dict__[obj](*args, **kwargs) >>> File "<decorator-gen-262>", line 2, in __init__ >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/utils.py", >>> line 130, in wrapper >>> return f(*args, **kwargs) >>> File >>> "/usr/not-backed-up/firedrake/2016-09-15/firedrake/lib/python2.7/site-packages/pyop2/base.py", >>> line 3999, in __init__ >>> fundecl = kernel._attached_info['fundecl'] >>> TypeError: 'bool' object has no attribute '__getitem__' >>> >>> >>> What needs to be changed to get it to compile again? >>> >>> Thanks >>> Will >>> >>> >>> >>> >>> >>

2 1

Strange MPI error/warning after upgrading homebrew
by Justin Chang 21 Sep '16

21 Sep '16

Hi all, I upgraded homebrew on my macbook and had to remove firedrake because the compiled libraries were pointing to old/nonexistent brew packages. So when I tried to install a fresh copy of firedrake, i get this message: $ python firedrake-install --developer --disable_ssh --log Installing command line tools... Installing required packages via homebrew. You can safely ignore warnings that packages are already installed Creating firedrake virtualenv in 'firedrake'. /Users/justin/Software/firedrake/bin/pip install -vvv -U pip Traceback (most recent call last): File "firedrake-install", line 1016, in <module> framework = fix_osx_virtualenv_python() File "firedrake-install", line 973, in fix_osx_virtualenv_python shutil.copytree(appsrc, appdest) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 208, in copytree raise Error, errors shutil.Error: [('/System/Library/Frameworks/Python.framework/Versions/2.7/ Resources/Python.app/Contents/Info.plist', '/Users/justin/Software/firedr ake/Python.app/Contents/Info.plist', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/MacOS/Python', '/Users/justin/Software/firedr ake/Python.app/Contents/MacOS/Python', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/MacOS', '/Users/justin/Software/firedr ake/Python.app/Contents/MacOS', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/MacOS'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/PkgInfo', '/Users/justin/Software/firedr ake/Python.app/Contents/PkgInfo', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/Resources/PythonApplet.icns', '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedr ake/Python.app/Contents/Resources/PythonApplet.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/Resources/PythonInterpreter.icns', '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedr ake/Python.app/Contents/Resources/PythonInterpreter.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/Resources', '/Users/justin/Software/firedr ake/Python.app/Contents/Resources', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Resources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/R esources/Python.app/Contents/version.plist', '/Users/justin/Software/firedr ake/Python.app/Contents/version.plist', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/version.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', '/Users/justin/Software/firedrake/Python.app/Contents', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', '/Users/justin/Software/firedrake/Python.app', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app'")] And when I run the script again, it installs correctly. I guess this meant the virtualenv was "successfully" installed the first time. However, I get this strange MPI warning/error that I have never before seen: $ python -c "from firedrake import *" [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] bind() failed on error Address already in use (48) [Justins-MacBook-Pro-2.local:88453] [[15547,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228 My firedrake programs appear to run without any error, but these messages still seem very suspicious. Any ideas what this could be? My homebrew upgrade/update has now given me Open MPI 2.0.1, and I am wondering if anyone else is having this issue. Thanks, Justin

2 4

Floriane Gidel [RPG] wants to share the file BL.py with you
by Floriane Gidel [RPG] 20 Sep '16

20 Sep '16

To view BL.py, sign in<https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/_layouts/15/ac…> or create an account.

1 0

Floriane Gidel [RPG] wants to share the file horizontal.msh with you
by Floriane Gidel [RPG] 20 Sep '16

20 Sep '16

To view horizontal.msh, sign in<https://leeds365-my.sharepoint.com/personal/mmfg_leeds_ac_uk/_layouts/15/ac…> or create an account.

1 0