August 2015 - firedrake - imperial.ac.uk

Grantham Institute talk, Mon 10th August 14:40
by Andrew McRae 07 Aug '15

07 Aug '15

Dear Firedrakers, I will be giving my Grantham third year presentation on Monday afternoon, with the title "Compatible finite element methods for atmospheric dynamical cores". I know that several people are currently on holiday, at a conference, or otherwise occupied, but I invite any of you still in SW7 to attend. As the Grantham Institute is multidisciplinary, my talk will not be particularly technical and should be accessible to a general audience. The schedule is below. Coffee will be served from 14:30. Feel free to leave immediately after my talk, or during the break, if the other talk titles don't appeal to you. Best, Andrew *Monday 10th August* *14:30-14:40* *Arr/coffee* Martin Siegert (chair) 14:40-15:10 Andrew McRae Compatible finite element methods for atmospheric dynamical cores 15:10-15:40 Ragnhild Noven Statistical Modelling of Tempo-Spatial Extrema and Dependencies *15:40-16:00* *Break* 16:00-16:30 Jonathan Ritson Peatland carbon sequestration and drinking water provision in an uncertain future 16:30-17:00 Joseph Yao Pressurised Carbonation Experiments in the presence of Steam in a Spouted Bed Reactor *17:00-18:00* *Drinks*

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Re: [firedrake] error installing PyOP2
by Fabio Luporini 06 Aug '15

06 Aug '15

If everything is up-to-date, you might have to clean the caches (run firedrake/scripts/firedrake-clean) -- Fabio 2015-08-06 2:19 GMT+01:00 Justin Chang <jychang48(a)gmail.com>: > Lawrence, > > Upgrading "six" resolved that issue. However, when I attempt to run my > mixed-poisson.py I get this error: > > Traceback (most recent call last): > > File "mixed-poisson.py", line 79, in <module> > > solver_parameters=selfp_parameters) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py", > line 231, in __init__ > > super(LinearVariationalSolver, self).__init__(*args, **kwargs) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py", > line 110, in __init__ > > ctx = solving_utils._SNESContext(problem) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py", > line 105, in __init__ > > for problem in problems) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py", > line 105, in <genexpr> > > for problem in problems) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py", > line 67, in assemble > > inverse=inverse, nest=nest) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py", > line 100, in _assemble > > inverse=inverse) > > File > "/Users/justin/Software/firedrake-deps/firedrake/firedrake/ffc_interface.py", > line 285, in compile_form > > ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 201, in __new__ > > return cls._cache_lookup(key) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 253, in _cache_lookup > > return cls._cache.get(key) or cls._read_from_disk(key) > > File > "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py", > line 279, in _read_from_disk > > val = cPickle.loads(val) > AttributeError: 'module' object has no attribute 'ColSparseArrayInit' > > This was after pulling the latest PyOP2 and firedrake repositories. > > Thanks, > Justin > > On Wed, Aug 5, 2015 at 3:50 AM, Lawrence Mitchell < > lawrence.mitchell(a)imperial.ac.uk> wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Hi Justin, >> >> On 04/08/15 23:05, Justin Chang wrote: >> > Coming back to this. >> > >> > I believe I have puled the latest petsc, petsc4py, and PyOP2 >> > repositories onto my laptop. Following through with all the >> > (re)installation, I come across this error when I run 'make test' >> > in PyOP2: >> > >> > Error in atexit._run_exitfuncs: >> >> Sorry for these continued pains! >> >> So PyOP2 imports cPickle elsewhere, so I think this module most exist. >> Plausibly the "six" module on your system is not sufficiently up-to-date. >> >> Does the following fail: >> >> python -c "from six.moves.cPickle import dumps" >> >> If that works, I'm very confused, but I suspect it won't. >> >> If it doesn't work, can you try installing an updated "six" module: >> >> pip install --user six >> >> and then go again. >> >> Lawrence >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1 >> >> iQEcBAEBAgAGBQJVwc5PAAoJECOc1kQ8PEYvSFwIALqHqS606QbklFGoQmmlFTJL >> zKzWvTk38907Jkz+028F5MrNSdrNAXSKUlkV/M90KWqBOKILk+n5mQfpz5P/rgbd >> ql/h2JTQMMBre3M9McacgdlHT5KIfOYPhmZcOudcgHo1hX03luOY4fzWM+shGpv9 >> woEooMJoIKXfyyxfiz8GO4xHakE4xnfzEiy3gJBoD1X0PyBo/ItKXEnMYwBcEF/1 >> 1/okUeJgmTI2y11CfA0zYpKCEMUkWa/ZK0iCD37tLnkawVtbc8s3+z/pKUeCnB2W >> jWKh2713ECCPBDCWMybXRDQsu1zFZL9HGh/VToVMT+uV+7V8/hSknRWVzSjIJxo= >> =gNYd >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > >

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error installing PyOP2
by Justin Chang 06 Aug '15

06 Aug '15

Hi everyone, I am trying to installing firedrake on my Ubuntu machine. Following the instructions for PyOP2, I get this error when I run "make test" cd test; py.test unit --backend=sequential Segmentation fault (core dumped) make: *** [unit_sequential] Error 139 I have installed everything via sudo pip install ... with the exception of petsc4py which was installed via pip install --user -U --no-deps ... python -c 'from pprint import pprint; import sys; pprint(sys.path)' gives the following: ['', '/usr/lib/python2.7/dist-packages', '/home/justin/.local/lib/python2.7/site-packages', '/home/justin/Software/firedrake-deps/PyOP2', '/home/justin/Software/firedrake-deps/firedrake', '/home/justin/.local/lib/python2.7/dist-packages', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client'] and py.test test/unit -vsx --tb=short --backend=sequential gives the following: [pacotaco-xps:29386] *** Process received signal *** [pacotaco-xps:29386] Signal: Segmentation fault (11) [pacotaco-xps:29386] Signal code: Address not mapped (1) [pacotaco-xps:29386] Failing at address: 0x44000098 [pacotaco-xps:29386] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f7eafdd8340] [pacotaco-xps:29386] [ 1] /usr/lib/libmpi.so.1(MPI_Comm_set_errhandler+0x4d) [0x7f7ead7fca1d] [pacotaco-xps:29386] [ 2] /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06(PetscInitialize+0x2a7) [0x7f7e9063f6b6] [pacotaco-xps:29386] [ 3] /home/justin/.local/lib/python2.7/site-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so(+0x11d3e8) [0x7f7e8e33c3e8] [pacotaco-xps:29386] [ 4] /usr/bin/python(PyEval_EvalFrameEx+0x40d) [0x49968d] [pacotaco-xps:29386] [ 5] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [ 6] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [ 7] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [ 8] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] [ 9] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [10] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [11] /usr/bin/python() [0x541510] [pacotaco-xps:29386] [12] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [13] /usr/bin/python(PyObject_Call+0x36) [0x505f96] [pacotaco-xps:29386] [14] /usr/bin/python() [0x536095] [pacotaco-xps:29386] [15] /usr/bin/python(PyObject_CallFunction+0xa5) [0x4ca095] [pacotaco-xps:29386] [16] /usr/bin/python(PyImport_Import+0xdd) [0x525e8d] [pacotaco-xps:29386] [17] /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(+0x770a) [0x7f7e915de70a] [pacotaco-xps:29386] [18] /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(initsparsity+0x1244) [0x7f7e915f91a4] [pacotaco-xps:29386] [19] /usr/bin/python(_PyImport_LoadDynamicModule+0x9b) [0x42266c] [pacotaco-xps:29386] [20] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [21] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [22] /usr/bin/python() [0x54111b] [pacotaco-xps:29386] [23] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [24] /usr/bin/python(PyEval_CallObjectWithKeywords+0x6b) [0x4dc9cb] [pacotaco-xps:29386] [25] /usr/bin/python(PyEval_EvalFrameEx+0x25fe) [0x49b87e] [pacotaco-xps:29386] [26] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [27] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [28] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [29] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] *** End of error message *** Segmentation fault (core dumped) Any idea what's going on? Thanks, Justin PS - this is a slightly separate issue from the petsc4py issue I posted in petsc-users (though it might be related?) But I figured I should try to resolve this one first.

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Counting FLOPS for assembling residual and Jacobian
by Justin Chang 05 Aug '15

05 Aug '15

Hi all, Is it possible to include manual/PETSc counts within the assembly of the FormResidual and FormJacobian routines? Because I think it would be nice to look at the performance of how firedrake is assembling these finite element discretization instead of always relying on hardware counters. Thanks, Justin

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