- firedrake - imperial.ac.uk

Re: [firedrake] compile problem
by Andrew McRae 03 Jul '14

03 Jul '14

Can you try the FFC branch "const-access"? On 3 July 2014 18:57, Shipton, Jemma <j.shipton(a)imperial.ac.uk> wrote: > Hi All, > > Sorry to post a question in the chat and then disappear - I'd lost track > of time and needed to dash home. Anyway, I've copied and pasted my > question... > > 18:26 < jemma> I have pulled some code Colin added this morning > 18:27 < jemma> and it doesn't work - although Colin was quite happily > running > it before he went to watch tennis > 18:27 < jemma> can anyone see why there'd be a problem with this: > 18:27 < jemma> u = project(Expression(("1.0 + > > sin(pi*(x[0]-t))*sin(pi*x[1])*cos(pi*t/T0)","cos(pi*(x[0]-t))*cos(pi*x[1])*cos(pi*t/T0)")t=t,T0=T0),V1) > 18:28 < jemma> where V1 comes from: > 18:28 < jemma> V1_v = OuterProductElement(IUh1, IUv0) > 18:28 < jemma> V1_h = OuterProductElement(IUh0, IUv1) > 18:28 < jemma> V1_elt = HDiv(V1_v) + HDiv(V1_h) > 18:28 < jemma> V1 = FunctionSpace(mesh,V1_elt) > 18:28 < jemma> t and T0 are defined > 18:29 < jemma> maybe I'm missing a ufl/pyop2/something update - I haven't > updated in a while... > > When I run the code won't even compile: > > pyop2.exceptions.CompilationError: Unable to compile code > > I've attached the log and err files. The problem seems to be the variables > t and T0 in the expression - although they are defined in previous lines: > > t = 0.0 > T0 = 1.0 > > The script I'm trying to run is at: > https://bitbucket.org/colinjcotter/vertical-tests/src/c1a2a565912564897fdbe… > > Thanks! > > Jemma >

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compile problem
by Shipton, Jemma 03 Jul '14

03 Jul '14

Hi All, Sorry to post a question in the chat and then disappear - I'd lost track of time and needed to dash home. Anyway, I've copied and pasted my question... 18:26 < jemma> I have pulled some code Colin added this morning 18:27 < jemma> and it doesn't work - although Colin was quite happily running it before he went to watch tennis 18:27 < jemma> can anyone see why there'd be a problem with this: 18:27 < jemma> u = project(Expression(("1.0 + sin(pi*(x[0]-t))*sin(pi*x[1])*cos(pi*t/T0)","cos(pi*(x[0]-t))*cos(pi*x[1])*cos(pi*t/T0)")t=t,T0=T0),V1) 18:28 < jemma> where V1 comes from: 18:28 < jemma> V1_v = OuterProductElement(IUh1, IUv0) 18:28 < jemma> V1_h = OuterProductElement(IUh0, IUv1) 18:28 < jemma> V1_elt = HDiv(V1_v) + HDiv(V1_h) 18:28 < jemma> V1 = FunctionSpace(mesh,V1_elt) 18:28 < jemma> t and T0 are defined 18:29 < jemma> maybe I'm missing a ufl/pyop2/something update - I haven't updated in a while... When I run the code won't even compile: pyop2.exceptions.CompilationError: Unable to compile code I've attached the log and err files. The problem seems to be the variables t and T0 in the expression - although they are defined in previous lines: t = 0.0 T0 = 1.0 The script I'm trying to run is at: https://bitbucket.org/colinjcotter/vertical-tests/src/c1a2a565912564897fdbe… Thanks! Jemma

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Meeting tomorrow
by Lawrence Mitchell 03 Jul '14

03 Jul '14

Dear firedrakers, for the avoidance of doubt, those of us currently local to Imperial will be holding our weekly meeting tomorrow at 1pm in WPL 301. Lawrence

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Fwd: [PRISM] PRISM Technical Seminar: 10th July 10am
by Lawrence Mitchell 02 Jul '14

02 Jul '14

Dear firedrakers, next week, I'll be continuing the PRISM technical seminar series with an overview of the design and implementation of Firedrake and PyOP2. If you're interested, do come along. 10am Thursday 10th July in Room 266 Roderic Hill (Aeronautic). See abstract below. Cheers, Lawrence -------- Original Message -------- Subject: [PRISM] PRISM Technical Seminar: 10th July 10am Date: Wed, 11 Jun 2014 15:34:11 +0100 From: Chris Cantwell <c.cantwell(a)imperial.ac.uk> Organization: Imperial College London To: <prism(a)imperial.ac.uk> Dear all, The next PRISM technical seminar will take place as follows: Speaker: Lawrence Mitchell Title: The design and implementation of Firedrake and PyOP2 Time: Thursday 10th July, 10am Place: TBC Abstract: The guiding principle in the development of PyOP2 and Firedrake is "get the abstraction right and everything else is easy". In this talk, I will present the abstractions in PyOP2 and and Firedrake (and their implementation). Starting with the data structures and parallel iteration construct in PyOP2 for execution on unstructured meshes, I will move on to explain how these handcuffs influence the design of Firedrake, and why we think they're a good thing. Although Firedrake itself is designed as a finite element package, the separation of mesh iteration into a PyOP2 level leads to the ability to "escape" out of the variational jail in a clean way, and I will describe why we might want to do so. Finally, I'll motivate why we don't want to implement any solvers ourselves, and describe how we interact with PETSc to provide us with both linear and non-linear solvers. Cheers, Chris -- Chris Cantwell Department of Aeronautics Roderic Hill Building Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell _______________________________________________ prism mailing list prism(a)imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/prism

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Looks like a relevant conference
by Colin Cotter 01 Jul '14

01 Jul '14

http://conan.iwr.uni-heidelberg.de/sppexa-workshop/

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GitHub private repositories for OP2 and firedrake
by Florian Rathgeber 30 Jun '14

30 Jun '14

I have applied for an academic upgrade and we have been granted a free silver plan with 20 private repositories each for the OP2 and firedrake organisations. Florian

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Re: [firedrake] Fwd: [FEniCS] Summer intern to work on python 3 support / FIAT PR
by David Ham 30 Jun '14

30 Jun '14

Does this actually change anything we care about, or is it orthogonal? On 29 June 2014 21:27, McRae, Andrew <a.mcrae12(a)imperial.ac.uk> wrote: > Originally posted to the FEniCS mailing list. This is relevant for us > (or maybe just "me"), too. > > Andrew > > ---------- Forwarded message ---------- > From: Nico Schlömer <nico.schloemer(a)gmail.com> > Date: 29 June 2014 21:18 > Subject: Re: [FEniCS] Summer intern to work on python 3 support > To: Martin Sandve Alnæs <martinal(a)simula.no> > Cc: Jan Blechta <blechta(a)karlin.mff.cuni.cz>, Aslak Bergersen < > aslak.bergersen(a)gmail.com>, "fenics(a)fenicsproject.org" < > fenics(a)fenicsproject.org> > > > FWIW, I created a pull request that improves FIAT and removes almost > all of ScientificPython, cf. > < > https://bitbucket.org/fenics-project/fiat/pull-request/2/remove-almost-all-… > >. > If this gets reviewed (and possibly improved) soon, we might get to > Python3-ready FEniCS quiet quick. > > Cheers, > Nico > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Fwd: [FEniCS] Summer intern to work on python 3 support / FIAT PR
by Andrew McRae 29 Jun '14

29 Jun '14

Originally posted to the FEniCS mailing list. This is relevant for us (or maybe just "me"), too. Andrew ---------- Forwarded message ---------- From: Nico Schlömer <nico.schloemer(a)gmail.com> Date: 29 June 2014 21:18 Subject: Re: [FEniCS] Summer intern to work on python 3 support To: Martin Sandve Alnæs <martinal(a)simula.no> Cc: Jan Blechta <blechta(a)karlin.mff.cuni.cz>, Aslak Bergersen < aslak.bergersen(a)gmail.com>, "fenics(a)fenicsproject.org" < fenics(a)fenicsproject.org> FWIW, I created a pull request that improves FIAT and removes almost all of ScientificPython, cf. < https://bitbucket.org/fenics-project/fiat/pull-request/2/remove-almost-all-… >. If this gets reviewed (and possibly improved) soon, we might get to Python3-ready FEniCS quiet quick. Cheers, Nico

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petsc
by Colin Cotter 25 Jun '14

25 Jun '14

Hi Folks, I've tried to update my petsc4py. I started by re-pip-installing petsc, and then ran "sudo python setup.py --install" in an updated petsc4py directory, and got the output which can be read at the bottom of this email, which was unexpected. cheers --cjc cjc1@ae-gauss:~/firedrake/petsc4py$ sudo python setup.py install running install running build running build_src running build_py running build_ext PETSC_DIR: /usr/local/lib/python2.7/dist-packages/petsc PETSC_ARCH: scalar-type: real precision: double language: CONLY compiler: /usr/bin/mpicc.openmpi linker: /usr/bin/mpicc.openmpi building 'PETSc' extension /usr/bin/mpicc.openmpi -pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DPETSC_DIR=/usr/local/lib/python2.7/dist-packages/petsc -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include -I/usr/local/lib/python2.7/dist-packages/petsc/include -Isrc/include -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/PETSc.c -o build/temp.linux-x86_64-2.7/src/PETSc.o In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from src/include/petsc4py/numpy.h:11, from src/petsc4py.PETSc.c:347, from src/PETSc.c:3: /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_8create’: src/petsc4py.PETSc.c:71088:3: warning: passing argument 3 of ‘ISLocalToGlobalMappingCreate’ makes pointer from integer without a cast [enabled by default] /usr/local/lib/python2.7/dist-packages/petsc/include/petscis.h:143:29: note: expected ‘const PetscInt *’ but argument is of type ‘PetscInt’ src/petsc4py.PETSc.c:71088:3: error: incompatible type for argument 4 of ‘ISLocalToGlobalMappingCreate’ /usr/local/lib/python2.7/dist-packages/petsc/include/petscis.h:143:29: note: expected ‘PetscCopyMode’ but argument is of type ‘PetscInt *’ src/petsc4py.PETSc.c:71088:3: error: incompatible type for argument 5 of ‘ISLocalToGlobalMappingCreate’ /usr/local/lib/python2.7/dist-packages/petsc/include/petscis.h:143:29: note: expected ‘struct _p_ISLocalToGlobalMapping **’ but argument is of type ‘PetscCopyMode’ src/petsc4py.PETSc.c:71088:3: error: too many arguments to function ‘ISLocalToGlobalMappingCreate’ /usr/local/lib/python2.7/dist-packages/petsc/include/petscis.h:143:29: note: declared here src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_14getBlockSize’: src/petsc4py.PETSc.c:71405:3: warning: implicit declaration of function ‘ISLocalToGlobalMappingGetBlockSize’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_18getBlockIndices’: src/petsc4py.PETSc.c:71752:3: warning: implicit declaration of function ‘ISLocalToGlobalMappingGetBlockIndices’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c:71803:7: warning: implicit declaration of function ‘ISLocalToGlobalMappingRestoreBlockIndices’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_22getBlockInfo’: src/petsc4py.PETSc.c:72204:3: warning: implicit declaration of function ‘ISLocalToGlobalMappingGetBlockInfo’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c:72259:7: warning: implicit declaration of function ‘ISLocalToGlobalMappingRestoreBlockInfo’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_26applyBlock’: src/petsc4py.PETSc.c:72724:3: warning: implicit declaration of function ‘ISLocalToGlobalMappingApplyBlock’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_5LGMap_32applyBlockInverse’: src/petsc4py.PETSc.c:73315:3: warning: implicit declaration of function ‘ISGlobalToLocalMappingApplyBlock’ [-Wimplicit-function-declaration] src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_4DMDA_62getScatter’: src/petsc4py.PETSc.c:186920:3: error: too few arguments to function ‘DMDAGetScatter’ /usr/local/lib/python2.7/dist-packages/petsc/include/petscdmda.h:71:29: note: declared here error: command '/usr/bin/mpicc.openmpi' failed with exit status 1

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reproducible parallel summation
by Kelly, Paul H J 23 Jun '14

23 Jun '14

Further to various discussions of reproducibility, I thought you might be interested in this paper: http://hal.archives-ouvertes.fr/docs/00/94/93/55/PDF/superaccumulator.pdf Full-Speed Deterministic Bit-Accurate Parallel Floating-Point Summation on Multi- and Many-Core Architectures Abstract. On modern multi-core, many-core, and heterogeneous architectures, ﬂoating-point computations, especially reductions, may become non-deterministic and thus non-reproducible mainly due to non-associativity of ﬂoating-point operations. We introduce a solution to compute deterministic sums of ﬂoating-point numbers efﬁciently and with the best possible accuracy. Our multi-level algorithm consists of two main stages: a ﬁltering stage that uses fast vectorized ﬂoating-point expansions; an accumulation stage based on superaccumulators in a high-radix carry-save representation. We present implementations on recent Intel desktop and server processors, on Intel Xeon Phi accelerator, and on AMD and NVIDIA GPUs. We show that the numerical reproducibility and bit-perfect accuracy can be achieved at no additional cost for large sums that have dynamic ranges of up to 90 orders of magnitude by leveraging arithmetic units that are left underused by standard reduction algorithms. Paul

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