March 2014 - firedrake - imperial.ac.uk

FEniCS/PDESoft Abstracts
by Florian Rathgeber 14 Apr '14

14 Apr '14

Hi all, Here are my drafts of potential talks to submit: FEniCS'14: https://gist.github.com/kynan/9c9c048b0c05fa8d0188 "Firedrake: Composing Domain-specific Abstractions for Productive and Efficient Computational Science" PDESoft 14: https://gist.github.com/kynan/025857adaa21bfabdd59 "PyOP2: a performance-portable framework for parallel computations on unstructured meshes" Cheers, Florian

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environment
by Cotter, Colin J 27 Mar '14

27 Mar '14

Dear Firedrakers, I've opened a new terminal and there is something not right with my environment: cjc1@richardson:~/mercurial/vertical-tests$ python Traceback (most recent call last): File "/usr/lib/python2.7/site.py", line 68, in <module> import os File "/usr/lib/python2.7/os.py", line 49, in <module> import posixpath as path File "/usr/lib/python2.7/posixpath.py", line 17, in <module> import warnings File "/usr/lib/python2.7/warnings.py", line 8, in <module> import types File "/home/cjc1/firedrake/firedrake/firedrake/types.py", line 1, in <module> import numpy as np ImportError: No module named numpy I had this yesterday on my workstation but I've forgotten how I fixed it. What do I need to do? cheers --cjc

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Fwd: K40
by Kelly, Paul H J 27 Mar '14

27 Mar '14

We now have access to a shiny new Nvidia K40 GPU on CX1, see below. This is a kind donation from Nvidia, as a result of Imperial becoming an official CUDA Research Centre (the process was led by Peter Vincent). Paul Begin forwarded message: From: "Harvey, M J" <m.j.harvey(a)imperial.ac.uk<mailto:m.j.harvey@imperial.ac.uk>> Date: 27 March 2014 16:40:53 GMT To: "Kelly, Paul H J" <p.kelly(a)imperial.ac.uk<mailto:p.kelly@imperial.ac.uk>>, "Vincent, Peter E" <p.vincent(a)imperial.ac.uk<mailto:p.vincent@imperial.ac.uk>> Subject: Re: K40 Paul, Yes. For the moment, you can get it with: #PBS -lselect=1:ncpus=1:ngpus=1:host=cx1-30-12-1 #PBS -q pqkelly ________________________________________ De: Kelly, Paul H J Enviado: jueves, 27 de marzo de 2014 16:36 Para: Vincent, Peter E CC: Harvey, M J Asunto: Re: K40 Hi Peter, hi Matt Did this card get installed? Cheers, Paul On 16 Mar 2014, at 23:46, Vincent, Peter E wrote: Dear All, Regarding below, the consensus was to put the card in a shared machine in HPC. I plan to meet Matt Harvey later this week to hand over the card. I will send out further details of how to access it once it is in place. Cheers Peter Dr Peter Vincent MSci ARCS DIC PhD Lecturer and EPSRC Early Career Fellow Department of Aeronautics Imperial College London South Kensington London SW7 2AZ UK web: www.imperial.ac.uk/aeronautics/research<http://www.imperial.ac.uk/aeronautics/research>/vincentlab<http://www.imperial.ac.uk/aeronautics/research/vincentlab> twitter: @Vincent_Lab<https://twitter.com/Vincent_Lab> On 10 Mar 2014, at 19:09, Peter Vincent <p.vincent(a)imperial.ac.uk<mailto:p.vincent@imperial.ac.uk>> wrote: Dear All, Nvidia have sent us a K40 as part of the CRC. Can I please have suggestions for what to do with it. Options include: 1.) Put it in a box that we can all access remotely. 2.) Pass it around between us so we can each play with it for a few weeks in our local systems. Cheers Peter Dr Peter Vincent MSci ARCS DIC PhD Lecturer and EPSRC Early Career Fellow Department of Aeronautics Imperial College London South Kensington London SW7 2AZ email: p.vincent(a)imperial.ac.uk<mailto:p.vincent@imperial.ac.uk> web: www.imperial.ac.uk/aeronautics/research/vincentlab<http://www.imperial.ac.uk/aeronautics/research/vincentlab>/<http://www.imperial.ac.uk/aeronautics/research/vincentlab/> twitter: @Vincent_Lab<https://twitter.com/#!/Vincent_Lab>

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Expressions compiler
by Cotter, Colin J 27 Mar '14

27 Mar '14

Dear Firedrakers, Please excuse my excitement, but the expressions compiler is extremely cool. For example, it allows an application of an SSPRK timestepping scheme in the following compact form: while (t <= end): solve(lhsA == action(rhsA,oldT), newT) T1.assign(newT) solve(lhsA == action(rhsA,T1), newT) T2.assign(0.75*oldT + 0.25*newT) solve(lhsA == action(rhsA,T2), newT) newT.assign((1.0/3.0)*oldT + (2.0/3.0)*newT) oldT.assign(newT) cheers --cjc

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Fwd: PDESoft Abstract
by Lawrence Mitchell 27 Mar '14

27 Mar '14

Begin forwarded message: > From: "Bercea, Gheorghe-teodor" <gheorghe-teodor.bercea08(a)imperial.ac.uk> > Subject: PDESoft Abstract > Date: 20 March 2014 16:28:51 GMT > To: "Ham, David A" <david.ham(a)imperial.ac.uk> > Cc: "Kelly, Paul H J" <p.kelly(a)imperial.ac.uk>, "McRae, Andrew" <a.mcrae12(a)imperial.ac.uk>, "Luporini, Fabio" <f.luporini12(a)imperial.ac.uk>, "Loriant, Nicolas" <n.loriant(a)imperial.ac.uk>, Lawrence Mitchell <lawrence.mitchell(a)ed.ac.uk> > > Hi everyone, > > Here's my abstract for PDESoft. It's a tentative abstract, it's longer than it should be, and the results section contains a bit of wishful thinking. With that in mind, I would like to know if the message matches the audience. > > Let me know what you think. > > Best wishes, > > Doru > >

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FW: PRISM talk: Thursday 3rd April 12:00 RH254
by Cotter, Colin J 27 Mar '14

27 Mar '14

I'm away next week, but would be good if some others could get to this to help cement our college computational science connections. cheers --cjc ________________________________________ From: Chris Cantwell [c.cantwell(a)imperial.ac.uk] Sent: 27 March 2014 08:34 To: Sherwin, Spencer J; Kelly, Paul H J; Pain, Christopher; Piggott, Matthew D; Cotter, Colin J; Ham, David A; Peiro, Joaquim; Gorman, Gerard J; Vincent, Peter E Subject: PRISM talk: Thursday 3rd April 12:00 RH254 Dear all, We have a visitor, Kilian Lackhove from the Technische Universitat Darmstadt, funded under the PRISM platform visiting on Thursday and Friday next week and he will be giving a brief talk on his work. Title: "Using Nektar++ as CAA solver in a coupled setup for combustion noise modeling" Time: Thursday 1st April, 12:00 Room: Aeronautics, RH254 I would be grateful if you could circulate to your groups and anyone interested is welcome to attend. Please let me know if you would also like to meet with him during his visit. Cheers, Chris -- Chris Cantwell Research Fellow National Heart & Lung Institute Imperial College London South Kensington Campus Room L57, Roderic Hill Building, Department of Aeronautics London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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Re: [firedrake] dmplex migration
by Fabio Luporini 25 Mar '14

25 Mar '14

Hi, Right - let's go for option (a), then. Thanks -- Fabio 2014-03-25 9:55 GMT+00:00 Ham, David A <david.ham(a)imperial.ac.uk>: > Hi Fabio, > > I think there might be some confusion here. Option c is not to continue > development at the point of master from which you have currently branched. > We're dropping support for pre-dmplex firedrake so that branch is going to > stop working on all our systems. Option c means that you rebase the branch > yourself rather than Lawrence doing it. > > Regards, > > David > > > On 24 March 2014 16:33, Luporini, Fabio <f.luporini12(a)imperial.ac.uk>wrote: > >> For my branch: >> - pyop2-ir-perf-eval >> >> I choose option (c). It's still under development, but it's there just, >> as you said, for benchmarking. >> >> Thanks >> >> -- Fabio >> >> >> 2014-03-24 14:59 GMT+00:00 Mitchell, Lawrence < >> lawrence.mitchell(a)imperial.ac.uk>: >> >>> Dear firedrakers, >>> >>> >>> if you've been paying attention recently, you'll have noticed we just >>> transitioned to a dmplex based mesh infrastructure. Now would appear to be >>> a good time to do a little bit of branch spring cleaning. For each of the >>> branches listed please tell me if you would like it: >>> >>> (a) kept and pulled forward onto master (still under active development) >>> (b) pulled forward onto master and proposed for merging >>> (c) left alone (under development but you'll do it yourself) >>> (d) removed (the branch is abandoned) >>> >>> I've organised the branches by "owner", that is the person who has made >>> the most commits on it, but please check the entire list. >>> >>> David's branches: >>> >>> - form_cache is in (a), but already rebased >>> - public_coordinates is in (b) >>> - real-function-space >>> Discussions suggest we need to actually implement these, but we >>> probably need to sit down and think about how to do it properly. >>> - wave-demo >>> This made the video on the front page of the website, should probably >>> be pulled forward and documented in the same way as the other demos. >>> >>> Doru's branches: >>> >>> - extrusion-facets-rhs >>> This appears under active development as in in review I think >>> - rebased-efr >>> I think this is the same functionality as extrusion-facets-rhs but >>> rebased on a different commit, abandon? >>> - extrusion-facets >>> Abandoned in favour of extrusion-facets-rhs? >>> - extrusion-documentation >>> In review but needing multiple fixes to text before merging >>> - extrusion-mixed-bcs >>> I think this is abandoned, it's got a blowing up discretisation of >>> extruded linear boussinesq we wrote for the October gung-ho meeting. >>> - ext_bc_demo >>> no clue >>> - extrusion-vfs >>> Has some tests, I don't know if they're in master >>> - extrusion-vfs-new >>> has some tests and some IR-related changes. >>> - extrusion >>> has some tests >>> >>> Florian's branches: >>> >>> - split-forms >>> Needs pulling forward and merging, I think. >>> - split-kernels >>> Abandoned in favour of split-forms? >>> - fenics-1.3 >>> Needs to come forward I think >>> - pytest-2.5.2 >>> Asks for newer pytest versions on travis >>> - petsc-ppa >>> Probably abandon ware, since we don't have petsc packages for now. >>> - moar-lint >>> Adds even tighter linking to travis >>> >>> >>> Lawrence's branches: >>> >>> - more-nullspace >>> In progress >>> - matrix-free >>> Needs updating to master, I don't know what state the stuff Rod has >>> been working on is in, that may be a better bet. >>> - blocked-matrices >>> Abandon ware, will drop. >>> >>> Fabio's branches: >>> >>> - pyop2-ir-perf-eval >>> A bunch of stuff implementing a benchmarking test suite I think. >>> >>> Colin's branches: >>> >>> - hydrostatic: >>> A test case where the test and trial spaces differ. Colin, do you >>> want to keep this one? >>> >>> Simon's branches: >>> >>> - firedrake-adjoint >>> Various bits and pieces of firedrake-adjoint testing, I think this can >>> be dropped. >>> >>> Cheers, >>> >>> Lawrence >>> >> >> > > > -- > Dr David Ham > Departments of Mathematics and Computing > Imperial College London > > http://www.imperial.ac.uk/people/david.ham >

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dmplex migration
by Lawrence Mitchell 25 Mar '14

25 Mar '14

Dear firedrakers, if you've been paying attention recently, you'll have noticed we just transitioned to a dmplex based mesh infrastructure. Now would appear to be a good time to do a little bit of branch spring cleaning. For each of the branches listed please tell me if you would like it: (a) kept and pulled forward onto master (still under active development) (b) pulled forward onto master and proposed for merging (c) left alone (under development but you'll do it yourself) (d) removed (the branch is abandoned) I've organised the branches by "owner", that is the person who has made the most commits on it, but please check the entire list. David's branches: - form_cache is in (a), but already rebased - public_coordinates is in (b) - real-function-space Discussions suggest we need to actually implement these, but we probably need to sit down and think about how to do it properly. - wave-demo This made the video on the front page of the website, should probably be pulled forward and documented in the same way as the other demos. Doru's branches: - extrusion-facets-rhs This appears under active development as in in review I think - rebased-efr I think this is the same functionality as extrusion-facets-rhs but rebased on a different commit, abandon? - extrusion-facets Abandoned in favour of extrusion-facets-rhs? - extrusion-documentation In review but needing multiple fixes to text before merging - extrusion-mixed-bcs I think this is abandoned, it's got a blowing up discretisation of extruded linear boussinesq we wrote for the October gung-ho meeting. - ext_bc_demo no clue - extrusion-vfs Has some tests, I don't know if they're in master - extrusion-vfs-new has some tests and some IR-related changes. - extrusion has some tests Florian's branches: - split-forms Needs pulling forward and merging, I think. - split-kernels Abandoned in favour of split-forms? - fenics-1.3 Needs to come forward I think - pytest-2.5.2 Asks for newer pytest versions on travis - petsc-ppa Probably abandon ware, since we don't have petsc packages for now. - moar-lint Adds even tighter linking to travis Lawrence's branches: - more-nullspace In progress - matrix-free Needs updating to master, I don't know what state the stuff Rod has been working on is in, that may be a better bet. - blocked-matrices Abandon ware, will drop. Fabio's branches: - pyop2-ir-perf-eval A bunch of stuff implementing a benchmarking test suite I think. Colin's branches: - hydrostatic: A test case where the test and trial spaces differ. Colin, do you want to keep this one? Simon's branches: - firedrake-adjoint Various bits and pieces of firedrake-adjoint testing, I think this can be dropped. Cheers, Lawrence

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Re: [firedrake] dmplex migration
by Andrew McRae 25 Mar '14

25 Mar '14

I will handle ext_bc_demo. It has an extruded mixed Helmholtz test in development, IIRC. On 25 March 2014 10:42, Bercea, Gheorghe-teodor < gheorghe-teodor.bercea08(a)imperial.ac.uk> wrote: > Hi Lawrence, > > As for my branches. > > - extrusion-facets-rhs (b) > - rebased-efr (c) > - extrusion-facets (d) > - extrusion-documentation (b) > - extrusion-mixed-bcs (d) > - ext_bc_demo (d) > - extrusion-vfs (c) > - extrusion-vfs-new (c) > - extrusion (c) > > Andrew, any objections on the extrusion-mixed-bcs and ext_bc_demo? Do you > still want to have those two branches around? > > Best wishes, > > Doru > > > > > > ________________________________________ > From: firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Lawrence Mitchell [lawrence.mitchell(a)imperial.ac.uk] > Sent: 24 March 2014 14:59 > To: firedrake > Subject: [firedrake] dmplex migration > > Dear firedrakers, > > if you've been paying attention recently, you'll have noticed we just > transitioned to a dmplex based mesh infrastructure. Now would appear to be > a good time to do a little bit of branch spring cleaning. For each of the > branches listed please tell me if you would like it: > > (a) kept and pulled forward onto master (still under active development) > (b) pulled forward onto master and proposed for merging > (c) left alone (under development but you'll do it yourself) > (d) removed (the branch is abandoned) > > I've organised the branches by "owner", that is the person who has made > the most commits on it, but please check the entire list. > > David's branches: > > - form_cache is in (a), but already rebased > - public_coordinates is in (b) > - real-function-space > Discussions suggest we need to actually implement these, but we probably > need to sit down and think about how to do it properly. > - wave-demo > This made the video on the front page of the website, should probably be > pulled forward and documented in the same way as the other demos. > > Doru's branches: > > - extrusion-facets-rhs > This appears under active development as in in review I think > - rebased-efr > I think this is the same functionality as extrusion-facets-rhs but > rebased on a different commit, abandon? > - extrusion-facets > Abandoned in favour of extrusion-facets-rhs? > - extrusion-documentation > In review but needing multiple fixes to text before merging > - extrusion-mixed-bcs > I think this is abandoned, it's got a blowing up discretisation of > extruded linear boussinesq we wrote for the October gung-ho meeting. > - ext_bc_demo > no clue > - extrusion-vfs > Has some tests, I don't know if they're in master > - extrusion-vfs-new > has some tests and some IR-related changes. > - extrusion > has some tests > > Florian's branches: > > - split-forms > Needs pulling forward and merging, I think. > - split-kernels > Abandoned in favour of split-forms? > - fenics-1.3 > Needs to come forward I think > - pytest-2.5.2 > Asks for newer pytest versions on travis > - petsc-ppa > Probably abandon ware, since we don't have petsc packages for now. > - moar-lint > Adds even tighter linking to travis > > > Lawrence's branches: > > - more-nullspace > In progress > - matrix-free > Needs updating to master, I don't know what state the stuff Rod has been > working on is in, that may be a better bet. > - blocked-matrices > Abandon ware, will drop. > > Fabio's branches: > > - pyop2-ir-perf-eval > A bunch of stuff implementing a benchmarking test suite I think. > > Colin's branches: > > - hydrostatic: > A test case where the test and trial spaces differ. Colin, do you want > to keep this one? > > Simon's branches: > > - firedrake-adjoint > Various bits and pieces of firedrake-adjoint testing, I think this can > be dropped. > > Cheers, > > Lawrence >

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Re: [firedrake] dmplex migration
by David Ham 25 Mar '14

25 Mar '14

Hi Fabio, I think there might be some confusion here. Option c is not to continue development at the point of master from which you have currently branched. We're dropping support for pre-dmplex firedrake so that branch is going to stop working on all our systems. Option c means that you rebase the branch yourself rather than Lawrence doing it. Regards, David On 24 March 2014 16:33, Luporini, Fabio <f.luporini12(a)imperial.ac.uk> wrote: > For my branch: > - pyop2-ir-perf-eval > > I choose option (c). It's still under development, but it's there just, > as you said, for benchmarking. > > Thanks > > -- Fabio > > > 2014-03-24 14:59 GMT+00:00 Mitchell, Lawrence < > lawrence.mitchell(a)imperial.ac.uk>: > >> Dear firedrakers, >> >> if you've been paying attention recently, you'll have noticed we just >> transitioned to a dmplex based mesh infrastructure. Now would appear to be >> a good time to do a little bit of branch spring cleaning. For each of the >> branches listed please tell me if you would like it: >> >> (a) kept and pulled forward onto master (still under active development) >> (b) pulled forward onto master and proposed for merging >> (c) left alone (under development but you'll do it yourself) >> (d) removed (the branch is abandoned) >> >> I've organised the branches by "owner", that is the person who has made >> the most commits on it, but please check the entire list. >> >> David's branches: >> >> - form_cache is in (a), but already rebased >> - public_coordinates is in (b) >> - real-function-space >> Discussions suggest we need to actually implement these, but we >> probably need to sit down and think about how to do it properly. >> - wave-demo >> This made the video on the front page of the website, should probably >> be pulled forward and documented in the same way as the other demos. >> >> Doru's branches: >> >> - extrusion-facets-rhs >> This appears under active development as in in review I think >> - rebased-efr >> I think this is the same functionality as extrusion-facets-rhs but >> rebased on a different commit, abandon? >> - extrusion-facets >> Abandoned in favour of extrusion-facets-rhs? >> - extrusion-documentation >> In review but needing multiple fixes to text before merging >> - extrusion-mixed-bcs >> I think this is abandoned, it's got a blowing up discretisation of >> extruded linear boussinesq we wrote for the October gung-ho meeting. >> - ext_bc_demo >> no clue >> - extrusion-vfs >> Has some tests, I don't know if they're in master >> - extrusion-vfs-new >> has some tests and some IR-related changes. >> - extrusion >> has some tests >> >> Florian's branches: >> >> - split-forms >> Needs pulling forward and merging, I think. >> - split-kernels >> Abandoned in favour of split-forms? >> - fenics-1.3 >> Needs to come forward I think >> - pytest-2.5.2 >> Asks for newer pytest versions on travis >> - petsc-ppa >> Probably abandon ware, since we don't have petsc packages for now. >> - moar-lint >> Adds even tighter linking to travis >> >> >> Lawrence's branches: >> >> - more-nullspace >> In progress >> - matrix-free >> Needs updating to master, I don't know what state the stuff Rod has >> been working on is in, that may be a better bet. >> - blocked-matrices >> Abandon ware, will drop. >> >> Fabio's branches: >> >> - pyop2-ir-perf-eval >> A bunch of stuff implementing a benchmarking test suite I think. >> >> Colin's branches: >> >> - hydrostatic: >> A test case where the test and trial spaces differ. Colin, do you want >> to keep this one? >> >> Simon's branches: >> >> - firedrake-adjoint >> Various bits and pieces of firedrake-adjoint testing, I think this can >> be dropped. >> >> Cheers, >> >> Lawrence >> > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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