October 2014 - firedrake - imperial.ac.uk

Firedrake paper results
by Florian Rathgeber 11 Nov '14

11 Nov '14

Dear all, I finished a first draft of the results section for the Firedrake paper. Any feedback gratefully received! If you don't have access to the repository you can get a PDF from https://wwwhomes.doc.ic.ac.uk/~fr710/paper.pdf Cheers, Florian

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Re: [firedrake] PyOp2 Installation Issue
by David Ham 31 Oct '14

31 Oct '14

On 31 October 2014 10:18, Cotter, Colin J <colin.cotter(a)imperial.ac.uk> wrote: > I still think that the install instructions for different systems should > be on entirely different pages. > This simply means having multiple sets of almost identical instructions to maintain. Are you volunteering to do the maintenance? > > --cjc > > On 30/10/14 09:56, Lawrence Mitchell wrote: > > Hi Brian, > > > > On 30/10/14 09:28, Brian Weston wrote: > >> Hello, > >> > >> I am trying to install PyOp2 on my Macbook (10.9) and I'm having an > >> issue. In my terminal, I typed: > >> > >> wget -O - https://github.com/OP2/PyOP2/raw/master/install.sh | sudo > bash > >> > >> and at the end of my install log file: > > > > Hmmm, I'm not sure that we believe the install script will work on > > MacOS, it's pretty much specific to apt-based Linux systems, so I'm > > somewhat surprised it got this far. On MacOS, we recommend obtaining a > > build environment for PyOP2 using homebrew. Can you try following the > > instructions for install given here: > > > > > http://firedrakeproject.org/obtaining_pyop2.html#obtaining-a-build-environm… > > > > Suggestions as to how to make the different install descriptions clearer > > very welcome. > > > > Unfortunately, this isn't an automated script, however, it's quite a > > short list. > > > > Once you have the build environment you can then install PETSc and > > petsc4py using pip. With the homebrew setup we describe, you don't need > > to use sudo with pip. With that out of the way you can then follow the > > instructions at > > > > http://firedrakeproject.org/obtaining_pyop2.html#building-pyop2 > > > > To build PyOP2 itself. > > > > Cheers, > > > > Lawrence > > > > _______________________________________________ > > firedrake mailing list > > firedrake(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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PyOp2 Installation Issue
by Brian Weston 31 Oct '14

31 Oct '14

Hello, I am trying to install PyOp2 on my Macbook (10.9) and I'm having an issue. In my terminal, I typed: wget -O - https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash and at the end of my install log file: "Successfully installed petsc4py Cleaning up... *** Installing PyOP2 *** Cloning into 'PyOP2'... Checking connectivity... done Traceback (most recent call last): File "setup.py", line 45, in <module> import petsc4py ImportError: No module named petsc4py" Sincerely, Brian

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ARCHER
by Colin Cotter 27 Oct '14

27 Oct '14

Dear all, Is there some information on the web somewhere about how to build and execute Firedrake on ARCHER? all the best --cjc

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memory leak?
by Colin Cotter 21 Oct '14

21 Oct '14

Dear all, We are getting a memory leak in our slice model solver and we can't work out where we are making it. The time loop pretty much just consists of some solver calls and Function += calls. To see our test, please check out https://bitbucket.org/colinjcotter/slicemodels and run test_linear.py. We are observing a slow and steady increase in memory usage. cheers Colin and Hiroe

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Re: [firedrake] PETSc install instructions update
by David Ham 19 Oct '14

19 Oct '14

Yes, I forgot to push the website. It's up now. On 19 October 2014 10:54, McRae, Andrew <a.mcrae12(a)imperial.ac.uk> wrote: > I assume unintended, since it was updated in both the unattended install > script and the buildbot script. > > I've done the commit -- > https://github.com/OP2/PyOP2/commit/e06ecaf41c8eea7803850e1085c0bd80e6005a4c > -- but I think someone else needs to rebuild the website manually. > > On 19 October 2014 10:44, Eike Mueller <e.mueller(a)bath.ac.uk> wrote: > >> Hi Lawrence, >> >> this fixes it and it runs fine again on my laptop. >> >> As far as I can see the petsc4py installation instructions on >> >> http://www.firedrakeproject.org/obtaining_pyop2.html#petsc >> >> still point to https://bitbucket.org/petsc/petsc4py.git, is this >> intended, or does the firedrake trunk indeed work with this setup? >> >> Thanks a lot, >> >> Eike >> >> -- >> >> Dr Eike Hermann Mueller >> Research Associate (PostDoc) >> >> Department of Mathematical Sciences >> University of Bath >> Bath BA2 7AY, United Kingdom >> >> +44 1225 38 5803 >> e.mueller(a)bath.ac.uk >> http://people.bath.ac.uk/em459/ >> >> On 17 Oct 2014, at 15:26, David Ham <David.Ham(a)imperial.ac.uk> wrote: >> >> Dear Firedrakers, >> >> Some of you have recently had problems with installing PETSc recently. >> There is now a fix for this, and also new install URLs for PETSc and >> petsc4py which will hopefully reduce the number of ongoing PETSc install >> issues that people have. >> >> The short version is that the instructions for installing PETSc and >> petsc4py on our websites have been updated, so if you are installing or >> upgrading PETSc you should follow the new instructions: >> http://www.firedrakeproject.org/obtaining_pyop2.html#petsc >> >> The ever so slightly longer version is that we now point to our own >> fork of PETSc rather than the upstream master. We will update our forks as >> necessary and only after checking that the version we update to appears to >> work. This should hopefully reduce the number of random breakages users >> encounter in PETSc. >> >> Cheers, >> >> David >> >> -- >> Dr David Ham >> Departments of Mathematics and Computing >> Imperial College London >> >> http://www.imperial.ac.uk/people/david.ham >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> >> > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] PETSc install instructions update
by Andrew McRae 19 Oct '14

19 Oct '14

I assume unintended, since it was updated in both the unattended install script and the buildbot script. I've done the commit -- https://github.com/OP2/PyOP2/commit/e06ecaf41c8eea7803850e1085c0bd80e6005a4c -- but I think someone else needs to rebuild the website manually. On 19 October 2014 10:44, Eike Mueller <e.mueller(a)bath.ac.uk> wrote: > Hi Lawrence, > > this fixes it and it runs fine again on my laptop. > > As far as I can see the petsc4py installation instructions on > > http://www.firedrakeproject.org/obtaining_pyop2.html#petsc > > still point to https://bitbucket.org/petsc/petsc4py.git, is this > intended, or does the firedrake trunk indeed work with this setup? > > Thanks a lot, > > Eike > > -- > > Dr Eike Hermann Mueller > Research Associate (PostDoc) > > Department of Mathematical Sciences > University of Bath > Bath BA2 7AY, United Kingdom > > +44 1225 38 5803 > e.mueller(a)bath.ac.uk > http://people.bath.ac.uk/em459/ > > On 17 Oct 2014, at 15:26, David Ham <David.Ham(a)imperial.ac.uk> wrote: > > Dear Firedrakers, > > Some of you have recently had problems with installing PETSc recently. > There is now a fix for this, and also new install URLs for PETSc and > petsc4py which will hopefully reduce the number of ongoing PETSc install > issues that people have. > > The short version is that the instructions for installing PETSc and > petsc4py on our websites have been updated, so if you are installing or > upgrading PETSc you should follow the new instructions: > http://www.firedrakeproject.org/obtaining_pyop2.html#petsc > > The ever so slightly longer version is that we now point to our own fork > of PETSc rather than the upstream master. We will update our forks as > necessary and only after checking that the version we update to appears to > work. This should hopefully reduce the number of random breakages users > encounter in PETSc. > > Cheers, > > David > > -- > Dr David Ham > Departments of Mathematics and Computing > Imperial College London > > http://www.imperial.ac.uk/people/david.ham > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

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PETSc install instructions update
by David Ham 19 Oct '14

19 Oct '14

Dear Firedrakers, Some of you have recently had problems with installing PETSc recently. There is now a fix for this, and also new install URLs for PETSc and petsc4py which will hopefully reduce the number of ongoing PETSc install issues that people have. The short version is that the instructions for installing PETSc and petsc4py on our websites have been updated, so if you are installing or upgrading PETSc you should follow the new instructions: http://www.firedrakeproject.org/obtaining_pyop2.html#petsc The ever so slightly longer version is that we now point to our own fork of PETSc rather than the upstream master. We will update our forks as necessary and only after checking that the version we update to appears to work. This should hopefully reduce the number of random breakages users encounter in PETSc. Cheers, David -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] firedrake on ARCHER - helmholtz solver for larger core counts
by Andrew McRae 18 Oct '14

18 Oct '14

Question to others: could this be related to the 'subtract a large number to apply BCs' hack, or is that only for extruded meshes? On 18 Oct 2014 11:43, "Eike Mueller" <e.mueller(a)bath.ac.uk> wrote: > Dear all, > > with Lawrence's fix it now works with 10 levels (20,971,520 cells) on > two full nodes. If I increase both the number of cells and the number of > nodes by a factor of 4 (i.e. same #dof/core) I get a crash again. However, > the position in the code where it crashes varies, here are two example: > > https://gist.github.com/eikehmueller/a07007af72b34a57efff > > In the 1st and 3rd run, I had cleared the PyOP2/firedrake cashes, > whereas in the second case I'm not entirely sure what the state of the > cache was. > In the 3rd run I also set PYOP2_DEBUG=1, whereas it was 0 in the first two > runs. > The weird thing is also that the 3rd run seems to complete, but still > generates the dreaded PETSc seg fault. > > Thanks, > > Eike > > > -- > > Dr Eike Hermann Mueller > Research Associate (PostDoc) > > Department of Mathematical Sciences > University of Bath > Bath BA2 7AY, United Kingdom > > +44 1225 38 5803 > e.mueller(a)bath.ac.uk > http://people.bath.ac.uk/em459/ > > On 13 Oct 2014, at 11:22, Eike Mueller <E.Mueller(a)bath.ac.uk> wrote: > > Dear all, > > I rebuilt 'my' PETSc with debugging enabled, and then also rebuilt > petsc4py and firedrake. I could run on 48 cores with 7 levels once, but > this was not reproducible. When I tried again it crashed with a PETSc error. > > Is there any chance that the branches below help? Do I need > mlange/plex-distributed-overlap or can I use the PETSc master now? > > Thanks a lot, > > Eike > > firedrake: multigrid-parallel > pyop2: local-par_loop > petsc4py: bitbucket.org/mapdes/petsc4py branch moar-plex > petsc: mlange/plex-distributed-overlap > > > Functionality similar to the latter should hopefully arrive in petsc > master this week > > Lawrence > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- > Dr Eike Hermann Mueller > Research Associate (PostDoc) > > Department of Mathematical Sciences > University of Bath > Bath BA2 7AY, United Kingdom > > +44 1225 38 5803 > e.mueller(a)bath.ac.uk > http://people.bath.ac.uk/em459/ > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

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firedrake on ARCHER - helmholtz solver for larger core counts
by Eike Mueller 18 Oct '14

18 Oct '14

Dear firedrakers, I tried to run the Helmholtz multigrid solver on higher core counts on ARCHER. In certain configurations it works, but in others it crashes. The number of fine grid cells is 20*4^(4+refcount_coarse). In particular, I was not able to run on 48 cores (i.e. 2 full nodes) 1 node, 16 cores/node = 16 cores, refcount_coarse=5: Runs 2 nores, 16 cores/node = 48 cores, refcount_coarse=4: hangs without printing error message 2 nores, 16 cores/node = 48 cores, refcount_coarse=5: crashes with PETSc error message 2 nores, 16 cores/node = 48 cores, refcount_coarse=5: crashes with different error message Output logs for all cases are attached, as well as the pbs scripts for running on 48 cores. I also tried running the poisson example in firedrake-benchmark in different configurations: 1 node, 16 cores/node = 16 cores => works 2 nodes, 8 cores/node = 16 cores => works 2 nodes, 24 cores/node = 48 cores => crashes with PETSc error I did use the generic ARCHER firedrake installation in this case, though. In the Helmholtz solver runs I used my own version of firedrake and PyOP2 since I need the multigrid and local_par-loop branches. This makes me suspicious that it is not a problem specific to my code, but then I thought that you did run firedrake on relatively large core counts before, didn't you? The output of the Poisson benchmarks is also attached. Any ideas what might be going wrong and what is the best way for debugging this? Thanks, Eike -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5803 e.mueller(a)bath.ac.uk http://people.bath.ac.uk/em459/

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