July 2016 - firedrake - imperial.ac.uk

Re: [firedrake] Saving txt files while running in parallel
by Andrew McRae 30 Aug '16

30 Aug '16

Yes, I guess that in Floriane's original code, each process is computing its own max_eta (since eta.dat.data contains the values for degrees of freedom on that MPI process). Then all process are trying to write (or append?) to the same file(?). You could get the separate max values by making the filename depend on op2.MPI.comm.rank, so that each process writes to a separate file. Otherwise, computing the max over all subdomains indeed requires a parallel operation. On 8 June 2016 at 09:53, Shipton, Jemma <j.shipton(a)imperial.ac.uk> wrote: > Hi Floriane, > > > We have defined a max method that works in parallel for our code... try > something like: > > > def max(f): fmax = op2.Global(1, [-1000], dtype=float) op2.par_loop(op2.Kernel("""void maxify(double *a, double *b) { a[0] = a[0] < fabs(b[0]) ? fabs(b[0]) : a[0]; }""", "maxify"), f.dof_dset.set, fmax(op2.MAX), f.dat(op2.READ)) return fmax.data[0] > > > But I agree, it would be nice if that weren't necessary. > > > Hope that helps, > > > Jemma > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > on behalf of Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > *Sent:* 08 June 2016 09:33:46 > *To:* firedrake > *Subject:* [firedrake] Saving txt files while running in parallel > > > Dear all, > > > I am running a Firedrake code in parallel with 4 cores, in which I save > the maximal value of the amplitude of the wave at each time, with the > command: > > > max_eta = max(eta.dat.data) > > Eta_file.write('%-10s %-10s %-10s\n' % (t,'', eta_max)) > > > > But when opening the .txt file, I notice two issues: > > - the data are not saved continuously: time goes from 0 to 100 (let's say) > and then starts from 90 again; > > - the values of max_eta are not the maximal values of eta, except at the > beginning. So it looks like the function max takes the maximum value of eta > only in one subdomain, so that after the wave has crossed the subdomain, > the maximal value of eta goes back to the depth of rest value. > > > How can I force this command to be applied on the full domain, even if the > code is run in parallel? > > > Thanks, > > Floriane > > > >

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Mixed system
by Anna Kalogirou 05 Aug '16

05 Aug '16

Dear all, I am trying to solve the system found in the attached pdf as a mixed system. I want to solve the same problem as the one found here <https://bitbucket.org/annakalog/buoy2d/src/14334d3c20b9f10ed7c1246cde9e3cb6…>, but with the use of Schur complements and not linear algebra. In a previous discussion about this problem, Lawrence mentioned that the test function for integral(lambda*Theta(x-Lp)dx) needs to be considered as coming from the real space of constant functions. Could you please elaborate on this? Regards, Anna. <https://bitbucket.org/annakalog/buoy2d/src/14334d3c20b9f10ed7c1246cde9e3cb6…> -- Dr Anna Kalogirou Research Fellow School of Mathematics University of Leeds http://www1.maths.leeds.ac.uk/~matak/

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Re: [firedrake] problems updating and running firedrake
by David Ham 05 Aug '16

05 Aug '16

Hi Francis, Please provide the full output, because the following is based on guesswork because I can't see what is going on. It is true that curl depends on librtmp. If your curl can't find your rtmp, then something is broken on your system. This has nothing to do with Firedrake. I *think* that the only time you use curl is to download the firedrake-install script. If you really can't unbreak curl on your system then you can obtain this script by any of the usual ways (wget, download it with a web browser etc.) Regards, David On Mon, 27 Jun 2016 at 19:35 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello David, > > Thanks for finding that. > > I tried a) and that didn't help the update. > > I then tried b) and get an curl error, "error while loading shared > libraries: librtmp.so.0". > > I have done this before but not sure why this is not working now. > > Cheers, Francis > > > > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of David Ham [David.Ham(a)imperial.ac.uk] > *Sent:* Monday, June 27, 2016 10:48 AM > *To:* firedrake > *Subject:* Re: [firedrake] problems updating and running firedrake > > Hi Francis, > > It looks like you might have hit the issue they describe here: > http://askubuntu.com/questions/509283/python-no-module-named-datetime > > Basically datetime was apparently rolled into the python binary in a 2.7 > point release. I don't know why this was changed but it makes the python > binary in your virtualenv incompatible with your system python install. > > According to the thread on askubuntu, you have two options. > > a) Apparently you can re-initialise the virtualenv by running: > > virtualenv . > > in your top Firedrake directory. I'm guessing you should do this with the > virtualenv deactivated. > > or > > b) A fresh Firedrake install should work because it will create a fresh > virtualenv based on current Python binary. > > Regards, > > David > > On Mon, 27 Jun 2016 at 15:20 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > >> Hello, >> >> I recently updated my ubuntu from 14.04 to 16.04. I tried running >> firedrake and it failed. >> >> I also tried updating firedrake and it failed, see below. >> >> Do I need to install it from scratch or should it be possible to update >> it with a new OS? >> >> Cheers, Francis >> >> >> >> Installing pip dependencies for COFFEE >> /home/fpoulin/software/firedrake/bin/pip install -r >> COFFEE/requirements.txt >> >> Traceback (most recent call last): >> File "/home/fpoulin/software/firedrake/bin/pip", line 7, in <module> >> from pip import main >> File >> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/pip/__init__.py", >> line 14, in <module> >> from pip.utils import get_installed_distributions, get_prog >> File >> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/pip/utils/__init__.py", >> line 27, in <module> >> from pip._vendor import pkg_resources >> File >> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", >> line 36, in <module> >> import plistlib >> File "/usr/lib/python2.7/plistlib.py", line 62, in <module> >> import datetime >> ImportError: No module named datetime >> Traceback (most recent call last): >> File "../bin/firedrake-update", line 974, in <module> >> pip_requirements(p) >> File "../bin/firedrake-update", line 377, in pip_requirements >> run_pip_install(["-r", "%s/requirements.txt" % package]) >> File "../bin/firedrake-update", line 364, in run_pip_install >> check_call(pipinstall + pipargs) >> File "../bin/firedrake-update", line 211, in check_call >> subprocess.check_call(arguments, env=env) >> File "/usr/lib/python2.7/subprocess.py", line 541, in check_call >> raise CalledProcessError(retcode, cmd) >> subprocess.CalledProcessError: Command >> '['/home/fpoulin/software/firedrake/bin/pip', 'install', '-r', >> 'COFFEE/requirements.txt']' returned non-zero exit status 1 >> >> ------------------ >> Francis Poulin >> Associate Professor >> Department of Applied Mathematics >> University of Waterloo >> >> email: fpoulin(a)uwaterloo.ca >> Web: https://uwaterloo.ca/poulin-research-group/ >> Telephone: +1 519 888 4567 x32637 >> >>

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out of memory error during assemble
by moritz braun 02 Aug '16

02 Aug '16

Dear Colleagues I have a strange out or memory error when calling assemble on a bilinear form How can that happen in firedrake? Regards Moritz -- Prof M Braun Tel.:27-12-4298006/8027 Physics Department Fax.: 27-12-4293643 University of South Africa (UNISA) moritz.braun(a)gmail.com P.O. Box 392 0003 UNISA South Africa http://moritz-braun.blogspot.com

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DirichletBC not working anymore
by Justin Chang 30 Jul '16

30 Jul '16

Hi all, Last year (~8 months ago) the following worked: mesh = UnitSquareMesh(10,10) V = VectorFunctionSpace(mesh, "CG", 1) P = FunctionSpace(mesh, "CG", 1) W = V*Q bc1 = DirichletBC(W.sub(0).sub(0), Expression("cos(pi*x[0])*sin(pi*x[1])"), (1,2)) Today, I get these errors: Traceback (most recent call last): File "Darcy_LS.py", line 32, in <module> bc1 = DirichletBC(W.sub(0).sub(0), Expression("cos(pi*x[0])*sin(pi*x[1])"), (1,2)) File "/Users/jychang48/Software/firedrake/src/firedrake/firedrake/bcs.py", line 54, in __init__ self.function_arg = g File "/Users/jychang48/Software/firedrake/src/firedrake/firedrake/bcs.py", line 100, in function_arg g = function.Function(self._function_space).interpolate(g) File "/Users/jychang48/Software/firedrake/src/firedrake/firedrake/function.py", line 243, in __init__ val=val, name=name, dtype=dtype) File "/Users/jychang48/Software/firedrake/src/firedrake/firedrake/function.py", line 79, in __init__ self.dat = function_space.make_dat(val, dtype, self.name(), uid=self.uid) File "/Users/jychang48/Software/firedrake/src/firedrake/firedrake/functionspaceimpl.py", line 798, in make_dat raise ValueError("Can't build Function on %s function space" % self.typ) AttributeError: 'ProxyFunctionSpace' object has no attribute 'typ' What's going on, and how do I work around this? Also, is it suppose to say 'self.type' instead of 'self.typ'? Thanks, Justin

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Re: [firedrake] Runtime visualization
by David Ham 28 Jul '16

28 Jul '16

Hi Justin, That's a very well timed question. Happily Fangyi (Thomas) Zhou is with us as a summer student working on this precise problem. He's started out by implementing some functionality for 1 and 2 dimensions using matplotlib. If you're feeling brave you can try the plotting and plotting-1d branches but they will hopefully land in master in the next week or so. Meanwhile I'm at WCCM and was in a visualisation session this morning. It appears that what both PyFR and GMSH are now doing is using catalyst, which is a runtime paraview interface (http://www.paraview.org/in-situ/) I think it would be really cool if Thomas has a look at that next (although I haven't yet had a chance to discuss that with him since we're not in the same location or timezone right now). Regards, David On Wed, 27 Jul 2016 at 13:56 Justin Chang <jychang48(a)gmail.com> wrote: > Hi all, > > One of the beautiful things about FEniCS is its ability to produce runtime > plots of the solution. Is there (or will there be) a way to do this in > Firedrake? It is a little bit cumbersome to dump the solution into a pvd > file and (re)open it in paraview/VisIt each time you want to tweak > something. > > Thanks, > Justin >

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Re: [firedrake] different SNES convergence on different machine?
by Colin Cotter 27 Jul '16

27 Jul '16

Hi TJ, We are currently discussing this in Slack if you would like to pop in? On 27 July 2016 at 13:54, Sun, Tianjiao <tianjiao.sun14(a)imperial.ac.uk> wrote: > Hi Lawrence, > > 20x20 is the smallest I tried. For smaller mesh the problem is not > well-conditioned. I can think of some other test cases for smaller mesh. > > I tried to run with snes_fd, and I got much similar but not still not > identical results on both machines, so it does look like something to do > with the Jacobian. I will try comparing the Jacobians and report back. > > Thanks, > > -TJ > > On 27/07/16 13:36, Lawrence Mitchell wrote: > > > On 27/07/16 13:09, Tianjiao Sun wrote: > > Hi team, > > The attached script is a trimmed down version of the sort of problem I'm > trying to run. Running it on most machines (I've tried 4 machines), I > got this output: > > $ python mytest.py > 0 SNES Function norm 0.873814 > 1 SNES Function norm 0.245545 > 2 SNES Function norm 0.0178611 > 3 SNES Function norm 0.000156473 > 4 SNES Function norm 1.26023e-09 > > However, on my workstation in college (where I do most work > unfortunately), I got: > > 0 SNES Function norm 0.873814 > 1 SNES Function norm 0.432782 > 2 SNES Function norm 0.0478636 > 3 SNES Function norm 0.0405004 > 4 SNES Function norm 0.0405004 > 5 SNES Function norm 0.0405004 > 6 SNES Function norm 0.0405004 > 7 SNES Function norm 0.0405004 > 8 SNES Function norm 0.0405004 > 9 SNES Function norm 0.0405004 > 10 SNES Function norm 0.0405004 > > I have tried to update and also reinstall firedrake, and pip list shows > same version for FIAT, petsc, petsc4py, UFL (firedrake version is shown > as 'unknown' though). The snes objects are identical as well. Is there > anything else that I can check to see where the discrepancy occurs? > > Does this problem exhibit on a small mesh? > > Can you try comparing the jacobians on a machine that works and one > that fails? > > Lawrence > > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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different SNES convergence on different machine?
by Tianjiao Sun 27 Jul '16

27 Jul '16

Hi team, The attached script is a trimmed down version of the sort of problem I'm trying to run. Running it on most machines (I've tried 4 machines), I got this output: $ python mytest.py 0 SNES Function norm 0.873814 1 SNES Function norm 0.245545 2 SNES Function norm 0.0178611 3 SNES Function norm 0.000156473 4 SNES Function norm 1.26023e-09 However, on my workstation in college (where I do most work unfortunately), I got: 0 SNES Function norm 0.873814 1 SNES Function norm 0.432782 2 SNES Function norm 0.0478636 3 SNES Function norm 0.0405004 4 SNES Function norm 0.0405004 5 SNES Function norm 0.0405004 6 SNES Function norm 0.0405004 7 SNES Function norm 0.0405004 8 SNES Function norm 0.0405004 9 SNES Function norm 0.0405004 10 SNES Function norm 0.0405004 I have tried to update and also reinstall firedrake, and pip list shows same version for FIAT, petsc, petsc4py, UFL (firedrake version is shown as 'unknown' though). The snes objects are identical as well. Is there anything else that I can check to see where the discrepancy occurs? Many thanks, -TJ

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segfaults on Xenial
by Stephan Kramer 27 Jul '16

27 Jul '16

Dear firedrake devs After upgrading my workstation to Ubuntu Xenial, and rebuilding firedrake from scratch I get several segfaults in the running of firedrake tests. The ones I've seen so far were segfaulting in petsc: kernel -> MatSetValuesLocal() -> ISLocalToGlobalMappingApply() If I switch on the debug PyOP2 option and run it in gdb, it seems the values passed to MatSetValuesLocal are all sensible. Unfortunately if I rebuild firedrake with a debugging-petsc the tests all pass (i.e. the segfault goes away). Any further hints how to debug this? Cheers Stephan

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Runtime visualization
by Justin Chang 27 Jul '16

27 Jul '16

Hi all, One of the beautiful things about FEniCS is its ability to produce runtime plots of the solution. Is there (or will there be) a way to do this in Firedrake? It is a little bit cumbersome to dump the solution into a pvd file and (re)open it in paraview/VisIt each time you want to tweak something. Thanks, Justin

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