January 2017 - firedrake - imperial.ac.uk

Firedrake workshop deadline 10 February
by David Ham 24 Mar '17

24 Mar '17

Dear all, This is a gentle reminder that the abstract and early registration deadline for the Firedrake users and developers workshop is next week already! As a reminder, the workshop will be at Imperial on 27 and 28 March, and we encourage users to present talks or posters showing how you are exploiting Firedrake (and possibly highlighting what you'd like us to add). We'll also be incorporating a Firedrake tutorial aimed at new Firedrake users on the Monday morning. New users who wish to only attend the tutorial can do so for free, but they still need to register so we can plan for the right number of participants. Full details on the workshop, registration, and abstract submission are available at: http://www.firedrakeproject.org/firedrake_17.html I hope to see many of you there. Regards, David -- Dr David Ham Department of Mathematics Imperial College London

3 2

Re: [firedrake] Parallel issues and projection issues
by David Ham 16 Feb '17

16 Feb '17

Dear Will, I think I understand your formulation a bit better now. My first question is why would I chose theta to be any value other than 0.5? Note that theta is not an upwinding value: the preferred direction is totally arbitrary at each face and does not depend on any aspect of the system state. I therefore don't understand why a value other than 0.5 would have better accuracy or stability than 0.5 itself, and at 0.5 the discretisation is invariant under renumbering the mesh (and therefore changing the arbitrary normal orderings). If there is indeed some good reason to introduce this asymmetry into the discretisation, then we do indeed hit the problem that Firedrake assumes your discretisation is invariant under renumbering and therefore may choose inconsistent numberings on different processors. In order to avoid this, you need to use an (arbitrary) numbering which is not dependent on the mesh numbering. One way to do this is to create a vector field which is guaranteed to have non-zero normal component on every edge: fs = FunctionSpace(mymesh, "RT", 1) f = Function(fs) f.dat.data[:] = 1. Then your "upwinding" code can use conditional(ge(dot(f,n), 0.), upwind_expr, downwind_expr) conditional and ge are UFL functions designed for this sort of thing. Regards, David On Fri, 27 Jan 2017 at 07:11 William Booker <scwb(a)leeds.ac.uk> wrote: > Dear David and Lawrence, > > > Derivation is attached, with the explanation for DIV_u and the projection > issue. > > > The DIV operator is just to avoid repeating code, and is simply a sum of > my element internal terms and boundary flux. > > Is there any way to communicate the same left and right sense to the > processors and to guarantee it? > > > Thanks > > Will > ------------------------------ > *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:* 20 January 2017 16:47:22 > *To:* firedrake > *Subject:* Re: [firedrake] Parallel issues and projection issues > > Hi Will, > > the problem does not immediately appear to be solver tolerances. But > rather in your definition of the discrete divergence. > > You have: > > # Declare flux indicator function > theta = Constant(0.6) > > def div_u(u, p): > return (dot(u, grad(p)))*dx(domain=p.ufl_domain()) \ > + (jump(p)*dot((u('-')*(1-theta)+u('+')*theta), n('-')))*dS > > > The second term is the problematic one: > > dot((u('-')*(1-theta)+u('+')*theta), n('-')) > > is not symmetric under interchange of "+" and "-" restrictions. Remember > that these restrictions are *arbitrary* and their value is local to a > particular MPI process. > > As a result, you can end up in a situation where this integral "double > counts", because on one process you pick up a contribution from the local > "n('-')" restriction, and on the other process, where in serial you are > guaranteed that this would be an "n('+')" (and therefore not contribute), > you can also get an "n('-')". > > Make sense? > > Can you show how you derived this discrete divergence? > > Cheers, > > Lawrence > > > On 20 Jan 2017, at 14:01, David Ham <david.ham(a)imperial.ac.uk> wrote: > > > > Hi Will, > > > > I'll have a quick look at the parallel issue - I suspect it's just > solver tolerances. Can you please provide a maths write-up of the > variational problem you are solving so we can think more easily about > number 2? > > > > Regards, > > > > David > > > > > > On Fri, 20 Jan 2017 at 13:09 William Booker <scwb(a)leeds.ac.uk> wrote: > > Dear Firedrakers, > > > > Attached is a code for a skew symmetric FEM scheme, that should conserve > the discrete energy of the system. > > > > I have two issues: > > > > 1) When I run the code in serial, it conserves energy as expected but > when I run it in parallel there seems to be an error. Attached a graph of > energy drifts from running on 1/2 cores. > > > > 2) To make the code skew symmetric, I have to project physical variables > ( density, velocity) into their variational derivatives. Currently this is > done by extending the system from (vel, dens) to (vel, dens, vel_deriv, > den_deriv) and I include the projection as part of the mixed system. > Obviously this is rather expensive as I double the amount of variables > used, and I'm looking to use this for more complicated systems. > > > > I believe Colin mentioned to Onno, there may be a better way of > including this projection step without extending the mixed system. > > > > > > Thanks > > Will > > > > -- > > Dr David Ham > > Department of Mathematics > > Imperial College London > > _______________________________________________ > > 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 Department of Mathematics Imperial College London

4 10

Firedrake and xcode
by Francis Poulin 31 Jan '17

31 Jan '17

Hello, I have had several students install Firedrake on a MacMini and each time the full version of Xcode needed to be installed. Is this necessarily the case? If yes, what in particular is needed? 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

1 0

Re: [firedrake] Parallel issues and projection issues
by David Ham 27 Jan '17

27 Jan '17

Hi Will, I'll have a quick look at the parallel issue - I suspect it's just solver tolerances. Can you please provide a maths write-up of the variational problem you are solving so we can think more easily about number 2? Regards, David On Fri, 20 Jan 2017 at 13:09 William Booker <scwb(a)leeds.ac.uk> wrote: > Dear Firedrakers, > > Attached is a code for a skew symmetric FEM scheme, that should conserve > the discrete energy of the system. > > I have two issues: > > 1) When I run the code in serial, it conserves energy as expected but when > I run it in parallel there seems to be an error. Attached a graph of energy > drifts from running on 1/2 cores. > > 2) To make the code skew symmetric, I have to project physical variables ( > density, velocity) into their variational derivatives. Currently this is > done by extending the system from (vel, dens) to (vel, dens, vel_deriv, > den_deriv) and I include the projection as part of the mixed system. > Obviously this is rather expensive as I double the amount of variables > used, and I'm looking to use this for more complicated systems. > > I believe Colin mentioned to Onno, there may be a better way of including > this projection step without extending the mixed system. > > > Thanks > Will > -- Dr David Ham Department of Mathematics Imperial College London

3 2

Re: [firedrake] Firedrake update
by David Ham 24 Jan '17

24 Jan '17

Hi David, It looks to me as if you have managed to somehow alter the permissions of your Firedrake git repository. For example this might have happened if you made the mistake of running firedrake-update under sudo. If you understand how Unix permissions work, you can change the permissions or ownership back to the correct ones for your user and all should be well. Otherwise it might be easier to just reinstall Firedrake. Regards. David On Tue, 24 Jan 2017 at 15:37 Angwenyi David <kipkoej(a)gmail.com> wrote: > Hi Firedrakers, > > I am trying to update firedrake on mac. The following error turns out. > > error: cannot open .git/FETCH_HEAD: Permission denied > > Traceback (most recent call last): > File "/Users/master/firedrake/bin/firedrake-update", line 957, in > <module> > git_update("firedrake") > File "/Users/master/firedrake/bin/firedrake-update", line 381, in > git_update > check_call(["git", "pull"]) > File "/Users/master/firedrake/bin/firedrake-update", line 228, in > check_call > subprocess.check_call(arguments, env=env) > File > "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", > line 540, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command '['git', 'pull']' returned non-zero > exit status 1 > > > How can I resolve it? > > Thanks in advance. > > Angwenyi > -- Dr David Ham Department of Mathematics Imperial College London

2 1

Firedrake update
by Angwenyi David 24 Jan '17

24 Jan '17

Hi Firedrakers, I am trying to update firedrake on mac. The following error turns out. error: cannot open .git/FETCH_HEAD: Permission denied Traceback (most recent call last): File "/Users/master/firedrake/bin/firedrake-update", line 957, in <module> git_update("firedrake") File "/Users/master/firedrake/bin/firedrake-update", line 381, in git_update check_call(["git", "pull"]) File "/Users/master/firedrake/bin/firedrake-update", line 228, in check_call subprocess.check_call(arguments, env=env) File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['git', 'pull']' returned non-zero exit status 1 How can I resolve it? Thanks in advance. Angwenyi

1 0

Projecting a small piece of data set onto a larger one
by Justin Chang 23 Jan '17

23 Jan '17

Hi all, I am trying to run a density driven flow problem where the computational domain has some initial perturbation in the concentration field. I have a unit cube domain and I want the concentrations at z >= 0.9 to be randomly perturbed by some random values. So I have a text file 'initialfield.txt' containing these perturbations which looks something like this: <xcoord> <ycoord> <zcoord> <value1> <xcoord> <ycoord> <zcoord> <value 2> ... Which is for a specific coarse grid resolution, say h-size = 1/20. How would I best go about projecting this data into a Firedrake/UFL Function? Does the initialfield.txt data set have to have the same connectivity/mapping as the Mesh function? Also, if I wanted to project this data onto a finer grid, like h-size = 1/40 or 1/60, would I create two meshes, one coarse mesh for the initialfield.txt data and one fine grid that the data shall be projected onto? Any guidelines or tips on how to best do this appreciated, thanks! Justin

2 1

Parallel issues and projection issues
by William Booker 20 Jan '17

20 Jan '17

Dear Firedrakers, Attached is a code for a skew symmetric FEM scheme, that should conserve the discrete energy of the system. I have two issues: 1) When I run the code in serial, it conserves energy as expected but when I run it in parallel there seems to be an error. Attached a graph of energy drifts from running on 1/2 cores. 2) To make the code skew symmetric, I have to project physical variables ( density, velocity) into their variational derivatives. Currently this is done by extending the system from (vel, dens) to (vel, dens, vel_deriv, den_deriv) and I include the projection as part of the mixed system. Obviously this is rather expensive as I double the amount of variables used, and I'm looking to use this for more complicated systems. I believe Colin mentioned to Onno, there may be a better way of including this projection step without extending the mixed system. Thanks Will

1 0

DMRefine
by Justin Chang 11 Jan '17

11 Jan '17

Hi all, Is there a way to pass -dm_refine <number> into Firedrake? That or what's the best way to do a parallel mesh refinement after the initial mesh is created and distributed (I think I recall seeing another mail about this last month). Thanks, Justin

2 2

Installing firedrake with anaconda
by Tuomas Karna 11 Jan '17

11 Jan '17

Hi all, AFAIK firedrake-install does not work with anaconda python, because anaconda does not support virtualenv. Anaconda comes with conda environment manager instead. Perhaps an easy solution would be to optionally skip the creation of a virtualenv in the firedrake-install script. In this case, the installer assumes that the user has already created and activated an virtual environment, conda for instance, and just pip installs all the packages. - Tuomas

3 3