February 2016 - firedrake - imperial.ac.uk

firedrake's open-mpi dependency
by Tao Wang 11 Feb '16

11 Feb '16

Hi, all I notice firedrake has dependency on open-mpi. But, I want to use other mpi implementation. I already have impi installed on my machine. What should I do to make this change happen ? Thanks, Tao

3 11

Re: [firedrake] Periodic rectangle mesh in x-direction
by Andrew McRae 11 Feb '16

11 Feb '16

I think not, but do feel free to implement it. It shouldn't be difficult. On 10 February 2016 at 20:24, Tuomas Karna <tuomas.karna(a)gmail.com> wrote: > Hi all, > > Is there an easy way to create a rectangular mesh with two periodic > boundaries? PeriodicRectangleMesh is a torus so all 4 sides are > connected. I'd need a triangular RectangleMesh where only sides x=0 and > x=Lx are connected. > > - Tuomas > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

2 1

Periodic rectangle mesh in x-direction
by Tuomas Karna 10 Feb '16

10 Feb '16

Hi all, Is there an easy way to create a rectangular mesh with two periodic boundaries? PeriodicRectangleMesh is a torus so all 4 sides are connected. I'd need a triangular RectangleMesh where only sides x=0 and x=Lx are connected. - Tuomas

1 0

Student Travel grants for Workshop on “Higher-order DG methods and finite element software on modern architectures”, Bath 31 May - 2nd Jun 2016
by Eike Mueller 10 Feb '16

10 Feb '16

Dear all, We are organising a 3-day workshop on finite element software and applications in Bath this summer, see https://sites.google.com/site/bathdgworkshop/ for details. Confirmed plenary speakers are: Markus Geveler (Dortmund), Frank Giraldo (Monterey), David Ham (Imperial), Rob Kirby (Baylor), Martin Kronbichler (TUM), Tom Melvin (Met Office), Steffen Müthing (Heidelberg), Marie Rognes (Simula). In addition there will be representatives from major chip manufacturers and HPC vendors. Although participation is by invitation-only, we are offering a small number of grants for students to attend the meeting. The exact amount available depends on the number of successful applications, but is likely in the range of £100-£200 per person. To apply, please send us a brief statement (not more than 2 pages) with the following information by 29th Feb 2016: (1) Description of your research interests (2) Motivation for attending the workshop (3) List of publications (4) Short supporting statement from your supervisor In addition, please state whether you are interested in giving a presentation at the workshop. Successful applicants will be notified at the beginning of March. Rob Scheichl and Eike Mueller

1 0

mpirun for examples
by Francis Poulin 10 Feb '16

10 Feb '16

I have downloaded some demos and am starting to learn how they work. I learned that to run it in parallel I need to specify the path for my firedrake version of python /usr/local/bin/mpirun -np 4 ~/software/firedrake/bin/python burgers.py These run in parallel and do seem to take up the right number of cores. I am curious to do some tests on my laptop, desktop, and cluster to see how things scale. The actual problem doesn't matter so much but I would like it to be something like Shallow Water, Navier Stokes, or something in that line. Are there any examples that someone can point me towards that would be good to test parallelization on different machines? ------------------ 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

2 1

Re: [firedrake] mpirun for examples
by Colin Cotter 09 Feb '16

09 Feb '16

Dear Francis, I can fix you up with a QG code that you can play with, I'll hopefully get around to it in the next few days. all the best --cjc On 8 February 2016 at 20:48, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > I have downloaded some demos and am starting to learn how they work. I > learned that to run it in parallel I need to specify the path for my > firedrake version of python > > /usr/local/bin/mpirun -np 4 ~/software/firedrake/bin/python burgers.py > > > These run in parallel and do seem to take up the right number of cores. I > am curious to do some tests on my laptop, desktop, and cluster to see how > things scale. The actual problem doesn't matter so much but I would like > it to be something like Shallow Water, Navier Stokes, or something in that > line. > > > Are there any examples that someone can point me towards that would be > good to test parallelization on different machines? > > > ------------------ > 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 > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

1 0

Re: [firedrake] upgrading firedrake (problem found!)
by David Ham 05 Feb '16

05 Feb '16

On Fri, 5 Feb 2016 at 03:29 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > > I have set my default python and ipython to my homebrew version. (don't > think this did much) I reinstalled firedrake and found the following: > > -> on ubuntu firedrake, petsc4py, mpi4py are all located in > "firedrake/local/lib/python2.7/site-packages". > > On my mac the local folder does not exist. > > -> I see that these are all located in the following, which is not in my > path. > > firedrake/lib/python2.7/site-packages/petsc4py > I think you mean here that all the python packages are installed under firedrake/lib/python2.7/site-packages This is correct. It's just a minor difference in where virtualenv installs packages on Ubuntu and on Mac. Activating the virtualenv will put the appropriate site-packages in your path. Are you sure that the directory is not in sys.path after activating the virtualenv with: source firedrake/bin/activate ? > > When I open python and append to my path > > > sys.path.append("/Users/fpoulin/software/firedrake/lib/python2.7/site-packages") > > then I can import petsc4py, mpi4py, but firedrake cannot be imported > because of h5py. I am going to redo this now including all the options in > PETSC and wonder if that will fix this problem. > just adding sys.path is very unlikely to work. You really need to activate the virtualenv in order to properly access all the things which the install script installs. > > >>> import firedrake > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Users/fpoulin/software/firedrake/lib/python2.7/site-packages/firedrake/__init__.py", > line 33, in <module> > from firedrake.checkpointing import * > File > "/Users/fpoulin/software/firedrake/lib/python2.7/site-packages/firedrake/checkpointing.py", > line 4, in <module> > from firedrake import hdf5interface as h5i > File "firedrake/hdf5interface.pyx", line 1, in init > firedrake.hdf5interface (firedrake/hdf5interface.c:2016) > ImportError: No module named h5py > > But it seems to me that maybe there is a problem with the paths set up on > my mac, and maybe other macs as well? > I think it's just activating the virtualenv. Firedrake currently runs fine on our Macs and on the Macs at travis-ci (the online build test service we use). Regards, David > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

4 13

Re: [firedrake] upgrading firedrake (problem found!)
by Francis Poulin 05 Feb '16

05 Feb '16

I have set my default python and ipython to my homebrew version. (don't think this did much) I reinstalled firedrake and found the following: -> on ubuntu firedrake, petsc4py, mpi4py are all located in "firedrake/local/lib/python2.7/site-packages". On my mac the local folder does not exist. -> I see that these are all located in the following, which is not in my path. firedrake/lib/python2.7/site-packages/petsc4py When I open python and append to my path sys.path.append("/Users/fpoulin/software/firedrake/lib/python2.7/site-packages") then I can import petsc4py, mpi4py, but firedrake cannot be imported because of h5py. I am going to redo this now including all the options in PETSC and wonder if that will fix this problem. >>> import firedrake Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/fpoulin/software/firedrake/lib/python2.7/site-packages/firedrake/__init__.py", line 33, in <module> from firedrake.checkpointing import * File "/Users/fpoulin/software/firedrake/lib/python2.7/site-packages/firedrake/checkpointing.py", line 4, in <module> from firedrake import hdf5interface as h5i File "firedrake/hdf5interface.pyx", line 1, in init firedrake.hdf5interface (firedrake/hdf5interface.c:2016) ImportError: No module named h5py But it seems to me that maybe there is a problem with the paths set up on my mac, and maybe other macs as well?

1 0

Re: [firedrake] upgrading firedrake
by David Ham 04 Feb '16

04 Feb '16

Hello again Francis, You definitely should not be setting PETSC_DIR to run or upgrade Firedrake. We hadn't previously noticed that cleaning PyOP2 hit the PETSc dependency. Can you try running firedrake-install with the virtualenv active? That should ensure that PETSc is found. Regards, David On Tue, 2 Feb 2016 at 21:04 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > I am very new to firedrake and trying to install it on two machines: > ubuntu and mac. I am having problems with each and thought I would start > asking about the ubuntu. > > running firedrake-install seemed to work. At least I didn’t notice any > errors. > > However, when I do an upgrade, I get that there is a problem with > PETSC_DIR not being defined. Is this something that we should specify > ourselves? > > Thank you in advance. > > Francis > > firedrake/bin/pip install --no-deps --ignore-installed ffc/ > Processing ./ffc > Installing collected packages: FFC > Running setup.py install for FFC ... done > Successfully installed FFC-1.7.0.dev0 > Cleaning PyOP2 > Error: Could not find PETSc library. > > Set the environment variable PETSC_DIR to your local PETSc base > directory or install PETSc from PyPI: pip install petsc > Traceback (most recent call last): > File "firedrake/bin/firedrake-update", line 777, in <module> > clean(p) > File "firedrake/bin/firedrake-update", line 438, in clean > check_call(["python", "setup.py", "clean"]) > File "firedrake/bin/firedrake-update", line 182, in check_call > subprocess.check_call(arguments) > File "/usr/lib/python2.7/subprocess.py", line 540, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command '['python', 'setup.py', 'clean']' > returned non-zero exit status 1 > > > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: http://www.math.uwaterloo.ca/~fpoulin/ > Telephone: +1 519 888 4567 x32637 > > > > > > > > > > >

5 22

New form compiler -- IMPORTANT UPDATE INFO
by Homolya, Miklós 04 Feb '16

04 Feb '16

Dear Firedrakers, The new form compiler has just landed. Since this changes the set of dependencies that Firedrake needs, one must rebuild the install script before updating. Follow these instructions for updating: cd to the top directory of the firedrake virtualenv . ./bin/activate cd src/firedrake/ git pull ./scripts/firedrake-install --rebuild-script --your-install-options Replace --your-install-options with the options you used to install Firedrake. Then run: firedrake-update --clean If the update script asks you to run it again, then please do so. When the update finished, do not forget to clean your cache: firedrake-clean New installations should just work. Kind regards, Miklós

1 0