[guide] Build the Fluidity PyOP2 branch

The following assumes you have the fluidity-dev package from the fluidity-core PPA installed, which contains all dependencies for building fluidity:

sudo add-apt-repository ppa:fluidity-core/ppa
sudo apt-get update
sudo apt-get install fluidity-dev

Build the floppy_bn branch of fluidity:

bzr branch lp:~fluidity-core/fluidity/firedrake
cd firedrake
# This MUST be the same PETSc you've used to build PyOP2
export PETSC_DIR=/path/to/petsc
./configure --without-adjoint --enable-sam --enable-shared --enable-2d-adaptivity --enable-debugging
make -j12 &&
make -j12 fltools &&
make -j12 shared &&
make -j12 python_build

Dump a decomposed mesh

There is an flml to dump decomposed meshes in tests/ufl_common/dump.flml.template. Use it from the tests/ufl_dump folder as follows:

To generate the decomposed mesh for the adv_diff_mpi run

make run

To generate custom decomposed meshes run

make custom

which accepts the following parameters:

• NPROCS to set the number of MPI processes
• X to set the number of layers in the x-direction
• Y to set the number of layers in the y-direction
• NAME for the output mesh file name

The output files are gzipped pickle dumps named NAME_PROC.pickle.gz, which can be loaded in PyOP2 with

import gzip
from cPickle import load
with gzip.open(opt['mesh'] + '.' + str(op2.MPI.comm.rank) + '.pickle.gz') as f:
    elements, nodes, elem_node, coords = load(f)