def backend(request):
backend, lazy = request.param
# Initialise the backend
try:
op2.init(backend=backend, lazy_evaluation=(lazy == 'lazy'))
# Skip test if initialisation failed
except:
pytest.skip('Backend %s is not available' % backend)
return backend
def _init():
"""Cause :func:`pyop2.init` to be called in case the user has not done it
for themselves. The result of this is that the user need only call
:func:`pyop2.init` if she wants to set a non-default option, for example
to switch the backend or the debug or log level."""
from pyop2 import op2
from firedrake.parameters import parameters
if not op2.initialised():
op2.init(**parameters["pyop2_options"])
def backend(request):
backend, lazy = request.param
# Initialise the backend
try:
op2.init(backend=backend, lazy_evaluation=(lazy == 'lazy'))
# Skip test if initialisation failed
except:
pytest.skip('Backend %s is not available' % backend)
return backend
def _init():
"""Cause :func:`pyop2.init` to be called in case the user has not done it
for themselves. The result of this is that the user need only call
:func:`pyop2.init` if she wants to set a non-default option, for example
to switch the backend or the debug or log level."""
from pyop2 import op2
from firedrake.parameters import parameters
if not op2.initialised():
op2.init(**parameters["pyop2_options"])
def backend(request):
# Initialise the backend
try:
op2.init(backend=request.param)
# Skip test if initialisation failed
except:
pytest.skip('Backend %s is not available' % request.param)
request.addfinalizer(op2.exit)
return request.param
def _init():
"""Cause :func:`pyop2.init` to be called in case the user has not done it
for themselves. The result of this is that the user need only call
:func:`pyop2.init` if she wants to set a non-default option, for example
to switch the backend or the debug or log level."""
from pyop2 import op2
from parameters import parameters
if not op2.initialised():
op2.init(log_level="INFO", compiler=parameters["coffee"]["compiler"], simd_isa=parameters["coffee"]["simd_isa"])
def test_invalid_init(self):
"init should not accept an invalid backend."
with pytest.raises(ImportError):
op2.init(backend='invalid_backend')
This may also depend on development trunk versions of other FEniCS programs.
"""
from pyop2 import op2, utils
from pyop2.ffc_interface import compile_form
from ufl import *
import ffc
import numpy as np
parser = utils.parser(group=True, description=__doc__)
parser.add_argument('-s', '--save-output',
action='store_true',
help='Save the output of the run (used for testing)')
opt = vars(parser.parse_args())
op2.init(**opt)
# Set up finite element identity problem
E = FiniteElement("Lagrange", "triangle", 1)
v = TestFunction(E)
u = TrialFunction(E)
f = Coefficient(E)
a = v*u*dx
L = v*f*dx
# Generate code for mass and rhs assembly.
mass, = compile_form(a, "mass")
def run(diffusivity, current_time, dt, endtime, **kwargs):
op2.init(**kwargs)
# Set up finite element problem
T = FiniteElement("Lagrange", "triangle", 1)
V = VectorElement("Lagrange", "triangle", 1)
p = TrialFunction(T)
q = TestFunction(T)
t = Coefficient(T)
u = Coefficient(V)
diffusivity = 0.1
M = p * q * dx
adv_rhs = (q * t + dt * dot(grad(q), u) * t) * dx
d = -dt * diffusivity * dot(grad(q), grad(p)) * dx
diff_matrix = M - 0.5 * d
diff_rhs = action(M + 0.5 * d, t)
# Generate code for mass and rhs assembly.
mass = compile_form(M, "mass")[0]
adv_rhs = compile_form(adv_rhs, "adv_rhs")[0]
diff_matrix = compile_form(diff_matrix, "diff_matrix")[0]
diff_rhs = compile_form(diff_rhs, "diff_rhs")[0]
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(kwargs['mesh'])
num_nodes = nodes.size
sparsity = op2.Sparsity((elem_node, elem_node), 1, "sparsity")
mat = op2.Mat(sparsity, valuetype, "mat")
tracer_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
tracer = op2.Dat(nodes, 1, tracer_vals, valuetype, "tracer")
b_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
b = op2.Dat(nodes, 1, b_vals, valuetype, "b")
velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype)
velocity = op2.Dat(nodes, 2, velocity_vals, valuetype, "velocity")
# Set initial condition
i_cond_code = """
void i_cond(double *c, double *t)
{
double i_t = 0.01; // Initial time
double A = 0.1; // Normalisation
double D = 0.1; // Diffusivity
double pi = 3.141459265358979;
double x = c[0]-0.5;
double y = c[1]-0.5;
double r = sqrt(x*x+y*y);
if (r<0.25)
*t = A*(exp((-(r*r))/(4*D*i_t))/(4*pi*D*i_t));
else
*t = 0.0;
}
"""
i_cond = op2.Kernel(i_cond_code, "i_cond")
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ),
tracer(op2.IdentityMap, op2.WRITE))
zero_dat_code = """
void zero_dat(double *dat)
{
*dat = 0.0;
}
"""
zero_dat = op2.Kernel(zero_dat_code, "zero_dat")
# Assemble and solve
have_advection = True
have_diffusion = True
def timestep_iteration():
# Advection
if have_advection:
tic('advection')
tic('assembly')
mat.zero()
op2.par_loop(
mass, elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ))
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(adv_rhs, elements(3), b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
velocity(elem_node, op2.READ))
toc('assembly')
tic('solve')
op2.solve(mat, tracer, b)
toc('solve')
toc('advection')
# Diffusion
if have_diffusion:
tic('diffusion')
tic('assembly')
mat.zero()
op2.par_loop(
diff_matrix, elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ))
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(diff_rhs, elements(3), b(elem_node[op2.i[0]],
op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ))
toc('assembly')
tic('solve')
op2.solve(mat, tracer, b)
toc('solve')
toc('diffusion')
# Perform 1 iteration to warm up plan cache then reset initial condition
timestep_iteration()
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ),
tracer(op2.IdentityMap, op2.WRITE))
reset()
# Timed iteration
t1 = clock()
while current_time < endtime:
timestep_iteration()
current_time += dt
runtime = clock() - t1
print "/fluidity :: %f" % runtime
summary('profile_pyop2_%s_%s.csv' %
(opt['mesh'].split('/')[-1], opt['backend']))
from math import sqrt
parser = utils.parser(group=True, description=__doc__)
parser.add_argument('-s',
'--single',
action='store_true',
help='single precision floating point mode')
parser.add_argument('-n',
'--niter',
action='store',
default=2,
type=int,
help='set the number of iteration')
opt = vars(parser.parse_args())
op2.init(**opt)
fp_type = np.float32 if opt['single'] else np.float64
NN = 6
NITER = opt['niter']
nnode = (NN - 1)**2
nedge = nnode + 4 * (NN - 1) * (NN - 2)
pp = np.zeros((2 * nedge, ), dtype=np.int)
A = np.zeros((nedge, ), dtype=fp_type)
r = np.zeros((nnode, ), dtype=fp_type)
u = np.zeros((nnode, ), dtype=fp_type)
du = np.zeros((nnode, ), dtype=fp_type)
def run(diffusivity, current_time, dt, endtime, **kwargs):
op2.init(**kwargs)
# Set up finite element problem
T = FiniteElement("Lagrange", "triangle", 1)
V = VectorElement("Lagrange", "triangle", 1)
p = TrialFunction(T)
q = TestFunction(T)
t = Coefficient(T)
u = Coefficient(V)
diffusivity = 0.1
M = p * q * dx
adv_rhs = (q * t + dt * dot(grad(q), u) * t) * dx
d = -dt * diffusivity * dot(grad(q), grad(p)) * dx
diff_matrix = M - 0.5 * d
diff_rhs = action(M + 0.5 * d, t)
# Generate code for mass and rhs assembly.
mass = compile_form(M, "mass")[0]
adv_rhs = compile_form(adv_rhs, "adv_rhs")[0]
diff_matrix = compile_form(diff_matrix, "diff_matrix")[0]
diff_rhs = compile_form(diff_rhs, "diff_rhs")[0]
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(kwargs["mesh"])
num_nodes = nodes.size
sparsity = op2.Sparsity((elem_node, elem_node), 1, "sparsity")
mat = op2.Mat(sparsity, valuetype, "mat")
tracer_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
tracer = op2.Dat(nodes, 1, tracer_vals, valuetype, "tracer")
b_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
b = op2.Dat(nodes, 1, b_vals, valuetype, "b")
velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype)
velocity = op2.Dat(nodes, 2, velocity_vals, valuetype, "velocity")
# Set initial condition
i_cond_code = """
void i_cond(double *c, double *t)
{
double i_t = 0.01; // Initial time
double A = 0.1; // Normalisation
double D = 0.1; // Diffusivity
double pi = 3.141459265358979;
double x = c[0]-0.5;
double y = c[1]-0.5;
double r = sqrt(x*x+y*y);
if (r<0.25)
*t = A*(exp((-(r*r))/(4*D*i_t))/(4*pi*D*i_t));
else
*t = 0.0;
}
"""
i_cond = op2.Kernel(i_cond_code, "i_cond")
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ), tracer(op2.IdentityMap, op2.WRITE))
zero_dat_code = """
void zero_dat(double *dat)
{
*dat = 0.0;
}
"""
zero_dat = op2.Kernel(zero_dat_code, "zero_dat")
# Assemble and solve
have_advection = True
have_diffusion = True
def timestep_iteration():
# Advection
if have_advection:
tic("advection")
tic("assembly")
mat.zero()
op2.par_loop(
mass,
elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ),
)
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(
adv_rhs,
elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
velocity(elem_node, op2.READ),
)
toc("assembly")
tic("solve")
op2.solve(mat, tracer, b)
toc("solve")
toc("advection")
# Diffusion
if have_diffusion:
tic("diffusion")
tic("assembly")
mat.zero()
op2.par_loop(
diff_matrix,
elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ),
)
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(
diff_rhs,
elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
)
toc("assembly")
tic("solve")
op2.solve(mat, tracer, b)
toc("solve")
toc("diffusion")
# Perform 1 iteration to warm up plan cache then reset initial condition
timestep_iteration()
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ), tracer(op2.IdentityMap, op2.WRITE))
reset()
# Timed iteration
t1 = clock()
while current_time < endtime:
timestep_iteration()
current_time += dt
runtime = clock() - t1
print "/fluidity :: %f" % runtime
summary("profile_pyop2_%s_%s.csv" % (opt["mesh"].split("/")[-1], opt["backend"]))
def initializer(request):
lazy = request.param
op2.init(lazy_evaluation=(lazy == "lazy"))
return lazy
"""PyOP2 sparsity building benchmark"""
import numpy as np
from time import clock
from pyop2 import op2, utils
def time_sparsity(n):
nodes = op2.Set(n)
cells = op2.Set(n - 1)
m = op2.Map(cells, nodes, 2,
np.concatenate((np.arange(n - 1), np.arange(1, n))))
t = clock()
s = op2.Sparsity((m, m), 1)
return clock() - t
if __name__ == '__main__':
import pylab
parser = utils.parser(group=True, description=__doc__)
op2.init(**vars(parser.parse_args()))
n = [2**i for i in range(10, 18)]
t = [time_sparsity(i) for i in n]
pylab.plot(n, t)
pylab.xlabel('Sparsity size')
pylab.ylabel('Sparsity build time (s)')
pylab.show()
def initializer(request):
lazy = request.param
op2.init(lazy_evaluation=(lazy == "lazy"))
return lazy
_expr_count = 0
V, E = badata.quickLoad(badata.MANHATTAN)
if _VERBOSE:
print V.head()
print E.head()
POSES_PER_CONSTRAINT = 2
POSES_DIM = balib.dim_lookup[V.label.unique()[0]]
CONSTRAINT_DIM = balib.dim_lookup[E.label.unique()[0]]
OMEGA_DOF = balib.omega_dof(CONSTRAINT_DIM)
NUM_POSES = len(V)
NUM_CONSTRAINTS = len(E)
op2.init(backend='sequential')
def testKernel(data=None, op2set=None, op2map=None):
""" for testing purposes, it just prints out the data Dat array
(assuming) it has dimension 3 in its Map (op2map). The kernel
iterates over the Set op2set, if no arguments are passed in,
this creates dummy values and prints them out
"""
if not op2set:
op2set = op2.Set(5, 'fromset')
if not op2map:
op2toset = op2.Set(4, 'toset')
npmapping = np.array([0, 1, 1, 2, 2, 3, 3, 1, 3, 2], np.uint32)
print '-' * 80
print 'mapping: ', npmapping, npmapping.dtype, npmapping.shape
def test_double_init(self, backend):
"Calling init again with the same backend should update the configuration."
op2.init(backend=backend, foo='bar')
assert op2.backends.get_backend() == 'pyop2.' + backend
assert cfg.foo == 'bar'
def test_change_backend_fails(self, backend):
"Calling init again with a different backend should fail."
with pytest.raises(RuntimeError):
op2.init(backend='other')
"""PyOP2 sparsity building benchmark"""
import numpy as np
from time import clock
from pyop2 import op2, utils
def time_sparsity(n):
nodes = op2.Set(n)
cells = op2.Set(n-1)
m = op2.Map(cells, nodes, 2, np.concatenate((np.arange(n-1), np.arange(1,n))))
t = clock()
s = op2.Sparsity((m,m), 1)
return clock() - t
if __name__=='__main__':
import pylab
parser = utils.parser(group=True, description=__doc__)
op2.init(**vars(parser.parse_args()))
n = [2**i for i in range(10,18)]
t = [time_sparsity(i) for i in n]
pylab.plot(n,t)
pylab.xlabel('Sparsity size')
pylab.ylabel('Sparsity build time (s)')
pylab.show()