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__copyright__ = "Copyright (C) 2013 Andreas Kloeckner"
__license__ = """
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
import numpy as np
import numpy.linalg as la
from arraycontext import pytest_generate_tests_for_array_contexts
from boxtree.array_context import _acf # noqa: F401
from boxtree.array_context import PytestPyOpenCLArrayContextFactory
from boxtree.constant_one import (
ConstantOneExpansionWrangler, ConstantOneTreeIndependentDataForWrangler)
from boxtree.tools import ( # noqa: F401
make_normal_particle_array as p_normal, make_surface_particle_array as p_surface,
make_uniform_particle_array as p_uniform, particle_array_to_host)
logger = logging.getLogger(__name__)
pytest_generate_tests = pytest_generate_tests_for_array_contexts([
PytestPyOpenCLArrayContextFactory,
])
# {{{ ref fmmlib pot computation
def get_fmmlib_ref_pot(wrangler, weights, sources_host, targets_host,
helmholtz_k, dipole_vec=None):
dims = sources_host.shape[0]
eqn_letter = "h" if helmholtz_k else "l"
use_dipoles = dipole_vec is not None
import pyfmmlib
fmmlib_routine = getattr(
pyfmmlib,
"%spot%s%ddall%s_vec" % (
eqn_letter,
"fld" if dims == 3 else "grad",
dims,
"_dp" if use_dipoles else ""))
kwargs = {}
if dims == 3:
kwargs["iffld"] = False
else:
kwargs["ifgrad"] = False
kwargs["ifhess"] = False
if use_dipoles:
if helmholtz_k == 0 and dims == 2:
kwargs["dipstr"] = -weights * (dipole_vec[0] + 1j * dipole_vec[1])
else:
kwargs["dipstr"] = weights
kwargs["dipvec"] = dipole_vec
else:
kwargs["charge"] = weights
if helmholtz_k:
kwargs["zk"] = helmholtz_k
return wrangler.finalize_potentials(
fmmlib_routine(
sources=sources_host, targets=targets_host,
**kwargs)[0],
template_ary=weights)
class ConstantOneExpansionWranglerWithFilteredTargetsInTreeOrder(
ConstantOneExpansionWrangler):
def __init__(self, tree_indep, traversal, filtered_targets):
super().__init__(tree_indep, traversal)
self.filtered_targets = filtered_targets
def _get_target_slice(self, ibox):
pstart = self.filtered_targets.box_target_starts[ibox]
return slice(
pstart, pstart
+ self.filtered_targets.box_target_counts_nonchild[ibox])
def output_zeros(self):
return np.zeros(self.filtered_targets.nfiltered_targets, dtype=np.float64)
def reorder_potentials(self, potentials):
tree_order_all_potentials = np.zeros(self.tree.ntargets, potentials.dtype)
tree_order_all_potentials[
self.filtered_targets.unfiltered_from_filtered_target_indices] \
= potentials
return tree_order_all_potentials[self.tree.sorted_target_ids]
class ConstantOneExpansionWranglerWithFilteredTargetsInUserOrder(
ConstantOneExpansionWrangler):
def __init__(self, tree_indep, traversal, filtered_targets):
super().__init__(tree_indep, traversal)
self.filtered_targets = filtered_targets
def _get_target_slice(self, ibox):
user_target_ids = self.filtered_targets.target_lists[
self.filtered_targets.target_starts[ibox]:
self.filtered_targets.target_starts[ibox+1]]
return self.tree.sorted_target_ids[user_target_ids]
@pytest.mark.parametrize("well_sep_is_n_away", [1, 2])
@pytest.mark.parametrize(("dims", "nsources_req", "ntargets_req",
"who_has_extent", "source_gen", "target_gen", "filter_kind",
"extent_norm", "from_sep_smaller_crit"),
(1, 10**5, None, "", p_normal, p_normal, None, "linf", "static_linf"),
(2, 10**5, None, "", p_normal, p_normal, None, "linf", "static_linf"),
(2, 5 * 10**4, 4*10**4, "", p_normal, p_normal, None, "linf", "static_linf"), # noqa: E501
(2, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "linf", "static_linf"), # noqa: E501
(3, 10**5, None, "", p_normal, p_normal, None, "linf", "static_linf"),
(3, 5 * 10**5, 4*10**4, "", p_normal, p_normal, None, "linf", "static_linf"), # noqa: E501
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "linf", "static_linf"), # noqa: E501
(2, 10**5, None, "", p_normal, p_normal, "user", "linf", "static_linf"),
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, "user", "linf", "static_linf"), # noqa: E501
(2, 10**5, None, "", p_normal, p_normal, "tree", "linf", "static_linf"),
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, "tree", "linf", "static_linf"), # noqa: E501
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "linf", "static_linf"), # noqa: E501
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "linf", "precise_linf"), # noqa: E501
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "l2", "precise_linf"), # noqa: E501
(3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None, "l2", "static_l2"), # noqa: E501
def test_fmm_completeness(actx_factory, dims, nsources_req, ntargets_req,
Andreas Klöckner
committed
who_has_extent, source_gen, target_gen, filter_kind, well_sep_is_n_away,
extent_norm, from_sep_smaller_crit):
"""Tests whether the built FMM traversal structures and driver completely
capture all interactions.
"""
devname = actx.queue.device.name.lower()
if (dims == 1
and actx.queue.device.platform.name == "Portable Computing Language"
and ("nvidia" in devname or "tesla" in devname)):
pytest.xfail("1D FMM fails to build on POCL Nvidia")
sources_have_extent = "s" in who_has_extent
targets_have_extent = "t" in who_has_extent
dtype = np.float64
sources = source_gen(actx.queue, nsources_req, dims, dtype, seed=15)
nsources = len(sources[0])
if ntargets_req is None:
# This says "same as sources" to the tree builder.
targets = None
ntargets = ntargets_req
else:
targets = target_gen(actx.queue, ntargets_req, dims, dtype, seed=16)
ntargets = len(targets[0])
except ImportError:
pytest.skip("loopy not available, but needed for particle array "
if sources_have_extent:
source_radii = actx.from_numpy(
2**rng.uniform(-10, 0, (nsources)).astype(dtype)
)
else:
source_radii = None
if targets_have_extent:
target_radii = actx.from_numpy(
2**rng.uniform(-10, 0, (ntargets,)).astype(dtype)
)
else:
target_radii = None
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=30,
source_radii=source_radii, target_radii=target_radii,
Andreas Klöckner
committed
debug=True, stick_out_factor=0.25, extent_norm=extent_norm)
tree = tree.get(queue=actx.queue)
tree.plot()
import matplotlib.pyplot as pt
pt.show()
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context,
Andreas Klöckner
committed
well_sep_is_n_away=well_sep_is_n_away,
from_sep_smaller_crit=from_sep_smaller_crit)
trav, _ = tbuild(actx.queue, tree, debug=True)
if who_has_extent:
pre_merge_trav = trav
trav = trav.merge_close_lists(actx.queue)
#weights = np.random.randn(nsources)
weights = np.ones(nsources)
weights_sum = np.sum(weights)
host_trav = trav.get(queue=actx.queue)
if who_has_extent:
pre_merge_host_trav = pre_merge_trav.get(queue=actx.queue)
from boxtree.tree import ParticleListFilter
plfilt = ParticleListFilter(actx.context)
tree_indep = ConstantOneTreeIndependentDataForWrangler()
flags = actx.from_numpy(
rng.integers(0, 2, ntargets or nsources, dtype=np.int8)
)
filtered_targets = plfilt.filter_target_lists_in_user_order(
wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInUserOrder(
filtered_targets.get(queue=actx.queue))
filtered_targets = plfilt.filter_target_lists_in_tree_order(
wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInTreeOrder(
filtered_targets.get(queue=actx.queue))
else:
raise ValueError("unsupported value of 'filter_kind'")
else:
wrangler = ConstantOneExpansionWrangler(tree_indep, host_trav)
flags = 1 + actx.zeros(ntargets or nsources, dtype=np.int8)
if ntargets is None and not filter_kind:
# This check only works for targets == sources.
assert np.all(
wrangler.reorder_potentials(wrangler.reorder_sources(weights))
== weights)
pot = drive_fmm(wrangler, (weights,))
rel_err = la.norm((pot - weights_sum) / nsources)
good = rel_err < 1e-8
# {{{ build, evaluate matrix (and identify incorrect interactions)
if 0 and not good:
mat = np.zeros((ntargets, nsources), dtype)
from pytools import ProgressBar
pb = ProgressBar("matrix", nsources)
unit_vec = np.zeros(nsources, dtype=dtype)
unit_vec[i] = 1
mat[:, i] = drive_fmm(host_trav, wrangler, (unit_vec,))
pb.progress()
pb.finished()
import matplotlib.pyplot as pt
if 0:
pt.imshow(mat)
pt.colorbar()
incorrect_tgts, incorrect_srcs = np.where(mat != 1)
from boxtree.visualization import TreePlotter
plotter.draw_tree(fill=False, edgecolor="black")
plotter.draw_box_numbers()
plotter.set_bounding_box()
tree_order_incorrect_tgts = \
host_tree.indices_to_tree_target_order(incorrect_tgts)
tree_order_incorrect_srcs = \
host_tree.indices_to_tree_source_order(incorrect_srcs)
src_boxes = [
for i in tree_order_incorrect_srcs]
tgt_boxes = [
for i in tree_order_incorrect_tgts]
# plot all sources/targets
if 0:
pt.plot(
host_tree.targets[0],
host_tree.targets[1],
"v", alpha=0.9)
pt.plot(
host_tree.sources[0],
host_tree.sources[1],
"gx", alpha=0.9)
# plot offending sources/targets
if 0:
pt.plot(
host_tree.targets[0][tree_order_incorrect_tgts],
host_tree.targets[1][tree_order_incorrect_tgts],
"rv")
pt.plot(
host_tree.sources[0][tree_order_incorrect_srcs],
host_tree.sources[1][tree_order_incorrect_srcs],
"go")
pt.gca().set_aspect("equal")
from boxtree.visualization import draw_box_lists
draw_box_lists(
plotter,
pre_merge_host_trav if who_has_extent else host_trav,
22)
# from boxtree.visualization import draw_same_level_non_well_sep_boxes
# draw_same_level_non_well_sep_boxes(plotter, host_trav, 2)
pt.show()
# }}}
import matplotlib.pyplot as pt
pt.plot(pot-weights_sum)
pt.show()
if 0 and not good:
import matplotlib.pyplot as pt
filt_targets = [
host_tree.targets[0][actx.to_numpy(flags > 0)],
host_tree.targets[1][actx.to_numpy(flags > 0)],
]
host_tree.plot()
bad = np.abs(pot - weights_sum) >= 1e-3
bad_targets = [
filt_targets[0][bad],
filt_targets[1][bad],
]
pt.plot(filt_targets[0], filt_targets[1], "x")
pt.plot(bad_targets[0], bad_targets[1], "v")
pt.show()
assert good
# {{{ test fmmlib integration
@pytest.mark.parametrize("dims", [2, 3])
@pytest.mark.parametrize("use_dipoles", [True, False])
@pytest.mark.parametrize("helmholtz_k", [0, 2])
def test_pyfmmlib_fmm(actx_factory, dims, use_dipoles, helmholtz_k):
pytest.importorskip("pyfmmlib")
actx = actx_factory()
nsources = 3000
ntargets = 1000
sources = p_normal(actx.queue, nsources, dims, dtype, seed=15)
p_normal(actx.queue, ntargets, dims, dtype, seed=18)
+ np.array([2, 0, 0])[:dims])
sources_host = particle_array_to_host(sources)
targets_host = particle_array_to_host(targets)
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=30, debug=True)
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context)
trav, _ = tbuild(actx.queue, tree, debug=True)
rng = np.random.default_rng(20)
weights = rng.uniform(0.0, 1.0, (nsources,))
dipole_vec = np.random.randn(dims, nsources)
else:
dipole_vec = None
if dims == 2 and helmholtz_k == 0:
def fmm_level_to_order(tree, lev):
result = base_order
if lev < 3 and helmholtz_k:
# exercise order-varies-by-level capability
result += 5
if use_dipoles:
result += 1
return result
from boxtree.pyfmmlib_integration import (
FMMLibExpansionWrangler, FMMLibTreeIndependentDataForWrangler, Kernel)
tree_indep = FMMLibTreeIndependentDataForWrangler(
trav.tree.dimensions,
Kernel.HELMHOLTZ if helmholtz_k else Kernel.LAPLACE)
wrangler = FMMLibExpansionWrangler(
tree_indep, trav,
helmholtz_k=helmholtz_k,
timing_data = {}
pot = drive_fmm(wrangler, (weights,), timing_data=timing_data)
assert timing_data
# {{{ ref fmmlib computation
logger.info("computing direct (reference) result")
ref_pot = get_fmmlib_ref_pot(wrangler, weights, sources_host.T,
targets_host.T, helmholtz_k, dipole_vec)
rel_err = la.norm(pot - ref_pot, np.inf) / la.norm(ref_pot, np.inf)
logger.info("relative l2 error vs fmmlib direct: %g", rel_err)
assert rel_err < 1e-5, rel_err
# }}}
# {{{ check against sumpy
try:
import sumpy # noqa
except ImportError:
have_sumpy = False
from warnings import warn
warn("sumpy unavailable: cannot compute independent reference "
"values for pyfmmlib")
else:
have_sumpy = True
if have_sumpy:
from sumpy.kernel import ( # pylint:disable=import-error
DirectionalSourceDerivative, HelmholtzKernel, LaplaceKernel)
from sumpy.p2p import P2P # pylint:disable=import-error
sumpy_extra_kwargs = {}
if helmholtz_k:
knl = HelmholtzKernel(dims)
sumpy_extra_kwargs["k"] = helmholtz_k
else:
knl = LaplaceKernel(dims)
if use_dipoles:
knl = DirectionalSourceDerivative(knl)
sumpy_extra_kwargs["src_derivative_dir"] = dipole_vec
[knl],
exclude_self=False)
evt, (sumpy_ref_pot,) = p2p(
actx.queue, targets, sources, (weights,),
out_host=True, **sumpy_extra_kwargs)
sumpy_rel_err = (
la.norm(pot - sumpy_ref_pot, np.inf)
logger.info("relative l2 error vs sumpy direct: %g", sumpy_rel_err)
assert sumpy_rel_err < 1e-5, sumpy_rel_err
# }}}
# {{{ test fmmlib numerical stability
@pytest.mark.parametrize("dims", [2, 3])
@pytest.mark.parametrize("helmholtz_k", [0, 2])
@pytest.mark.parametrize("order", [35])
def test_pyfmmlib_numerical_stability(actx_factory, dims, helmholtz_k, order):
pytest.importorskip("pyfmmlib")
actx = actx_factory()
# The input particles are arranged with geometrically increasing/decreasing
# spacing along a line, to build a deep tree that stress-tests the
# translations.
particle_line = np.array([2**-i for i in range(nsources//2)], dtype=dtype)
particle_line = np.hstack([particle_line, 3 - particle_line])
zero = np.zeros(nsources, dtype=dtype)
zero,
zero])[:dims]
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=2, debug=True)
assert tree.nlevels >= 15
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context)
trav, _ = tbuild(actx.queue, tree, debug=True)
weights = np.ones_like(sources[0])
from boxtree.pyfmmlib_integration import (
FMMLibExpansionWrangler, FMMLibRotationData,
FMMLibTreeIndependentDataForWrangler, Kernel)
tree_indep = FMMLibTreeIndependentDataForWrangler(
trav.tree.dimensions,
Kernel.HELMHOLTZ if helmholtz_k else Kernel.LAPLACE)
wrangler = FMMLibExpansionWrangler(
tree_indep, trav,
helmholtz_k=helmholtz_k,
rotation_data=FMMLibRotationData(actx.queue, trav))
from boxtree.fmm import drive_fmm
pot = drive_fmm(wrangler, (weights,))
assert not np.isnan(pot).any()
# {{{ ref fmmlib computation
logger.info("computing direct (reference) result")
ref_pot = get_fmmlib_ref_pot(wrangler, weights, sources, targets,
helmholtz_k)
rel_err = la.norm(pot - ref_pot, np.inf) / la.norm(ref_pot, np.inf)
logger.info("relative l2 error vs fmmlib direct: %g", rel_err)
if dims == 2:
error_bound = (1/2) ** (1 + order)
else:
error_bound = (3/4) ** (1 + order)
assert rel_err < error_bound, rel_err
# }}}
# }}}
# {{{ test particle count thresholding in traversal generation
@pytest.mark.parametrize("enable_extents", [True, False])
def test_interaction_list_particle_count_thresholding(actx_factory, enable_extents):
actx = actx_factory()
dims = 2
nsources = 1000
ntargets = 1000
dtype = np.float64
max_particles_in_box = 30
# Ensure that we have underfilled boxes.
from_sep_smaller_min_nsources_cumul = 1 + max_particles_in_box
from boxtree.fmm import drive_fmm
sources = p_normal(actx.queue, nsources, dims, dtype, seed=15)
targets = p_normal(actx.queue, ntargets, dims, dtype, seed=15)
if enable_extents:
target_radii = actx.from_numpy(
2**rng.uniform(-10, 0, (ntargets,)).astype(dtype)
)
else:
target_radii = None
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=max_particles_in_box,
target_radii=target_radii,
debug=True, stick_out_factor=0.25)
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context)
trav, _ = tbuild(actx.queue, tree, debug=True,
_from_sep_smaller_min_nsources_cumul=from_sep_smaller_min_nsources_cumul)
weights = np.ones(nsources)
weights_sum = np.sum(weights)
host_trav = trav.get(queue=actx.queue)
tree_indep = ConstantOneTreeIndependentDataForWrangler()
wrangler = ConstantOneExpansionWrangler(tree_indep, host_trav)
pot = drive_fmm(wrangler, (weights,))
# }}}
# {{{ test fmm with float32 dtype
@pytest.mark.parametrize("enable_extents", [True, False])
def test_fmm_float32(actx_factory, enable_extents):
actx = actx_factory()
from pyopencl.characterize import has_struct_arg_count_bug
if has_struct_arg_count_bug(actx.queue.device, actx.context):
pytest.xfail("won't work on devices with the struct arg count issue")
dims = 2
nsources = 1000
ntargets = 1000
dtype = np.float32
from boxtree.fmm import drive_fmm
sources = p_normal(actx.queue, nsources, dims, dtype, seed=15)
targets = p_normal(actx.queue, ntargets, dims, dtype, seed=15)
target_radii = actx.from_numpy(
2**rng.uniform(-10, 0, (ntargets,)).astype(dtype)
)
else:
target_radii = None
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=30,
target_radii=target_radii,
debug=True, stick_out_factor=0.25)
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context)
trav, _ = tbuild(actx.queue, tree, debug=True)
weights = np.ones(nsources)
weights_sum = np.sum(weights)
host_trav = trav.get(queue=actx.queue)
tree_indep = ConstantOneTreeIndependentDataForWrangler()
wrangler = ConstantOneExpansionWrangler(tree_indep, host_trav)
pot = drive_fmm(wrangler, (weights,))
# {{{ test with fmm optimized 3d m2l
@pytest.mark.parametrize("well_sep_is_n_away", (1, 2))
@pytest.mark.parametrize("helmholtz_k", (0, 2))
@pytest.mark.parametrize("nsrcntgts", (20, 10000))
def test_fmm_with_optimized_3d_m2l(actx_factory, nsrcntgts, helmholtz_k,
well_sep_is_n_away):
pytest.importorskip("pyfmmlib")
actx = actx_factory()
nsources = ntargets = nsrcntgts // 2
sources = p_normal(actx.queue, nsources, dims, dtype, seed=15)
p_normal(actx.queue, ntargets, dims, dtype, seed=18)
+ np.array([2, 0, 0])[:dims])
from boxtree import TreeBuilder
tree, _ = tb(actx.queue, sources, targets=targets,
max_particles_in_box=30, debug=True)
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(actx.context)
trav, _ = tbuild(actx.queue, tree, debug=True)
trav = trav.get(queue=actx.queue)
rng = np.random.default_rng(20)
weights = rng.uniform(0.0, 1.0, (nsources,))
def fmm_level_to_order(tree, lev):
result = base_order
if lev < 3 and helmholtz_k:
# exercise order-varies-by-level capability
result += 5
return result
from boxtree.pyfmmlib_integration import (
FMMLibExpansionWrangler, FMMLibRotationData,
FMMLibTreeIndependentDataForWrangler, Kernel)
tree_indep = FMMLibTreeIndependentDataForWrangler(
trav.tree.dimensions,
Kernel.HELMHOLTZ if helmholtz_k else Kernel.LAPLACE)
tree_indep, trav,
helmholtz_k=helmholtz_k,
tree_indep, trav,
helmholtz_k=helmholtz_k,
rotation_data=FMMLibRotationData(actx.queue, trav))
from boxtree.fmm import drive_fmm
baseline_timing_data = {}
baseline_pot = drive_fmm(
baseline_wrangler, (weights,), timing_data=baseline_timing_data)
optimized_wrangler, (weights,), timing_data=optimized_timing_data)
baseline_time = baseline_timing_data["multipole_to_local"]["process_elapsed"]
if baseline_time is not None:
print("Baseline M2L time : %#.4g s" % baseline_time)
opt_time = optimized_timing_data["multipole_to_local"]["process_elapsed"]
if opt_time is not None:
print("Optimized M2L time: %#.4g s" % opt_time)
assert np.allclose(baseline_pot, optimized_pot, atol=1e-13, rtol=1e-13)
# }}}
# $ python test_fmm.py 'test_routine(_acf)'
if __name__ == "__main__":
import sys
if len(sys.argv) > 1:
exec(sys.argv[1])
else: