from __future__ import division, absolute_import, print_function __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. """ from six.moves import range import numpy as np import numpy.linalg as la import pyopencl as cl import pytest from pyopencl.tools import ( # noqa pytest_generate_tests_for_pyopencl as pytest_generate_tests) 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) import logging logger = logging.getLogger(__name__) # {{{ fmm interaction completeness test class ConstantOneExpansionWrangler(object): """This implements the 'analytical routines' for a Green's function that is constant 1 everywhere. For 'charges' of 'ones', this should get every particle a copy of the particle count. """ def __init__(self, tree): self.tree = tree def multipole_expansion_zeros(self): return np.zeros(self.tree.nboxes, dtype=np.float64) local_expansion_zeros = multipole_expansion_zeros def potential_zeros(self): return np.zeros(self.tree.ntargets, dtype=np.float64) def _get_source_slice(self, ibox): pstart = self.tree.box_source_starts[ibox] return slice( pstart, pstart + self.tree.box_source_counts_nonchild[ibox]) def _get_target_slice(self, ibox): pstart = self.tree.box_target_starts[ibox] return slice( pstart, pstart + self.tree.box_target_counts_nonchild[ibox]) def reorder_sources(self, source_array): return source_array[self.tree.user_source_ids] def reorder_potentials(self, potentials): return potentials[self.tree.sorted_target_ids] def form_multipoles(self, level_start_source_box_nrs, source_boxes, src_weights): mpoles = self.multipole_expansion_zeros() for ibox in source_boxes: pslice = self._get_source_slice(ibox) mpoles[ibox] += np.sum(src_weights[pslice]) return mpoles def coarsen_multipoles(self, level_start_source_parent_box_nrs, source_parent_boxes, mpoles): tree = self.tree # nlevels-1 is the last valid level index # nlevels-2 is the last valid level that could have children # # 3 is the last relevant source_level. # 2 is the last relevant target_level. # (because no level 1 box will be well-separated from another) for source_level in range(tree.nlevels-1, 2, -1): target_level = source_level - 1 start, stop = level_start_source_parent_box_nrs[ target_level:target_level+2] for ibox in source_parent_boxes[start:stop]: for child in tree.box_child_ids[:, ibox]: if child: mpoles[ibox] += mpoles[child] def eval_direct(self, target_boxes, neighbor_sources_starts, neighbor_sources_lists, src_weights): pot = self.potential_zeros() for itgt_box, tgt_ibox in enumerate(target_boxes): tgt_pslice = self._get_target_slice(tgt_ibox) src_sum = 0 start, end = neighbor_sources_starts[itgt_box:itgt_box+2] #print "DIR: %s <- %s" % (tgt_ibox, neighbor_sources_lists[start:end]) for src_ibox in neighbor_sources_lists[start:end]: src_pslice = self._get_source_slice(src_ibox) src_sum += np.sum(src_weights[src_pslice]) pot[tgt_pslice] = src_sum return pot def multipole_to_local(self, level_start_target_or_target_parent_box_nrs, target_or_target_parent_boxes, starts, lists, mpole_exps): local_exps = self.local_expansion_zeros() for itgt_box, tgt_ibox in enumerate(target_or_target_parent_boxes): start, end = starts[itgt_box:itgt_box+2] contrib = 0 #print tgt_ibox, "<-", lists[start:end] for src_ibox in lists[start:end]: contrib += mpole_exps[src_ibox] local_exps[tgt_ibox] += contrib return local_exps def eval_multipoles(self, level_start_target_box_nrs, target_boxes, from_sep_smaller_nonsiblings_by_level, mpole_exps): pot = self.potential_zeros() for ssn in from_sep_smaller_nonsiblings_by_level: for itgt_box, tgt_ibox in enumerate(target_boxes): tgt_pslice = self._get_target_slice(tgt_ibox) contrib = 0 start, end = ssn.starts[itgt_box:itgt_box+2] for src_ibox in ssn.lists[start:end]: contrib += mpole_exps[src_ibox] pot[tgt_pslice] += contrib return pot def form_locals(self, level_start_target_or_target_parent_box_nrs, target_or_target_parent_boxes, starts, lists, src_weights): local_exps = self.local_expansion_zeros() for itgt_box, tgt_ibox in enumerate(target_or_target_parent_boxes): start, end = starts[itgt_box:itgt_box+2] #print "LIST 4", tgt_ibox, "<-", lists[start:end] contrib = 0 for src_ibox in lists[start:end]: src_pslice = self._get_source_slice(src_ibox) contrib += np.sum(src_weights[src_pslice]) local_exps[tgt_ibox] += contrib return local_exps def refine_locals(self, level_start_target_or_target_parent_box_nrs, target_or_target_parent_boxes, local_exps): for target_lev in range(1, self.tree.nlevels): start, stop = level_start_target_or_target_parent_box_nrs[ target_lev:target_lev+2] for ibox in target_or_target_parent_boxes[start:stop]: local_exps[ibox] += local_exps[self.tree.box_parent_ids[ibox]] return local_exps def eval_locals(self, level_start_target_box_nrs, target_boxes, local_exps): pot = self.potential_zeros() for ibox in target_boxes: tgt_pslice = self._get_target_slice(ibox) pot[tgt_pslice] += local_exps[ibox] return pot def finalize_potentials(self, potentials): return potentials class ConstantOneExpansionWranglerWithFilteredTargetsInTreeOrder( ConstantOneExpansionWrangler): def __init__(self, tree, filtered_targets): ConstantOneExpansionWrangler.__init__(self, tree) self.filtered_targets = filtered_targets def potential_zeros(self): return np.zeros(self.filtered_targets.nfiltered_targets, dtype=np.float64) 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 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, filtered_targets): ConstantOneExpansionWrangler.__init__(self, tree) 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(("extent_norm", "from_sep_smaller_crit"), [ ("linf", "static_linf"), ("linf", "precise_linf"), ("l2", "precise_linf"), ("l2", "static_l2"), ("l2", "precise_l2"), ]) @pytest.mark.parametrize(("dims", "nsources_req", "ntargets_req", "who_has_extent", "source_gen", "target_gen", "filter_kind"), [ (2, 10**5, None, "", p_normal, p_normal, None), (3, 5 * 10**4, 4*10**4, "", p_normal, p_normal, None), #(2, 5 * 10**5, 4*10**4, "s", p_normal, p_normal, None), #(2, 5 * 10**5, 4*10**4, "st", p_normal, p_normal, None), (2, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None), #(2, 5 * 10**5, 4*10**4, "st", p_surface, p_uniform, None), (3, 10**5, None, "", p_normal, p_normal, None), (3, 5 * 10**4, 4*10**4, "", p_normal, p_normal, None), #(3, 5 * 10**5, 4*10**4, "s", p_normal, p_normal, None), #(3, 5 * 10**5, 4*10**4, "st", p_normal, p_normal, None), (3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, None), #(3, 5 * 10**5, 4*10**4, "st", p_surface, p_uniform, None), (2, 10**5, None, "", p_normal, p_normal, "user"), (3, 5 * 10**4, 4*10**4, "", p_normal, p_normal, "user"), #(2, 5 * 10**5, 4*10**4, "s", p_normal, p_normal, "user"), #(2, 5 * 10**5, 4*10**4, "st", p_normal, p_normal, "user"), (3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, "user"), #(2, 5 * 10**5, 4*10**4, "st", p_surface, p_uniform, "user"), (2, 10**5, None, "", p_normal, p_normal, "tree"), (3, 5 * 10**4, 4*10**4, "", p_normal, p_normal, "tree"), #(2, 5 * 10**5, 4*10**4, "s", p_normal, p_normal, "tree"), #(2, 5 * 10**5, 4*10**4, "st", p_normal, p_normal, "tree"), (3, 5 * 10**5, 4*10**4, "t", p_normal, p_normal, "tree"), #(2, 5 * 10**5, 4*10**4, "st", p_surface, p_uniform, "tree"), ]) def test_fmm_completeness(ctx_getter, dims, nsources_req, ntargets_req, 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. """ sources_have_extent = "s" in who_has_extent targets_have_extent = "t" in who_has_extent logging.basicConfig(level=logging.INFO) ctx = ctx_getter() queue = cl.CommandQueue(ctx) dtype = np.float64 try: sources = source_gen(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(queue, ntargets_req, dims, dtype, seed=16) ntargets = len(targets[0]) except ImportError: pytest.skip("loo.py not available, but needed for particle array " "generation") from pyopencl.clrandom import PhiloxGenerator rng = PhiloxGenerator(queue.context, seed=12) if sources_have_extent: source_radii = 2**rng.uniform(queue, nsources, dtype=dtype, a=-10, b=0) else: source_radii = None if targets_have_extent: target_radii = 2**rng.uniform(queue, ntargets, dtype=dtype, a=-10, b=0) else: target_radii = None from boxtree import TreeBuilder tb = TreeBuilder(ctx) tree, _ = tb(queue, sources, targets=targets, max_particles_in_box=30, source_radii=source_radii, target_radii=target_radii, debug=True, stick_out_factor=0.25, extent_norm=extent_norm) if 0: tree.get().plot() import matplotlib.pyplot as pt pt.show() from boxtree.traversal import FMMTraversalBuilder tbuild = FMMTraversalBuilder(ctx, well_sep_is_n_away=well_sep_is_n_away, from_sep_smaller_crit=from_sep_smaller_crit) trav, _ = tbuild(queue, tree, debug=True) if who_has_extent: pre_merge_trav = trav trav = trav.merge_close_lists(queue) #weights = np.random.randn(nsources) weights = np.ones(nsources) weights_sum = np.sum(weights) host_trav = trav.get(queue=queue) host_tree = host_trav.tree if who_has_extent: pre_merge_host_trav = pre_merge_trav.get(queue=queue) from boxtree.tree import ParticleListFilter plfilt = ParticleListFilter(ctx) if filter_kind: flags = rng.uniform(queue, ntargets or nsources, np.int32, a=0, b=2) \ .astype(np.int8) if filter_kind == "user": filtered_targets = plfilt.filter_target_lists_in_user_order( queue, tree, flags) wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInUserOrder( host_tree, filtered_targets.get(queue=queue)) elif filter_kind == "tree": filtered_targets = plfilt.filter_target_lists_in_tree_order( queue, tree, flags) wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInTreeOrder( host_tree, filtered_targets.get(queue=queue)) else: raise ValueError("unsupported value of 'filter_kind'") else: wrangler = ConstantOneExpansionWrangler(host_tree) flags = cl.array.empty(queue, ntargets or nsources, dtype=np.int8) flags.fill(1) if ntargets is None and not filter_kind: # This check only works for targets == sources. assert (wrangler.reorder_potentials( wrangler.reorder_sources(weights)) == weights).all() from boxtree.fmm import drive_fmm pot = drive_fmm(host_trav, wrangler, weights) if filter_kind: pot = pot[flags.get() > 0] 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 logging.getLogger().setLevel(logging.WARNING) pb = ProgressBar("matrix", nsources) for i in range(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() logging.getLogger().setLevel(logging.INFO) import matplotlib.pyplot as pt if 0: pt.imshow(mat) pt.colorbar() pt.show() incorrect_tgts, incorrect_srcs = np.where(mat != 1) if 1 and len(incorrect_tgts): from boxtree.visualization import TreePlotter plotter = TreePlotter(host_tree) 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 = [ host_tree.find_box_nr_for_source(i) for i in tree_order_incorrect_srcs] tgt_boxes = [ host_tree.find_box_nr_for_target(i) for i in tree_order_incorrect_tgts] print(src_boxes) print(tgt_boxes) # 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() # }}} if 0 and not good: 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][flags.get() > 0], host_tree.targets[1][flags.get() > 0], ] host_tree.plot() bad = np.abs(pot - weights_sum) >= 1e-3 bad_targets = [ filt_targets[0][bad], filt_targets[1][bad], ] print(bad_targets[0].shape) 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(ctx_getter, dims, use_dipoles, helmholtz_k): logging.basicConfig(level=logging.INFO) from pytest import importorskip importorskip("pyfmmlib") ctx = ctx_getter() queue = cl.CommandQueue(ctx) nsources = 3000 ntargets = 1000 dtype = np.float64 sources = p_normal(queue, nsources, dims, dtype, seed=15) targets = ( p_normal(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 tb = TreeBuilder(ctx) tree, _ = tb(queue, sources, targets=targets, max_particles_in_box=30, debug=True) from boxtree.traversal import FMMTraversalBuilder tbuild = FMMTraversalBuilder(ctx) trav, _ = tbuild(queue, tree, debug=True) trav = trav.get(queue=queue) from pyopencl.clrandom import PhiloxGenerator rng = PhiloxGenerator(queue.context, seed=20) weights = rng.uniform(queue, nsources, dtype=np.float64).get() #weights = np.ones(nsources) if use_dipoles: np.random.seed(13) dipole_vec = np.random.randn(dims, nsources) else: dipole_vec = None if dims == 2 and helmholtz_k == 0: base_nterms = 20 else: base_nterms = 10 def fmm_level_to_nterms(tree, lev): result = base_nterms 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 wrangler = FMMLibExpansionWrangler( trav.tree, helmholtz_k, fmm_level_to_nterms=fmm_level_to_nterms, dipole_vec=dipole_vec) from boxtree.fmm import drive_fmm pot = drive_fmm(trav, wrangler, weights) # {{{ ref fmmlib computation logger.info("computing direct (reference) result") import pyfmmlib fmmlib_routine = getattr( pyfmmlib, "%spot%s%ddall%s_vec" % ( wrangler.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 ref_pot = wrangler.finalize_potentials( fmmlib_routine( sources=sources_host.T, targets=targets_host.T, **kwargs)[0] ) 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 ( LaplaceKernel, HelmholtzKernel, DirectionalSourceDerivative) from sumpy.p2p import P2P 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 p2p = P2P(ctx, [knl], exclude_self=False) evt, (sumpy_ref_pot,) = p2p( queue, targets, sources, [weights], out_host=True, **sumpy_extra_kwargs) sumpy_rel_err = ( la.norm(pot - sumpy_ref_pot, np.inf) / la.norm(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 # }}} # }}} # You can test individual routines by typing # $ python test_fmm.py 'test_routine(cl.create_some_context)' if __name__ == "__main__": import sys if len(sys.argv) > 1: exec(sys.argv[1]) else: from py.test.cmdline import main main([__file__]) # vim: fdm=marker