def make_normal_particle_array(queue, nparticles, dims, dtype, seed=15):
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=seed)
return make_obj_array([
rng.normal(queue, nparticles, dtype=dtype)
for i in range(dims)])
def test_random(ctx_factory):
context = ctx_factory()
queue = cl.CommandQueue(context)
from pyopencl.clrandom import RanluxGenerator
if has_double_support(context.devices[0]):
dtypes = [np.float32, np.float64]
else:
dtypes = [np.float32]
gen = RanluxGenerator(queue, 5120)
for ary_size in [300, 301, 302, 303, 10007]:
for dtype in dtypes:
ran = cl_array.zeros(queue, ary_size, dtype)
gen.fill_uniform(ran)
assert (0 < ran.get()).all()
assert (ran.get() < 1).all()
gen.synchronize(queue)
ran = cl_array.zeros(queue, ary_size, dtype)
gen.fill_uniform(ran, a=4, b=7)
assert (4 < ran.get()).all()
assert (ran.get() < 7).all()
ran = gen.normal(queue, (10007,), dtype, mu=4, sigma=3)
dtypes = [np.int32]
for dtype in dtypes:
ran = gen.uniform(queue, (10000007,), dtype, a=200, b=300)
assert (200 <= ran.get()).all()
assert (ran.get() < 300).all()
def valueMonteCarloGPU(ctx,queue,S_init,nPaths,Exp_Time, dtMonte,Strike,Int_Rate,Vol,PTYPE, nMonteLoops=1):
nextStepPathKernel = ElementwiseKernel(ctx,"float *latestStep, float *ran, float Strike, float Int_Rate, float Exp_Time, float dt, float Vol","float rval = exp((Int_Rate - 0.5f * Vol*Vol)*dt + Vol * sqrt(dt) * ran[i]); latestStep[i] *= rval;","nextStepPathKernel")
excersisePriceKernel = ElementwiseKernel(ctx,"float *latestStep, float Strike, float Int_Rate, float Exp_Time","float rval = (latestStep[i]-Strike); latestStep[i] = exp(-Int_Rate*Exp_Time) * max(rval,0.0f);","excersisePriceKernel")
sumKernel = ReductionKernel(ctx, numpy.float32, neutral="0", reduce_expr="a+b", map_expr="x[i]", arguments="__global float *x")
maxWorkItems = 1*2**9
multiplier = 1
if(nPaths > maxWorkItems):
multiplier = math.ceil(nPaths/maxWorkItems)
nPaths = multiplier * maxWorkItems
else:
maxWorkItems = nPaths
#print(maxWorkItems, multiplier, nPaths)
nTimeStepsMonte = math.ceil(Exp_Time/dtMonte)
#print(nTimeStepsMonte,nMonteLoops)
#set up random number generator
gen = RanluxGenerator(queue, maxWorkItems, luxury=4, seed=time.time())
#the arrays
ran = cl.array.zeros(queue, maxWorkItems, numpy.float32)
latestStep = cl.array.zeros_like(ran)
means = numpy.zeros(nMonteLoops)
theMean = 0
#the loop
for loop in range(nMonteLoops):
theSum = 0
for mult in range(multiplier):
latestStep.fill(S_init)
for t in range(nTimeStepsMonte):
gen.fill_normal(ran)
gen.synchronize(queue)
nextStepPathKernel(latestStep, ran, Strike, Int_Rate, Exp_Time, dtMonte, Vol)
excersisePriceKernel(latestStep, Strike, Int_Rate, Exp_Time)
#print(latestStep)
#add to array
theSum += sumKernel(latestStep, queue).get()
means[loop] = theSum / nPaths
monteAverage = numpy.mean(means)
monteStdDeviation = numpy.std(means)
return monteAverage,dtMonte, monteStdDeviation
def test_random_int_in_range(ctx_factory, dtype):
context = ctx_factory()
queue = cl.CommandQueue(context)
from pyopencl.clrandom import RanluxGenerator
gen = RanluxGenerator(queue, 5120)
if (dtype == np.int64
and context.devices[0].platform.vendor.startswith("Advanced Micro")):
pytest.xfail("AMD miscompiles 64-bit RNG math")
ran = gen.uniform(queue, (10000007,), dtype, a=200, b=300)
assert (200 <= ran.get()).all()
assert (ran.get() < 300).all()
def test_sort(ctx_factory, scan_kernel):
from pytest import importorskip
importorskip("mako")
context = ctx_factory()
queue = cl.CommandQueue(context)
dtype = np.int32
from pyopencl.algorithm import RadixSort
sort = RadixSort(context,
"int *ary",
key_expr="ary[i]",
sort_arg_names=["ary"],
scan_kernel=scan_kernel)
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from time import time
# intermediate arrays for largest size cause out-of-memory on low-end GPUs
for n in scan_test_counts[:-1]:
if n >= 2000 and isinstance(scan_kernel, GenericDebugScanKernel):
continue
print(n)
print(" rng")
a_dev = rng.uniform(queue, (n, ), dtype=dtype, a=0, b=2**16)
a = a_dev.get()
dev_start = time()
print(" device")
(a_dev_sorted, ), evt = sort(a_dev, key_bits=16)
queue.finish()
dev_end = time()
print(" numpy")
a_sorted = np.sort(a)
numpy_end = time()
numpy_elapsed = numpy_end - dev_end
dev_elapsed = dev_end - dev_start
print(" dev: %.2f MKeys/s numpy: %.2f MKeys/s ratio: %.2fx" %
(1e-6 * n / dev_elapsed, 1e-6 * n / numpy_elapsed,
numpy_elapsed / dev_elapsed))
assert (a_dev_sorted.get() == a_sorted).all()
def test_sort(ctx_factory):
from pytest import importorskip
importorskip("mako")
context = ctx_factory()
queue = cl.CommandQueue(context)
dtype = np.int32
from pyopencl.algorithm import RadixSort
sort = RadixSort(context, "int *ary", key_expr="ary[i]", sort_arg_names=["ary"])
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from time import time
# intermediate arrays for largest size cause out-of-memory on low-end GPUs
for n in scan_test_counts[:-1]:
print(n)
print(" rng")
a_dev = rng.uniform(queue, (n,), dtype=dtype, a=0, b=2 ** 16)
a = a_dev.get()
dev_start = time()
print(" device")
(a_dev_sorted,), evt = sort(a_dev, key_bits=16)
queue.finish()
dev_end = time()
print(" numpy")
a_sorted = np.sort(a)
numpy_end = time()
numpy_elapsed = numpy_end - dev_end
dev_elapsed = dev_end - dev_start
print(
" dev: %.2f MKeys/s numpy: %.2f MKeys/s ratio: %.2fx"
% (1e-6 * n / dev_elapsed, 1e-6 * n / numpy_elapsed, numpy_elapsed / dev_elapsed)
)
assert (a_dev_sorted.get() == a_sorted).all()
def test_sort(ctx_factory):
context = ctx_factory()
queue = cl.CommandQueue(context)
dtype = np.int32
from pyopencl.algorithm import RadixSort
sort = RadixSort(context, "int *ary", key_expr="ary[i]",
sort_arg_names=["ary"])
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from time import time
for n in scan_test_counts:
print(n)
print(" rng")
a_dev = rng.uniform(queue, (n,), dtype=dtype, a=0, b=2**16)
a = a_dev.get()
dev_start = time()
print(" device")
a_dev_sorted, = sort(a_dev, key_bits=16)
queue.finish()
dev_end = time()
print(" numpy")
a_sorted = np.sort(a)
numpy_end = time()
numpy_elapsed = numpy_end-dev_end
dev_elapsed = dev_end-dev_start
print (" dev: %.2f MKeys/s numpy: %.2f MKeys/s ratio: %.2fx" % (
1e-6*n/dev_elapsed, 1e-6*n/numpy_elapsed, numpy_elapsed/dev_elapsed))
assert (a_dev_sorted.get() == a_sorted).all()
def make_normal_particle_array(queue, nparticles, dims, dtype, seed=15):
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=seed)
return make_obj_array(
[rng.normal(queue, nparticles, dtype=dtype) for i in range(dims)])
# STARTEXAMPLE
import pyopencl as cl
import numpy as np
from six.moves import range
ctx = cl.create_some_context()
queue = cl.CommandQueue(ctx)
dims = 2
nparticles = 10**4
# -----------------------------------------------------------------------------
# generate some random particle positions
# -----------------------------------------------------------------------------
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from pytools.obj_array import make_obj_array
particles = make_obj_array(
[rng.normal(queue, nparticles, dtype=np.float64) for i in range(dims)])
# -----------------------------------------------------------------------------
# build tree and traversals (lists)
# -----------------------------------------------------------------------------
from boxtree import TreeBuilder
tb = TreeBuilder(ctx)
tree, _ = tb(queue, particles, max_particles_in_box=30)
from boxtree.traversal import FMMTraversalBuilder
tg = FMMTraversalBuilder(ctx)
trav, _ = tg(queue, tree)
def test_pyfmmlib_fmm(ctx_getter):
logging.basicConfig(level=logging.INFO)
from pytest import importorskip
importorskip("pyfmmlib")
ctx = ctx_getter()
queue = cl.CommandQueue(ctx)
nsources = 3000
ntargets = 1000
dims = 2
dtype = np.float64
helmholtz_k = 2
sources = p_normal(queue, nsources, dims, dtype, seed=15)
targets = p_normal(queue, ntargets, dims, dtype, seed=18) + np.array([2, 0])
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 RanluxGenerator
rng = RanluxGenerator(queue, seed=20)
weights = rng.uniform(queue, nsources, dtype=np.float64).get()
# weights = np.ones(nsources)
logger.info("computing direct (reference) result")
from pyfmmlib import hpotgrad2dall_vec
ref_pot, _, _ = hpotgrad2dall_vec(
ifgrad=False, ifhess=False, sources=sources_host.T, charge=weights, targets=targets_host.T, zk=helmholtz_k
)
from boxtree.pyfmmlib_integration import Helmholtz2DExpansionWrangler
wrangler = Helmholtz2DExpansionWrangler(trav.tree, helmholtz_k, nterms=10)
from boxtree.fmm import drive_fmm
pot = drive_fmm(trav, wrangler, weights)
rel_err = la.norm(pot - ref_pot) / la.norm(ref_pot)
logger.info("relative l2 error: %g" % rel_err)
assert rel_err < 1e-5
def test_fmm_completeness(
ctx_getter, dims, nsources_req, ntargets_req, who_has_extent, source_gen, target_gen, filter_kind
):
"""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 RanluxGenerator
rng = RanluxGenerator(queue, seed=13)
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,
)
if 0:
tree.get().plot()
import matplotlib.pyplot as pt
pt.show()
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(ctx)
trav, _ = tbuild(queue, tree, debug=True)
if trav.sep_close_smaller_starts is not None:
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 filter_kind:
flags = rng.uniform(queue, ntargets or nsources, np.int32, a=0, b=2).astype(np.int8)
if filter_kind == "user":
from boxtree.tree import filter_target_lists_in_user_order
filtered_targets = filter_target_lists_in_user_order(queue, tree, flags)
wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInUserOrder(
host_tree, filtered_targets.get(queue=queue)
)
elif filter_kind == "tree":
from boxtree.tree import filter_target_lists_in_tree_order
filtered_targets = 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)
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)
# {{{ build, evaluate matrix (and identify missing interactions)
if 0:
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 1:
pt.spy(mat)
pt.show()
missing_tgts, missing_srcs = np.where(mat == 0)
if 1 and len(missing_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_missing_tgts = host_tree.indices_to_tree_target_order(missing_tgts)
tree_order_missing_srcs = host_tree.indices_to_tree_source_order(missing_srcs)
src_boxes = [host_tree.find_box_nr_for_source(i) for i in tree_order_missing_srcs]
tgt_boxes = [host_tree.find_box_nr_for_target(i) for i in tree_order_missing_tgts]
print(src_boxes)
print(tgt_boxes)
pt.plot(host_tree.targets[0][tree_order_missing_tgts], host_tree.targets[1][tree_order_missing_tgts], "rv")
pt.plot(host_tree.sources[0][tree_order_missing_srcs], host_tree.sources[1][tree_order_missing_srcs], "go")
pt.gca().set_aspect("equal")
pt.show()
# }}}
if filter_kind:
pot = pot[flags.get() > 0]
rel_err = la.norm((pot - weights_sum) / nsources)
good = rel_err < 1e-8
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
def setup_rng(self):
self.rng = RanluxGenerator(self.cl_queue)
# STARTEXAMPLE
import pyopencl as cl
import numpy as np
from six.moves import range
ctx = cl.create_some_context()
queue = cl.CommandQueue(ctx)
dims = 2
nparticles = 500
# -----------------------------------------------------------------------------
# generate some random particle positions
# -----------------------------------------------------------------------------
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from pytools.obj_array import make_obj_array
particles = make_obj_array([
rng.normal(queue, nparticles, dtype=np.float64)
for i in range(dims)])
# -----------------------------------------------------------------------------
# build tree and traversals (lists)
# -----------------------------------------------------------------------------
from boxtree import TreeBuilder
tb = TreeBuilder(ctx)
tree, _ = tb(queue, particles, max_particles_in_box=5)
from boxtree.traversal import FMMTraversalBuilder
tg = FMMTraversalBuilder(ctx)
if ((local_index & mask) == 0) {
float other = scratch[local_index + offset];
float mine = scratch[local_index];
scratch[local_index] = (mine < other) ? mine : other;
}
barrier(CLK_LOCAL_MEM_FENCE);
}
if (local_index == 0) {
result[get_group_id(0)] = scratch[0];
}
}
"""
gen = RanluxGenerator(queue, nPaths, luxury=4, seed=time.time())
#gen = RanluxGenerator(queue, nPaths, luxury=4)
ran = cl.array.zeros(queue, nPaths, numpy.float32)
latestStep = cl.array.empty_like(ran)
averages = numpy.zeros(nLoops)
#averages = cl.array.zeros(queue, nLoops, numpy.float32)
tStartMonte = time.time()
theSum = 0
for loop in range(0, nLoops):
latestStep.fill(S_init)
def test_pyfmmlib_fmm(ctx_getter):
logging.basicConfig(level=logging.INFO)
from pytest import importorskip
importorskip("pyfmmlib")
ctx = ctx_getter()
queue = cl.CommandQueue(ctx)
nsources = 3000
ntargets = 1000
dims = 2
dtype = np.float64
helmholtz_k = 2
sources = p_normal(queue, nsources, dims, dtype, seed=15)
targets = (p_normal(queue, ntargets, dims, dtype, seed=18) +
np.array([2, 0]))
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 RanluxGenerator
rng = RanluxGenerator(queue, seed=20)
weights = rng.uniform(queue, nsources, dtype=np.float64).get()
#weights = np.ones(nsources)
logger.info("computing direct (reference) result")
from pyfmmlib import hpotgrad2dall_vec
ref_pot, _, _ = hpotgrad2dall_vec(ifgrad=False,
ifhess=False,
sources=sources_host.T,
charge=weights,
targets=targets_host.T,
zk=helmholtz_k)
from boxtree.pyfmmlib_integration import Helmholtz2DExpansionWrangler
wrangler = Helmholtz2DExpansionWrangler(trav.tree, helmholtz_k, nterms=10)
from boxtree.fmm import drive_fmm
pot = drive_fmm(trav, wrangler, weights)
rel_err = la.norm(pot - ref_pot) / la.norm(ref_pot)
logger.info("relative l2 error: %g" % rel_err)
assert rel_err < 1e-5
def test_fmm_completeness(ctx_getter, dims, nsources_req, ntargets_req,
who_has_extent, source_gen, target_gen, filter_kind):
"""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 RanluxGenerator
rng = RanluxGenerator(queue, seed=13)
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)
if 0:
tree.get().plot()
import matplotlib.pyplot as pt
pt.show()
from boxtree.traversal import FMMTraversalBuilder
tbuild = FMMTraversalBuilder(ctx)
trav, _ = tbuild(queue, tree, debug=True)
if trav.sep_close_smaller_starts is not None:
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 filter_kind:
flags = rng.uniform(queue, ntargets or nsources, np.int32, a=0, b=2) \
.astype(np.int8)
if filter_kind == "user":
from boxtree.tree import filter_target_lists_in_user_order
filtered_targets = filter_target_lists_in_user_order(
queue, tree, flags)
wrangler = ConstantOneExpansionWranglerWithFilteredTargetsInUserOrder(
host_tree, filtered_targets.get(queue=queue))
elif filter_kind == "tree":
from boxtree.tree import filter_target_lists_in_tree_order
filtered_targets = 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)
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)
# {{{ build, evaluate matrix (and identify missing interactions)
if 0:
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 1:
pt.spy(mat)
pt.show()
missing_tgts, missing_srcs = np.where(mat == 0)
if 1 and len(missing_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_missing_tgts = \
host_tree.indices_to_tree_target_order(missing_tgts)
tree_order_missing_srcs = \
host_tree.indices_to_tree_source_order(missing_srcs)
src_boxes = [
host_tree.find_box_nr_for_source(i)
for i in tree_order_missing_srcs
]
tgt_boxes = [
host_tree.find_box_nr_for_target(i)
for i in tree_order_missing_tgts
]
print(src_boxes)
print(tgt_boxes)
pt.plot(host_tree.targets[0][tree_order_missing_tgts],
host_tree.targets[1][tree_order_missing_tgts], "rv")
pt.plot(host_tree.sources[0][tree_order_missing_srcs],
host_tree.sources[1][tree_order_missing_srcs], "go")
pt.gca().set_aspect("equal")
pt.show()
# }}}
if filter_kind:
pot = pot[flags.get() > 0]
rel_err = la.norm((pot - weights_sum) / nsources)
good = rel_err < 1e-8
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
def plot_traversal(ctx_getter, do_plot=False):
ctx = ctx_getter()
queue = cl.CommandQueue(ctx)
#for dims in [2, 3]:
for dims in [2]:
nparticles = 10**4
dtype = np.float64
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from pytools.obj_array import make_obj_array
particles = make_obj_array([
rng.normal(queue, nparticles, dtype=dtype)
for i in range(dims)])
#if do_plot:
#pt.plot(particles[0].get(), particles[1].get(), "x")
from boxtree import TreeBuilder
tb = TreeBuilder(ctx)
queue.finish()
tree = tb(queue, particles, max_particles_in_box=30, debug=True)
from boxtree.traversal import FMMTraversalBuilder
tg = FMMTraversalBuilder(ctx)
trav = tg(queue, tree).get()
from boxtree.visualization import TreePlotter
plotter = TreePlotter(tree)
plotter.draw_tree(fill=False, edgecolor="black")
#plotter.draw_box_numbers()
plotter.set_bounding_box()
from random import randrange, seed
seed(7)
# {{{ generic box drawing helper
def draw_some_box_lists(starts, lists, key_to_box=None,
count=5):
actual_count = 0
while actual_count < count:
if key_to_box is not None:
key = randrange(len(key_to_box))
ibox = key_to_box[key]
else:
key = ibox = randrange(tree.nboxes)
start, end = starts[key:key+2]
if start == end:
continue
#print ibox, start, end, lists[start:end]
for jbox in lists[start:end]:
plotter.draw_box(jbox, facecolor='yellow')
plotter.draw_box(ibox, facecolor='red')
actual_count += 1
# }}}
if 0:
# colleagues
draw_some_box_lists(
trav.colleagues_starts,
trav.colleagues_lists)
elif 0:
# near neighbors ("list 1")
draw_some_box_lists(
trav.neighbor_leaves_starts,
trav.neighbor_leaves_lists,
key_to_box=trav.source_boxes)
elif 0:
# well-separated siblings (list 2)
draw_some_box_lists(
trav.sep_siblings_starts,
trav.sep_siblings_lists)
elif 1:
# separated smaller (list 3)
draw_some_box_lists(
trav.sep_smaller_starts,
trav.sep_smaller_lists,
key_to_box=trav.source_boxes)
elif 1:
# separated bigger (list 4)
draw_some_box_lists(
trav.sep_bigger_starts,
trav.sep_bigger_lists)
import matplotlib.pyplot as pt
pt.show()
def test_extent_tree(ctx_getter, dims, do_plot=False):
logging.basicConfig(level=logging.INFO)
ctx = ctx_getter()
queue = cl.CommandQueue(ctx)
nsources = 100000
ntargets = 200000
dtype = np.float64
npoint_sources_per_source = 16
sources = make_normal_particle_array(queue, nsources, dims, dtype,
seed=12)
targets = make_normal_particle_array(queue, ntargets, dims, dtype,
seed=19)
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=13)
source_radii = 2**rng.uniform(queue, nsources, dtype=dtype,
a=-10, b=0)
target_radii = 2**rng.uniform(queue, ntargets, dtype=dtype,
a=-10, b=0)
from boxtree import TreeBuilder
tb = TreeBuilder(ctx)
queue.finish()
dev_tree, _ = tb(queue, sources, targets=targets,
source_radii=source_radii, target_radii=target_radii,
max_particles_in_box=10, debug=True)
logger.info("transfer tree, check orderings")
tree = dev_tree.get(queue=queue)
sorted_sources = np.array(list(tree.sources))
sorted_targets = np.array(list(tree.targets))
sorted_source_radii = tree.source_radii
sorted_target_radii = tree.target_radii
unsorted_sources = np.array([pi.get() for pi in sources])
unsorted_targets = np.array([pi.get() for pi in targets])
unsorted_source_radii = source_radii.get()
unsorted_target_radii = target_radii.get()
assert (sorted_sources
== unsorted_sources[:, tree.user_source_ids]).all()
assert (sorted_source_radii
== unsorted_source_radii[tree.user_source_ids]).all()
# {{{ test box structure, stick-out criterion
logger.info("test box structure, stick-out criterion")
user_target_ids = np.empty(tree.ntargets, dtype=np.intp)
user_target_ids[tree.sorted_target_ids] = np.arange(tree.ntargets, dtype=np.intp)
if ntargets:
assert (sorted_targets
== unsorted_targets[:, user_target_ids]).all()
assert (sorted_target_radii
== unsorted_target_radii[user_target_ids]).all()
all_good_so_far = True
# {{{ check sources, targets
for ibox in range(tree.nboxes):
extent_low, extent_high = tree.get_box_extent(ibox)
box_radius = np.max(extent_high-extent_low) * 0.5
stick_out_dist = tree.stick_out_factor * box_radius
assert (extent_low >=
tree.bounding_box[0] - 1e-12*tree.root_extent).all(), ibox
assert (extent_high <=
tree.bounding_box[1] + 1e-12*tree.root_extent).all(), ibox
box_children = tree.box_child_ids[:, ibox]
existing_children = box_children[box_children != 0]
assert (tree.box_source_counts_nonchild[ibox]
+ np.sum(tree.box_source_counts_cumul[existing_children])
== tree.box_source_counts_cumul[ibox])
assert (tree.box_target_counts_nonchild[ibox]
+ np.sum(tree.box_target_counts_cumul[existing_children])
== tree.box_target_counts_cumul[ibox])
for what, starts, counts, points, radii in [
("source", tree.box_source_starts, tree.box_source_counts_cumul,
sorted_sources, sorted_source_radii),
("target", tree.box_target_starts, tree.box_target_counts_cumul,
sorted_targets, sorted_target_radii),
]:
bstart = starts[ibox]
bslice = slice(bstart, bstart+counts[ibox])
check_particles = points[:, bslice]
check_radii = radii[bslice]
good = (
(check_particles + check_radii
< extent_high[:, np.newaxis] + stick_out_dist)
&
(extent_low[:, np.newaxis] - stick_out_dist
<= check_particles - check_radii)
).all(axis=0)
all_good_here = good.all()
if not all_good_here:
print("BAD BOX %s %d level %d" % (what, ibox, tree.box_levels[ibox]))
all_good_so_far = all_good_so_far and all_good_here
assert all_good_here
# }}}
assert all_good_so_far
# }}}
# {{{ create, link point sources
logger.info("creating point sources")
np.random.seed(20)
from pytools.obj_array import make_obj_array
point_sources = make_obj_array([
cl.array.to_device(queue,
unsorted_sources[i][:, np.newaxis]
+ unsorted_source_radii[:, np.newaxis]
* np.random.uniform(
-1, 1, size=(nsources, npoint_sources_per_source))
)
for i in range(dims)])
point_source_starts = cl.array.arange(queue,
0, (nsources+1)*npoint_sources_per_source, npoint_sources_per_source,
dtype=tree.particle_id_dtype)
from boxtree.tree import link_point_sources
dev_tree = link_point_sources(queue, dev_tree,
point_source_starts, point_sources,
debug=True)
def valueMonteCarloGPU(ctx,
queue,
S_init,
nPaths,
Exp_Time,
dtMonte,
Strike,
Int_Rate,
Vol,
PTYPE,
nMonteLoops=1):
nextStepPathKernel = ElementwiseKernel(
ctx,
"float *latestStep, float *ran, float Strike, float Int_Rate, float Exp_Time, float dt, float Vol",
"float rval = exp((Int_Rate - 0.5f * Vol*Vol)*dt + Vol * sqrt(dt) * ran[i]); latestStep[i] *= rval;",
"nextStepPathKernel")
excersisePriceKernel = ElementwiseKernel(
ctx, "float *latestStep, float Strike, float Int_Rate, float Exp_Time",
"float rval = (latestStep[i]-Strike); latestStep[i] = exp(-Int_Rate*Exp_Time) * max(rval,0.0f);",
"excersisePriceKernel")
sumKernel = ReductionKernel(ctx,
numpy.float32,
neutral="0",
reduce_expr="a+b",
map_expr="x[i]",
arguments="__global float *x")
maxWorkItems = 1 * 2**9
multiplier = 1
if (nPaths > maxWorkItems):
multiplier = math.ceil(nPaths / maxWorkItems)
nPaths = multiplier * maxWorkItems
else:
maxWorkItems = nPaths
#print(maxWorkItems, multiplier, nPaths)
nTimeStepsMonte = math.ceil(Exp_Time / dtMonte)
#print(nTimeStepsMonte,nMonteLoops)
#set up random number generator
gen = RanluxGenerator(queue, maxWorkItems, luxury=4, seed=time.time())
#the arrays
ran = cl.array.zeros(queue, maxWorkItems, numpy.float32)
latestStep = cl.array.zeros_like(ran)
means = numpy.zeros(nMonteLoops)
theMean = 0
#the loop
for loop in range(nMonteLoops):
theSum = 0
for mult in range(multiplier):
latestStep.fill(S_init)
for t in range(nTimeStepsMonte):
gen.fill_normal(ran)
gen.synchronize(queue)
nextStepPathKernel(latestStep, ran, Strike, Int_Rate, Exp_Time,
dtMonte, Vol)
excersisePriceKernel(latestStep, Strike, Int_Rate, Exp_Time)
#print(latestStep)
#add to array
theSum += sumKernel(latestStep, queue).get()
means[loop] = theSum / nPaths
monteAverage = numpy.mean(means)
monteStdDeviation = numpy.std(means)
return monteAverage, dtMonte, monteStdDeviation
def plot_traversal(ctx_getter, do_plot=False):
ctx = ctx_getter()
queue = cl.CommandQueue(ctx)
#for dims in [2, 3]:
for dims in [2]:
nparticles = 10**4
dtype = np.float64
from pyopencl.clrandom import RanluxGenerator
rng = RanluxGenerator(queue, seed=15)
from pytools.obj_array import make_obj_array
particles = make_obj_array(
[rng.normal(queue, nparticles, dtype=dtype) for i in range(dims)])
#if do_plot:
#pt.plot(particles[0].get(), particles[1].get(), "x")
from boxtree import TreeBuilder
tb = TreeBuilder(ctx)
queue.finish()
tree = tb(queue, particles, max_particles_in_box=30, debug=True)
from boxtree.traversal import FMMTraversalBuilder
tg = FMMTraversalBuilder(ctx)
trav = tg(queue, tree).get()
from boxtree.visualization import TreePlotter
plotter = TreePlotter(tree)
plotter.draw_tree(fill=False, edgecolor="black")
#plotter.draw_box_numbers()
plotter.set_bounding_box()
from random import randrange, seed
seed(7)
# {{{ generic box drawing helper
def draw_some_box_lists(starts, lists, key_to_box=None, count=5):
actual_count = 0
while actual_count < count:
if key_to_box is not None:
key = randrange(len(key_to_box))
ibox = key_to_box[key]
else:
key = ibox = randrange(tree.nboxes)
start, end = starts[key:key + 2]
if start == end:
continue
#print ibox, start, end, lists[start:end]
for jbox in lists[start:end]:
plotter.draw_box(jbox, facecolor='yellow')
plotter.draw_box(ibox, facecolor='red')
actual_count += 1
# }}}
if 0:
# colleagues
draw_some_box_lists(trav.colleagues_starts, trav.colleagues_lists)
elif 0:
# near neighbors ("list 1")
draw_some_box_lists(trav.neighbor_leaves_starts,
trav.neighbor_leaves_lists,
key_to_box=trav.source_boxes)
elif 0:
# well-separated siblings (list 2)
draw_some_box_lists(trav.sep_siblings_starts,
trav.sep_siblings_lists)
elif 1:
# separated smaller (list 3)
draw_some_box_lists(trav.sep_smaller_starts,
trav.sep_smaller_lists,
key_to_box=trav.source_boxes)
elif 1:
# separated bigger (list 4)
draw_some_box_lists(trav.sep_bigger_starts, trav.sep_bigger_lists)
import matplotlib.pyplot as pt
pt.show()
if ((local_index & mask) == 0) {
float other = scratch[local_index + offset];
float mine = scratch[local_index];
scratch[local_index] = (mine < other) ? mine : other;
}
barrier(CLK_LOCAL_MEM_FENCE);
}
if (local_index == 0) {
result[get_group_id(0)] = scratch[0];
}
}
"""
gen = RanluxGenerator(queue, nPaths, luxury=4, seed=time.time())
#gen = RanluxGenerator(queue, nPaths, luxury=4)
ran = cl.array.zeros(queue, nPaths, numpy.float32)
latestStep = cl.array.empty_like(ran)
averages = numpy.zeros(nLoops)
#averages = cl.array.zeros(queue, nLoops, numpy.float32)
tStartMonte = time.time()
theSum = 0
for loop in range(0,nLoops):
latestStep.fill(S_init)
class GeneticAlgorithmOpenCL(GeneticAlgorithm):
class Population:
# Crossover modes
CM_SEPARATE = 0 # Separate probabilities for translation/rotation genes
CM_COMBINE = 1 # Combined probability for translation/rotation genes
def __init__(self, size = 0, dna_size = 0, \
cl_ctx = None, cl_queue = None, rng = None, cl_prg = None):
self.size = size
self.dna_size = dna_size
# OpenCL
self.cl_ctx = cl_ctx
self.cl_queue = cl_queue
self.rng = rng
self.cl_prg = cl_prg
# Matrix of i by j for individuals and genes (DNA) respectively
self.individuals_np = None
self.individuals_buf = None
self.new_individuals_np = None
self.new_individuals_buf = None
self.crossover_translation_mode_np = np.array([], dtype = int)
self.crossover_translation_mode_buf = None
self.crossover_rotation_mode_np = np.array([], dtype = int)
self.crossover_rotation_mode_buf = None
self.crossover_probability_np = np.array([], dtype = float)
self.crossover_probability_buf = None
self.mutation_probability_np = np.array([], dtype = float)
self.mutation_probability_buf = None
def setup_opencl(self):
mf = cl.mem_flags
# Setup device buffers
self.individuals_buf = cl.array.zeros(self.cl_queue, \
(self.size, self.dna_size), \
dtype = float)
self.new_individuals_buf = cl.array.zeros(self.cl_queue, \
(self.size, self.dna_size), \
dtype = float)
self.crossover_translation_mode_np = np.array([self.crossover_translation_mode], \
dtype = int)
self.crossover_translation_mode_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.crossover_translation_mode_np)
self.crossover_rotation_mode_np = np.array([self.crossover_rotation_mode], \
dtype = int)
self.crossover_rotation_mode_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.crossover_rotation_mode_np)
self.crossover_probability_np = np.array([self.crossover_probability], \
dtype = float)
self.crossover_probability_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.crossover_probability_np)
self.mutation_probability_np = np.array([self.mutation_probability], \
dtype = float)
self.mutation_probability_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.mutation_probability_np)
def __repr__(self):
self.individuals_np = self.individuals_buf.get()
ret = "Individuals:\n"
for idx, individual in enumerate(self.individuals_np):
ret += "[%3d] " % (idx + 1)
ret += "%6.2f %6.2f %6.2f | " % (individual[0], \
individual[1], \
individual[2])
ret += "%6.2f %6.2fi %6.2fj %6.2fk | " % (individual[3], \
individual[4], \
individual[5], \
individual[6])
for torsion in individual[7:]:
ret += " %5.2f" % torsion
ret += "\n"
return ret
def get_individual(self, idx = 0):
self.individuals_np = self.individuals_buf.get()
return self.individuals_np[idx]
def create(self, dna_size_buf = None, dock = None):
self.rng.fill_uniform(self.individuals_buf)
# Construct individuals
self.cl_prg.construct_individuals(self.cl_queue, \
(self.size,), None, \
dock.lo_grid_buf, \
dock.dist_grid_buf, \
dna_size_buf, \
self.individuals_buf.data)
def scoring(self, dock = None, \
cl_ctx = None, cl_queue = None):
dock.reset_poses(self.size, self.individuals_buf, \
cl_ctx, cl_queue)
dock.calc_energy()
def min_score(self, dock = None):
scores = dock.e_totals_buf.get()
return scores.min()
def crossover(self, parents_idx, ttl_torsions, rng):
return None
def mutate(self, individual, mutation_chance, \
lo_grid, hi_grid, ttl_torsions, rng):
return None
class Settler(Population):
def __init__(self, size = 0, dna_size = 0, \
cl_ctx = None, cl_queue = None, rng = None, cl_prg = None):
GeneticAlgorithmOpenCL.Population.__init__(self, size, dna_size, \
cl_ctx, cl_queue, \
rng, cl_prg)
self.crossover_translation_mode = self.CM_COMBINE
self.crossover_rotation_mode = self.CM_COMBINE
self.crossover_probability = 0.5
self.mutation_probability = 0.25
# OpenCL
self.setup_opencl()
class Nomad(Population):
def __init__(self, size = 0, dna_size = 0, \
cl_ctx = None, cl_queue = None, rng = None, cl_prg = None):
GeneticAlgorithmOpenCL.Population.__init__(self, size, dna_size, \
cl_ctx, cl_queue, \
rng, cl_prg)
self.crossover_translation_mode = self.CM_SEPARATE
self.crossover_rotation_mode = self.CM_SEPARATE
self.crossover_probability = 0.5
self.mutation_probability = 0.75
# OpenCL
self.setup_opencl()
def __init__(self, dock = None, cl_device_type = None):
GeneticAlgorithm.__init__(self, dock)
# OpenCL
self.cl_device_type = cl_device_type
if self.cl_device_type == "gpu":
self.cl_ctx = cl.Context(dev_type = cl.device_type.GPU)
elif self.cl_device_type == "cpu":
self.cl_ctx = cl.Context(dev_type = cl.device_type.CPU)
else: # manual selection
self.cl_ctx = cl.create_some_context()
self.cl_queue = cl.CommandQueue(self.cl_ctx)
self.cl_filename = "./OpenCL/GeneticAlgorithm.cl"
fh = open(self.cl_filename, 'r')
cl_code = "".join(fh.readlines())
self.cl_prg = cl.Program(self.cl_ctx, cl_code).build()
self.rng = None
# OpenCL buffer
self.population_size_np = np.array([], dtype = int)
self.population_size_buf = None
self.dna_size_np = np.array([], dtype = int)
self.dna_size_buf = None
self.max_inherited_prob_np = np.array([], dtype = int)
self.max_inherited_prob_buf = None
self.normalizer_np = np.array([], dtype = int)
self.normalizer_buf = None
self.chances_np = None
self.chances_buf = None
self.chances_sum_buf = None
self.dna1_buf = None
self.dna2_buf = None
self.ttl_reproduction_rns_np = np.array([], dtype = int)
self.ttl_reproduction_rns_buf = None
self.reproduction_rns_buf = None
self.mutation_chance_np = np.array([], dtype = float)
self.mutation_chance_buf = None
def setup_opencl(self):
# OpenCL setup
self.dock.setup_opencl(self.cl_ctx, self.cl_queue)
# Setup OpenCL device buffer
mf = cl.mem_flags
self.population_size_np = np.array([self.population_size], dtype = int)
self.population_size_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.population_size_np)
self.dna_size = 3 + 4 + self.dock.get_total_torsions()
self.dna_size_np = np.array([self.dna_size], dtype = int)
self.dna_size_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.dna_size_np)
self.max_inherited_prob_np = np.array([self.max_inherited_prob], \
dtype = int)
self.max_inherited_prob_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.max_inherited_prob_np)
self.normalizer_np = np.array([self.ttl_ligand_atoms], dtype = int)
self.normalizer_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.normalizer_np)
self.chances_buf = cl.array.zeros(self.cl_queue, (self.population_size), \
dtype = int)
self.chances_sum_buf = cl.array.zeros(self.cl_queue, (self.population_size), \
dtype = int)
self.dna1_buf = cl.array.zeros(self.cl_queue, \
(self.population_size, self.dna_size), \
dtype = float)
self.dna2_buf = cl.array.zeros(self.cl_queue, \
(self.population_size, self.dna_size), \
dtype = float)
# Reproduction random numbers needed per individual:
# - Selecting parents: 2
# - Crossing over: Use new_individuals_buf
# - Mutation: 1 + 2 + total torsions
# - Mutation pose: 3 + 4 + total torsions
ttl_reproduction_rns = 2 + 1 + 2 + self.ttl_torsions + \
3 + 4 + self.ttl_torsions
self.ttl_reproduction_rns_np = np.array([ttl_reproduction_rns], \
dtype = int)
self.ttl_reproduction_rns_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.ttl_reproduction_rns_np)
self.reproduction_rns_buf = cl.array.zeros(self.cl_queue, \
(self.population_size, ttl_reproduction_rns), \
dtype = float)
self.mutation_chance_np = np.array([self.mutation_chance], dtype = float)
self.mutation_chance_buf = cl.Buffer(self.cl_ctx, \
mf.READ_ONLY | mf.COPY_HOST_PTR, \
hostbuf = self.mutation_chance_np)
# Setup OpenCL buffer for docking object
self.dock.setup_opencl_buffer(self.population_size, \
self.cl_ctx, self.cl_queue)
def setup_rng(self):
self.rng = RanluxGenerator(self.cl_queue)
def setup(self):
# Call parent setup
GeneticAlgorithm.setup(self)
# OpenCL
self.setup_opencl()
def select(self, population):
# Get individual scores
population.scoring(self.dock, self.cl_ctx, self.cl_queue)
self.cl_prg.calc_chances(self.cl_queue, (self.population_size,), None, \
self.dock.e_totals_buf.data, \
self.normalizer_buf, \
self.max_inherited_prob_buf, \
self.chances_buf.data)
def reproduce(self, population):
self.rng.fill_uniform(population.new_individuals_buf)
self.rng.fill_uniform(self.reproduction_rns_buf)
self.cl_prg.reproduce(self.cl_queue, (self.population_size,), None, \
self.population_size_buf, \
self.chances_buf.data, \
self.ttl_reproduction_rns_buf, \
self.reproduction_rns_buf.data, \
self.dna_size_buf, \
population.individuals_buf.data, \
population.crossover_translation_mode_buf, \
population.crossover_rotation_mode_buf, \
population.crossover_probability_buf, \
self.mutation_chance_buf, \
population.mutation_probability_buf, \
self.dock.ttl_torsions_buf, \
self.dock.lo_grid_buf, \
self.dock.dist_grid_buf, \
self.chances_sum_buf.data, \
self.dna1_buf.data, \
self.dna2_buf.data, \
population.new_individuals_buf.data)
cl.enqueue_copy(self.cl_queue, population.individuals_buf.data, \
population.new_individuals_buf.data)
def run(self):
self.setup()
# Define multiple population
self.nomad = self.Nomad(self.population_size, self.dna_size, \
self.cl_ctx, self.cl_queue, \
self.rng, self.cl_prg)
self.settler = self.Settler(self.population_size, self.dna_size, \
self.cl_ctx, self.cl_queue, \
self.rng, self.cl_prg)
population_min_scores = []
for community_idx in xrange(self.community_size):
tic = time()
# Nomad portion
nomad_min_score = float("inf")
self.nomad.create(self.dna_size_buf, self.dock)
if VERBOSE: print self.nomad
for gen_idx in xrange(self.num_gen):
self.select(self.nomad)
self.reproduce(self.nomad)
nomad_min_score = self.nomad.min_score(self.dock)
# Settler portion
settler_min_score = float("inf")
cl.enqueue_copy(self.cl_queue, self.settler.individuals_buf.data, \
self.nomad.individuals_buf.data)
if VERBOSE: print self.settler
for gen_idx in xrange(self.num_gen):
self.select(self.settler)
self.reproduce(self.settler)
if VERBOSE: print self.settler
settler_min_score = self.settler.min_score(self.dock)
population_min_scores.append([nomad_min_score, settler_min_score])
toc = time()
print "Elapsed time community %4d: %10.2f - Minimum Scores: %12.3f, %12.3f" \
% (community_idx + 1, toc - tic, \
nomad_min_score, settler_min_score)
print "Community Minimum Scores: %s" % population_min_scores