From dcccfc94a350d92a4f7a342f6dafd12a7e408bca Mon Sep 17 00:00:00 2001
From: Rafael Ravedutti <rafaelravedutti@gmail.com>
Date: Thu, 24 Jun 2021 02:24:15 +0200
Subject: [PATCH] Add neighbor lists and consider ArrayND in LICM
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
---
ir/loops.py | 28 ++++++++++++++---------
new_syntax.py | 1 +
particle.py | 1 +
sim/cell_lists.py | 1 +
sim/neighbor_lists.py | 46 ++++++++++++++++++++++++++++++++++++++
sim/particle_simulation.py | 9 +++++++-
transformations/LICM.py | 14 +++++++++++-
7 files changed, 87 insertions(+), 13 deletions(-)
create mode 100644 sim/neighbor_lists.py
diff --git a/ir/loops.py b/ir/loops.py
index b4ce423..f035afa 100644
--- a/ir/loops.py
+++ b/ir/loops.py
@@ -102,22 +102,28 @@ class While(ASTNode):
class NeighborFor():
- def __init__(self, sim, particle, cell_lists):
+ def __init__(self, sim, particle, cell_lists, neighbor_lists=None):
self.sim = sim
self.particle = particle
self.cell_lists = cell_lists
+ self.neighbor_lists = neighbor_lists
def __str__(self):
return f"NeighborFor<particle: {self.particle}>"
def __iter__(self):
- cl = self.cell_lists
- for s in For(self.sim, 0, cl.nstencil):
- neigh_cell = cl.particle_cell[self.particle] + cl.stencil[s]
- for _ in Filter(self.sim,
- BinOp.and_op(neigh_cell >= 0,
- neigh_cell <= cl.ncells_all)):
- for nc in For(self.sim, 0, cl.cell_sizes[neigh_cell]):
- it = cl.cell_particles[neigh_cell][nc]
- for _ in Filter(self.sim, BinOp.neq(it, self.particle)):
- yield it
+ if self.neighbor_lists is None:
+ cl = self.cell_lists
+ for s in For(self.sim, 0, cl.nstencil):
+ neigh_cell = cl.particle_cell[self.particle] + cl.stencil[s]
+ for _ in Filter(self.sim,
+ BinOp.and_op(neigh_cell >= 0,
+ neigh_cell <= cl.ncells_all)):
+ for nc in For(self.sim, 0, cl.cell_sizes[neigh_cell]):
+ it = cl.cell_particles[neigh_cell][nc]
+ for _ in Filter(self.sim, BinOp.neq(it, self.particle)):
+ yield it
+ else:
+ neighbor_lists = self.neighbor_lists
+ for k in For(self.sim, 0, neighbor_lists.numneighs[self.particle]):
+ yield neighbor_lists.neighborlists[self.particle][k]
diff --git a/new_syntax.py b/new_syntax.py
index 28a1e06..bdbeb0d 100644
--- a/new_syntax.py
+++ b/new_syntax.py
@@ -184,6 +184,7 @@ psim.add_vector_property('velocity')
psim.add_vector_property('force', vol=True)
psim.from_file("data/minimd_setup_4x4x4.input", ['mass', 'position', 'velocity'])
psim.create_cell_lists(2.8, 2.8)
+psim.create_neighbor_lists()
psim.periodic(2.8)
psim.vtk_output("output/test")
diff --git a/particle.py b/particle.py
index 312a132..8680d2b 100644
--- a/particle.py
+++ b/particle.py
@@ -30,6 +30,7 @@ force = psim.add_vector_property('force', vol=True)
#psim.create_particle_lattice(grid, spacing=[0.82323, 0.82323, 0.82323])
psim.from_file("data/minimd_setup_4x4x4.input", ['mass', 'position', 'velocity'])
psim.create_cell_lists(2.8, 2.8)
+psim.create_neighbor_lists()
psim.periodic(2.8)
psim.vtk_output("output/test")
diff --git a/sim/cell_lists.py b/sim/cell_lists.py
index 923c4de..4c1400a 100644
--- a/sim/cell_lists.py
+++ b/sim/cell_lists.py
@@ -14,6 +14,7 @@ class CellLists:
self.sim = sim
self.grid = grid
self.spacing = spacing
+ self.cutoff_radius = cutoff_radius
self.nneighbor_cells = [
math.ceil(cutoff_radius / (
diff --git a/sim/neighbor_lists.py b/sim/neighbor_lists.py
new file mode 100644
index 0000000..f2fa90b
--- /dev/null
+++ b/sim/neighbor_lists.py
@@ -0,0 +1,46 @@
+from ir.branches import Branch, Filter
+from ir.data_types import Type_Int
+from ir.loops import For, ParticleFor, NeighborFor
+from ir.utils import Print
+from sim.resize import Resize
+
+
+class NeighborLists:
+ def __init__(self, cell_lists):
+ self.sim = cell_lists.sim
+ self.cell_lists = cell_lists
+ self.capacity = self.sim.add_var('neighborlist_capacity', Type_Int, 32)
+ self.neighborlists = self.sim.add_array('neighborlists', [self.sim.particle_capacity, self.capacity], Type_Int)
+ self.numneighs = self.sim.add_array('numneighs', self.sim.particle_capacity, Type_Int)
+
+
+class NeighborListsBuild:
+ def __init__(self, neighbor_lists):
+ self.neighbor_lists = neighbor_lists
+
+ def lower(self):
+ neighbor_lists = self.neighbor_lists
+ sim = neighbor_lists.sim
+ cell_lists = neighbor_lists.cell_lists
+ cutoff_radius = cell_lists.cutoff_radius
+ position = sim.property('position')
+
+ sim.clear_block()
+ sim.add_statement(Print(sim, "NeighborListsBuild"))
+ for resize in Resize(sim, neighbor_lists.capacity):
+ for i in ParticleFor(sim):
+ neighbor_lists.numneighs[i].set(0)
+ for j in NeighborFor(sim, i, cell_lists):
+ # TODO: find a way to not repeat this (already present in particle_pairs)
+ dp = position[i] - position[j]
+ rsq = dp.x() * dp.x() + dp.y() * dp.y() + dp.z() * dp.z()
+ for _ in Filter(sim, rsq < cutoff_radius):
+ numneighs = neighbor_lists.numneighs[i]
+ for cond in Branch(sim, numneighs >= neighbor_lists.capacity):
+ if cond:
+ resize.set(numneighs)
+ else:
+ neighbor_lists.neighborlists[i][numneighs].set(j)
+ neighbor_lists.numneighs[i].set(numneighs + 1)
+
+ return sim.block
diff --git a/sim/particle_simulation.py b/sim/particle_simulation.py
index 20efef8..5b82cd4 100644
--- a/sim/particle_simulation.py
+++ b/sim/particle_simulation.py
@@ -12,6 +12,7 @@ from sim.cell_lists import CellLists, CellListsBuild, CellListsStencilBuild
from sim.grid import Grid2D, Grid3D
from sim.kernel_wrapper import KernelWrapper
from sim.lattice import ParticleLattice
+from sim.neighbor_lists import NeighborLists, NeighborListsBuild
from sim.pbc import PBC, UpdatePBC, EnforcePBC, SetupPBC
from sim.properties import PropertiesAlloc, PropertiesResetVolatile
from sim.read_from_file import ReadFromFile
@@ -38,6 +39,7 @@ class ParticleSimulation:
self.nghost = self.add_var('nghost', Type_Int)
self.grid = None
self.cell_lists = None
+ self.neighbor_lists = None
self.pbc = None
self.scope = []
self.nested_count = 0
@@ -114,6 +116,10 @@ class ParticleSimulation:
self.cell_lists = CellLists(self, self.grid, spacing, cutoff_radius)
return self.cell_lists
+ def create_neighbor_lists(self):
+ self.neighbor_lists = NeighborLists(self.cell_lists)
+ return self.neighbor_lists
+
def periodic(self, cutneigh, flags=[1, 1, 1]):
self.pbc = PBC(self, self.grid, cutneigh, flags)
self.properties.add_capacity(self.pbc.pbc_capacity)
@@ -122,7 +128,7 @@ class ParticleSimulation:
def particle_pairs(self, cutoff_radius=None, position=None):
self.clear_block()
for i in ParticleFor(self):
- for j in NeighborFor(self, i, self.cell_lists):
+ for j in NeighborFor(self, i, self.cell_lists, self.neighbor_lists):
if cutoff_radius is not None and position is not None:
dp = position[i] - position[j]
rsq = dp.x() * dp.x() + dp.y() * dp.y() + dp.z() * dp.z()
@@ -177,6 +183,7 @@ class ParticleSimulation:
(EnforcePBC(self.pbc).lower(), 20),
(SetupPBC(self.pbc).lower(), UpdatePBC(self.pbc).lower(), 20),
(CellListsBuild(self.cell_lists).lower(), 20),
+ (NeighborListsBuild(self.neighbor_lists).lower(), 20),
PropertiesResetVolatile(self).lower(),
self.kernels.lower()
])
diff --git a/transformations/LICM.py b/transformations/LICM.py
index 74f9969..5b42d8c 100644
--- a/transformations/LICM.py
+++ b/transformations/LICM.py
@@ -38,9 +38,13 @@ class SetBlockVariants(Mutator):
return ast_node
def mutate_BinOp(self, ast_node):
+ ast_node.lhs = self.mutate(ast_node.lhs)
+
# For property accesses, we only want to include the property name, and not
# the index that is also present in the expression
- ast_node.lhs = self.mutate(ast_node.lhs)
+ if not ast_node.is_property_access():
+ ast_node.rhs = self.mutate(ast_node.rhs)
+
return ast_node
def mutate_ArrayAccess(self, ast_node):
@@ -52,6 +56,10 @@ class SetBlockVariants(Mutator):
def mutate_Array(self, ast_node):
return self.push_variant(ast_node)
+ # TODO: Array should be enough
+ def mutate_ArrayND(self, ast_node):
+ return self.push_variant(ast_node)
+
def mutate_Iter(self, ast_node):
return self.push_variant(ast_node)
@@ -130,6 +138,10 @@ class SetBinOpTerminals(Visitor):
def visit_Array(self, ast_node):
self.push_terminal(ast_node)
+ # TODO: Array should be enough
+ def visit_ArrayND(self, ast_node):
+ self.push_terminal(ast_node)
+
def visit_Iter(self, ast_node):
self.push_terminal(ast_node)
--
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