From 8e815ad99ba89d4ea7a5538b11ffd63f9de4a131 Mon Sep 17 00:00:00 2001
From: Jean-Matthieu Etancelin <jean-matthieu.etancelin@univ-reims.fr>
Date: Tue, 18 Nov 2014 17:52:28 +0100
Subject: [PATCH] Improve GPU-diffusion profiling. Add a full update ghost. fix
advection_dir topology parameters. fix tools parameters. Add update ghosts
test.
---
HySoP/hysop/gpu/gpu_diffusion.py | 14 +-
.../numerics/tests/test_update_ghosts.py | 170 ++++++++++++++++++
HySoP/hysop/numerics/update_ghosts.py | 25 ++-
HySoP/hysop/operator/advection_dir.py | 13 +-
HySoP/hysop/tools/parameters.py | 2 +-
5 files changed, 199 insertions(+), 25 deletions(-)
create mode 100644 HySoP/hysop/numerics/tests/test_update_ghosts.py
diff --git a/HySoP/hysop/gpu/gpu_diffusion.py b/HySoP/hysop/gpu/gpu_diffusion.py
index 4131d9d28..e70f3ab4a 100644
--- a/HySoP/hysop/gpu/gpu_diffusion.py
+++ b/HySoP/hysop/gpu/gpu_diffusion.py
@@ -158,6 +158,8 @@ class GPUDiffusion(DiscreteOperator, GPUOperator):
nb_part_per_wi, tile_size)
self.num_diffusion = KernelLauncher(
prg.diffusion, self.cl_env.queue, gwi, lwi)
+ self.copy = KernelLauncher(cl.enqueue_copy,
+ self.cl_env.queue)
def _compute_diffusion(self, simulation):
assert self.field_tmp is not None
@@ -168,8 +170,10 @@ class GPUDiffusion(DiscreteOperator, GPUOperator):
self.gpu_precision(self.viscosity * simulation.timeStep),
self._mesh_size,
wait_for=wait_evt)
- c_evt = cl.enqueue_copy(self.cl_env.queue, self.field.gpu_data[0],
- self.field_tmp, wait_for=[d_evt])
+ c_evt = self.copy.launch_sizes_in_args(
+ self.field.gpu_data[0], self.field_tmp, wait_for=[d_evt])
+ #c_evt = cl.enqueue_copy(self.cl_env.queue, self.field.gpu_data[0],
+ # self.field_tmp, wait_for=[d_evt])
self.field.events.append(c_evt)
def set_field_tmp(self, field_tmp):
@@ -277,3 +281,9 @@ class GPUDiffusion(DiscreteOperator, GPUOperator):
def apply(self, simulation):
self._compute(simulation)
+
+ def get_profiling_info(self):
+ for k in [self.num_diffusion, self.copy]:
+ if k is not None:
+ for p in k.profile:
+ self.profiler += p
diff --git a/HySoP/hysop/numerics/tests/test_update_ghosts.py b/HySoP/hysop/numerics/tests/test_update_ghosts.py
new file mode 100644
index 000000000..d050f43ff
--- /dev/null
+++ b/HySoP/hysop/numerics/tests/test_update_ghosts.py
@@ -0,0 +1,170 @@
+import parmepy.tools.numpywrappers as npw
+from parmepy.numerics.update_ghosts import UpdateGhosts, UpdateGhostsFull
+from parmepy.domain.box import Box
+from parmepy.fields.continuous import Field
+from parmepy.tools.parameters import Discretization
+import numpy as np
+
+
+def _setup(ghosts, topo_dim):
+ dom = Box()
+
+ f = Field(dom, isVector=True)
+ resolTopo = Discretization([33, 33, 33], ghosts=ghosts)
+ topo = dom.create_topology(resolTopo, dim=topo_dim)
+ f.discretize(topo)
+ df = f.discreteFields[topo]
+ for i, dfd in enumerate(df.data):
+ dfd[...] = 0.
+ dfd[topo.mesh.iCompute] = 1. * (i + 1)
+ return df, topo
+
+
+def verify(df, gh):
+ sli = (
+ (slice(0, gh[0]), slice(gh[1], -gh[1]), slice(gh[2], -gh[2])),
+ (slice(-gh[0], None), slice(gh[1], -gh[1]), slice(gh[2], -gh[2])),
+ (slice(gh[0], -gh[0]), slice(0, gh[1]), slice(gh[2], -gh[2])),
+ (slice(gh[0], -gh[0]), slice(-gh[1], None), slice(gh[2], -gh[2])),
+ (slice(gh[0], -gh[0]), slice(gh[1], -gh[1]), slice(0, gh[2])),
+ (slice(gh[0], -gh[0]), slice(gh[1], -gh[1]), slice(-gh[2], None)))
+ slni = (
+ (slice(0, gh[0]), slice(0, gh[1]), slice(None)),
+ (slice(0, gh[0]), slice(None), slice(0, gh[2])),
+ (slice(None), slice(0, gh[1]), slice(0, gh[2])),
+ (slice(-gh[0], None), slice(-gh[1], None), slice(None)),
+ (slice(-gh[0], None), slice(None), slice(-gh[2], None)),
+ (slice(None), slice(-gh[1], None), slice(-gh[2], None)))
+ for i, dfd in enumerate(df.data):
+ for s in sli:
+ assert np.max(dfd[s]) == np.min(dfd[s]) and \
+ np.max(dfd[s]) == 1. * (i + 1)
+ for s in slni:
+ assert np.max(dfd[s]) == np.min(dfd[s]) and \
+ np.max(dfd[s]) == 0.
+
+
+def verify_full(df, gh):
+ for i, dfd in enumerate(df.data):
+ for s in ((slice(0, gh[0]), slice(None), slice(None)),
+ (slice(-gh[0], None), slice(None), slice(None)),
+ (slice(None), slice(0, gh[1]), slice(None)),
+ (slice(None), slice(-gh[1], None), slice(None)),
+ (slice(None), slice(None), slice(0, gh[2])),
+ (slice(None), slice(None), slice(-gh[2], None))):
+ assert np.max(dfd[s]) == np.min(dfd[s]) and \
+ np.max(dfd[s]) == 1. * (i + 1)
+ assert np.max(dfd) == np.min(dfd) and \
+ np.max(dfd) == 1. * (i + 1)
+
+
+def test_update_ghosts_simple_1D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 1)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_simple_2D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 2)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_simple_3D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 3)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_1D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 1)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_2D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 2)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_3D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 3)
+ update = UpdateGhosts(topo, 3)
+ update(df.data)
+ verify(df, gh)
+
+
+def test_update_ghosts_full_simple_1D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 1)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+def test_update_ghosts_full_simple_2D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 2)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+def test_update_ghosts_full_simple_3D():
+ gh = [1, 1, 1]
+ df, topo, = _setup(gh, 3)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+def test_update_ghosts_full_1D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 1)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+def test_update_ghosts_full_2D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 2)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+def test_update_ghosts_full_3D():
+ gh = [2, 3, 4]
+ df, topo, = _setup(gh, 3)
+ update = UpdateGhostsFull(topo, 3)
+ update(df.data)
+ verify_full(df, gh)
+
+
+if __name__ == '__main__':
+ for f in (test_update_ghosts_simple_1D,
+ test_update_ghosts_simple_2D,
+ test_update_ghosts_simple_3D,
+ test_update_ghosts_1D,
+ test_update_ghosts_2D,
+ test_update_ghosts_3D,
+ test_update_ghosts_full_simple_1D,
+ test_update_ghosts_full_simple_2D,
+ test_update_ghosts_full_simple_3D,
+ test_update_ghosts_full_1D,
+ test_update_ghosts_full_2D,
+ test_update_ghosts_full_3D):
+ f()
diff --git a/HySoP/hysop/numerics/update_ghosts.py b/HySoP/hysop/numerics/update_ghosts.py
index f18dce221..8e9c9a997 100644
--- a/HySoP/hysop/numerics/update_ghosts.py
+++ b/HySoP/hysop/numerics/update_ghosts.py
@@ -46,7 +46,7 @@ class UpdateGhosts(object):
self._recvbuffer = []
# domain dimension
self._dim = self.topology.domain.dimension
-
+
self._setup_slices()
## shape of numpy arrays to be updated.
@@ -123,7 +123,7 @@ class UpdateGhosts(object):
if self.topology.shape[d] == 1]
for d in dirs:
self._applyBC_in_dir(variables, d)
-
+
def _applyBC_in_dir(self, variables, d):
"""Apply periodic boundary condition in direction d."""
for v in variables:
@@ -151,7 +151,7 @@ class UpdateGhosts(object):
self.applyBC(variables)
def _apply_in_dir(self, variables, d, i):
- """Communicate ghosts values in direction d for neighbour
+ """Communicate ghosts values in direction d for neighbour
in direction i of the topology"""
comm = self.topology.comm
rank = self.topology.rank
@@ -219,7 +219,7 @@ class UpdateGhostsFull(UpdateGhosts):
at each call.
nbElements and memshape will be used to allocate memory for local
buffers used for send-recv process.
- This version differs from UpdateGhosts by computing also ghosts values
+ This version differs from UpdateGhosts by computing also ghosts values
in edges and corners of the domain. The directions are computed in reversed order.
"""
super(UpdateGhostsFull, self).__init__(topo, nbElements)
@@ -244,13 +244,14 @@ class UpdateGhostsFull(UpdateGhosts):
self._g_tonext.append(list(defslice))
self._g_tonext[d][d] = slice(-2 * self.ghosts[d],
-self.ghosts[d])
-
- ## Slices for other directions corresmonding to directions not
- ## yet exchanged : x < d. For directions x > d, the slices is a
- ## full slice that includes ghosts. This assumes that directions
- ## x > d have already been computed (by communications or local
+
+ ## Slices for other directions corresponding to directions not
+ ## yet exchanged : x > d. For directions x < d, the slices is a
+ ## full slice that includes ghosts. This assumes that directions
+ ## x < d have already been computed (by communications or local
## exchanges)
- otherDim = [x for x in xrange(self._dim) if x < d]
+ # if d == 0:
+ otherDim = [x for x in xrange(self._dim) if x > d]
for d2 in otherDim:
self._g_fromprevious[d][d2] = slice(self.ghosts[d2],
-self.ghosts[d2])
@@ -285,7 +286,7 @@ class UpdateGhostsFull(UpdateGhosts):
assert len(exchange_dir) + len(localBC_dir) == self._dim
i = 0
- for d in xrange(self._dim-1, -1, -1):
+ for d in xrange(self._dim):
if d in localBC_dir:
self._applyBC_in_dir(variables, d)
elif d in exchange_dir:
@@ -293,5 +294,3 @@ class UpdateGhostsFull(UpdateGhosts):
# update index in neighbours list
i += 1
# End of loop through send/recv directions.
-
-
diff --git a/HySoP/hysop/operator/advection_dir.py b/HySoP/hysop/operator/advection_dir.py
index d08deff01..75c004af2 100644
--- a/HySoP/hysop/operator/advection_dir.py
+++ b/HySoP/hysop/operator/advection_dir.py
@@ -30,7 +30,7 @@ class AdvectionDir(Computational):
@debug
def __init__(self, velocity, direction, advected_fields=None,
- name_suffix='', cutdir=None, **kwds):
+ name_suffix='', **kwds):
## Get the other arguments to pass to the discrete operators
self._kwds = kwds.copy()
self._kwds.pop('discretization')
@@ -78,8 +78,6 @@ class AdvectionDir(Computational):
## Positions of the particles
self.particle_positions = None
- self._default_cutdir = cutdir
-
@debug
def discretize(self):
if self._is_discretized:
@@ -93,12 +91,9 @@ class AdvectionDir(Computational):
raise ValueError("Multiscale advection is not yet supported "
"in pure Python, use Scales or GPU.")
- ## Topology cutdir for parallel advection
- if self._default_cutdir is None:
- cutdir = [False] * self.domain.dimension
- cutdir[-1] = True
- else:
- cutdir = self._default_cutdir
+ ## Default topology cutdir for parallel advection
+ cutdir = [False] * self.domain.dimension
+ cutdir[-1] = True
if self._single_topo:
# One topo for all fields ...
diff --git a/HySoP/hysop/tools/parameters.py b/HySoP/hysop/tools/parameters.py
index 53db939b5..b24a6f9cf 100644
--- a/HySoP/hysop/tools/parameters.py
+++ b/HySoP/hysop/tools/parameters.py
@@ -61,7 +61,7 @@ class Discretization(namedtuple("Discretization", ['resolution', 'ghosts'])):
assert ghosts.size == resolution.size, msg
assert all(ghosts >= 0)
else:
- ghosts = npw.dim_zeros(resolution.size)
+ ghosts = npw.int_zeros(resolution.size)
return super(Discretization, cls).__new__(cls, resolution, ghosts)
def __eq__(self, other):
--
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