From 9665d6b23d83a7385e71684a65e9f839d9446608 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Wed, 5 Feb 2014 09:58:42 +0000
Subject: [PATCH] Review comm management in topo.
---
HySoP/hysop/fields/discrete.py | 4 +-
HySoP/hysop/mpi/topology.py | 17 ++++----
.../hysop/operator/monitors/compute_forces.py | 43 +++++++++----------
HySoP/hysop/operator/reprojection.py | 2 +-
4 files changed, 32 insertions(+), 34 deletions(-)
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
index 04b9778c2..db13fff4c 100644
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -11,7 +11,6 @@ import numpy as np
from parmepy.constants import ORDER, PARMES_REAL
import parmepy.tools.numpywrappers as npw
import numpy.linalg as la
-from parmepy.mpi import main_comm
class DiscreteField(object):
@@ -188,7 +187,7 @@ class DiscreteField(object):
indNoGhost = self.topology.mesh.iCompute
for d in range(self.nbComponents):
result[d] += la.norm(self.data[d][indNoGhost]) ** 2
- main_comm.Allreduce(result, gResult)
+ self.topology.comm.Allreduce(result, gResult)
return gResult ** (1. / 2)
def get_data_method(self):
@@ -235,4 +234,3 @@ class DiscreteField(object):
""" set all components to zero"""
for dim in xrange(self.nbComponents):
self.data[dim][...] = 0.0
-
diff --git a/HySoP/hysop/mpi/topology.py b/HySoP/hysop/mpi/topology.py
index 752b5d2da..3386a2705 100644
--- a/HySoP/hysop/mpi/topology.py
+++ b/HySoP/hysop/mpi/topology.py
@@ -72,8 +72,8 @@ class Cartesian(object):
self.dim = dim
# Mind the sequential case : dim from withConstr may be equal
# to 0 if shape[:] = 1
- ## Communicator used to build the topology
- self.comm = comm
+ ## (Source) Communicator used to build the topology
+ self._comm_origin = comm
## True if everything has been properly set for this topology
self.isUpToDate = False
## Grid of mpi process layout
@@ -122,15 +122,16 @@ class Cartesian(object):
if(periods is not None):
assert (periods.size == self.dim)
self.periods[:] = periods[:]
- self.topo = self.comm.Create_cart(self.shape[self.cutdir],
- periods=self.periods, reorder=True)
+ self.comm = self._comm_origin.Create_cart(self.shape[self.cutdir],
+ periods=self.periods,
+ reorder=True)
## Size of the topology (i.e. total number of mpi processes)
- self.size = self.topo.Get_size()
+ self.size = self.comm.Get_size()
## Rank of the current process in the topology
- self.rank = self.topo.Get_rank()
+ self.rank = self.comm.Get_rank()
## Coordinates of the current process
- self.reduced_coords = np.asarray(self.topo.Get_coords(self.rank),
+ self.reduced_coords = np.asarray(self.comm.Get_coords(self.rank),
dtype=PARMES_INDEX)
## Coordinates of the current process
## What is different between proc_coords and reduced_coords?
@@ -144,7 +145,7 @@ class Cartesian(object):
## (warning : direction in the grid of process).
self.neighbours = np.zeros((2, self.dim), dtype=PARMES_INTEGER)
for direction in range(self.dim):
- self.neighbours[:, direction] = self.topo.Shift(direction, 1)
+ self.neighbours[:, direction] = self.comm.Shift(direction, 1)
## ghost layer (default = 0)
if(ghosts is None):
diff --git a/HySoP/hysop/operator/monitors/compute_forces.py b/HySoP/hysop/operator/monitors/compute_forces.py
index 38099234b..021e9ab10 100644
--- a/HySoP/hysop/operator/monitors/compute_forces.py
+++ b/HySoP/hysop/operator/monitors/compute_forces.py
@@ -24,11 +24,13 @@ class DragAndLift(Monitoring):
The present class implements formula (52) of Plouhmans2002.
Integral inside the obstacle is not taken into account.
"""
- def __init__(self, velocity, vorticity, nu, coefForce, topo, volumeOfControl,
- obstacles=None, frequency=1, filename=None, safeOutput=None):
+ def __init__(self, velocity, vorticity, nu, coefForce, topo,
+ volumeOfControl, obstacles=None, frequency=1,
+ filename=None, safeOutput=True):
"""
@param velocity field
- @param vorticity field@
+ @param vorticity field
+ @param nu viscosity
@param the topology on which forces will be computed
@param a volume of control
(parmepy.domain.obstacle.controlBox.ControlBox object)
@@ -77,9 +79,9 @@ class DragAndLift(Monitoring):
self.vd = None
# discrete vorticity field
self.wd = None
- # viscosity
+ ## viscosity
self.nu = nu
- # Normalizing coefficient for forces
+ # Normalizing coefficient for forces
# (based on the physics of the flow)
self.coefForce = coefForce
# Output file
@@ -94,17 +96,14 @@ class DragAndLift(Monitoring):
d = os.path.dirname(self.filename)
if not os.path.exists(d):
os.makedirs(d)
- if safeOutput is None:
- ## Defines how often
- ## output file is written :
- ## True --> open/close file everytime
- ## data are written.
- ## False --> open at init and close
- ## during finalize. Cost less but if simu
- ## crashes, data are lost.
- self.safeOutput = True
- else:
- self.safeOutput = safeOutput
+ ## Defines how often
+ ## output file is written :
+ ## True --> open/close file everytime
+ ## data are written.
+ ## False --> open at init and close
+ ## during finalize. Cost less but if simu
+ ## crashes, data are lost.
+ self.safeOutput = safeOutput
if self.safeOutput:
self._writeFile = self._fullwrite
else:
@@ -191,9 +190,9 @@ class DragAndLift(Monitoring):
# Print results, if required
if self._writeOuput and self.topo.rank == 0 and (ite % self.freq) == 0:
- dataout = npw.zeros((1,4))
- dataout[0,0] = simulation.time
- dataout[0,1:] = self.force
+ dataout = npw.zeros((1, 4))
+ dataout[0, 0] = simulation.time
+ dataout[0, 1:] = self.force
self._writeFile(dataout)
return self.force
@@ -243,8 +242,8 @@ class DragAndLift(Monitoring):
self._laplacian.fd_scheme.computeIndices(sl)
for j in i2:
self._work[...] = self._laplacian(vdata[j], self._work)
- res[i1] += self._coeff * self.nu * normal[i1] * np.sum(coords[j]
- * self._work[sl])
+ res[i1] += self._coeff * self.nu * normal[i1]\
+ * np.sum(coords[j] * self._work[sl])
res[j] -= self._coeff * self.nu * normal[i1] * coords[i1] * \
np.sum(self._work[sl])
self._fd_scheme.computeIndices(sl)
@@ -572,7 +571,7 @@ class Forces(Monitoring):
# Reduction operation
if main_rank == 0:
- comm = main_comm
+ comm = self.topo.comm
comm.Reduce([localForce, MPI.DOUBLE], [force, MPI.DOUBLE],
op=MPI.SUM, root=0)
force = force * self.coef
diff --git a/HySoP/hysop/operator/reprojection.py b/HySoP/hysop/operator/reprojection.py
index 51f6085a3..c6d0f5355 100644
--- a/HySoP/hysop/operator/reprojection.py
+++ b/HySoP/hysop/operator/reprojection.py
@@ -11,7 +11,7 @@ from parmepy.numerics.finite_differences import FD_C_4, FD_C_2
from parmepy.numerics.differential_operations import GradV
import parmepy.tools.numpywrappers as npw
from parmepy.numerics.updateGhosts import UpdateGhosts
-from parmepy.mpi import main_rank, main_comm, main_size, MPI
+from parmepy.mpi import main_rank, MPI
from parmepy.tools.timers import timed_function
--
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