From 62f30c0ffa07ca990245931c24bb6b4689830758 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Fri, 24 May 2013 14:37:15 +0000
Subject: [PATCH] Add methods to serialize the problem and restart a simulation
from a file
---
HySoP/hysop/domain/box.py | 4 ++--
HySoP/hysop/fields/discrete.py | 3 +++
HySoP/hysop/operator/monitors/printer.py | 23 ++++++++++++----------
HySoP/hysop/operator/poisson.py | 4 ++--
HySoP/hysop/problem/problem.py | 25 +++++++++++++++---------
HySoP/hysop/problem/simulation.py | 10 ++++++----
HySoP/hysop/problem/transport.py | 5 +++--
7 files changed, 45 insertions(+), 29 deletions(-)
diff --git a/HySoP/hysop/domain/box.py b/HySoP/hysop/domain/box.py
index 650df43c4..92fcd9755 100644
--- a/HySoP/hysop/domain/box.py
+++ b/HySoP/hysop/domain/box.py
@@ -28,13 +28,13 @@ class Box(Domain):
@param dimension : Box dimension. Default: 3
@param length : Box length. Default [1.0, 1.0, 1.0]
@param origin : Box minimum position. Default [0., 0., 0.]
-
+ \code
>>> import parmepy as pp
>>> import numpy as np
>>> b = pp.Box()
>>> (b.max == np.asarray([1.0, 1.0, 1.0])).all()
True
-
+ \endcode
"""
if not (dimension == len(length) and dimension == len(origin)):
raise ValueError("Box parameters inconsistents dimensions")
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
index da71fd982..8502f487b 100644
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -145,8 +145,11 @@ class DiscreteField(object):
filename += '_rk_'
filename += str(main_rank)
db = NumPyDB_cPickle(filename, mode='load')
+ print "lllll", self.name
if self.isVector:
for dim in xrange(self.dimension):
+ print dim, len(self.data)
+ print db.load(self.name)
self.data[dim] = db.load(self.name)[0][dim]
else:
self.data = db.load(self.name)[0]
diff --git a/HySoP/hysop/operator/monitors/printer.py b/HySoP/hysop/operator/monitors/printer.py
index f433e94db..2e0f1c32d 100644
--- a/HySoP/hysop/operator/monitors/printer.py
+++ b/HySoP/hysop/operator/monitors/printer.py
@@ -3,7 +3,6 @@
Classes for handling ouputs.
"""
-from parmepy import __VERBOSE__
from parmepy.constants import np, S_DIR, PARMES_REAL, debug
from parmepy.operator.monitors.monitoring import Monitoring
import evtk.hl as evtk
@@ -48,6 +47,14 @@ class Printer(Monitoring):
self.step = self._printStep
else:
self.step = self._passStep
+ ## Internal counter
+ self._call_number = 0
+
+ def setUp(self):
+ """
+ Print initial state
+ """
+ self.step(0)
@debug
@timed_function
@@ -86,7 +93,7 @@ class Printer(Monitoring):
raise ValueError("Cannot set non callable method to get data " +
"to print. Given method : " + str(method))
- def _passStep(self, ite):
+ def _passStep(self, ite=None):
"""A code method that do nothing."""
pass
@@ -97,8 +104,7 @@ class Printer(Monitoring):
@param iter : current iteration number
"""
if (ite % self.freq) == 0:
- if __VERBOSE__:
- print "== IO"
+ self._call_number += 1
# Transfer from GPU to CPU if required
for f in self.variables:
for df in f.discreteFields.values():
@@ -109,8 +115,6 @@ class Printer(Monitoring):
# Set output file name
filename = self.prefix + '_it_' + str(ite) + self.ext
print "Print to file " + filename
- if __VERBOSE__:
- print "Print file : " + filename
## VTK output \todo: Need fix in 2D, getting an IOError.
try:
evtk.imageToVTK(filename, pointData=self._build_vtk_dict())
@@ -159,10 +163,9 @@ class Printer(Monitoring):
df[i, j, k]))
f.write("\n")
f.close()
- if __VERBOSE__:
- print "=="
+ print "==\n"
if __name__ == "__main__":
print __doc__
- print "- Provided class : " + providedClass
- print eval(providedClass).__doc__
+ print "- Provided class : " + Printer
+ print Printer.__doc__
diff --git a/HySoP/hysop/operator/poisson.py b/HySoP/hysop/operator/poisson.py
index 43967904a..0782abf01 100644
--- a/HySoP/hysop/operator/poisson.py
+++ b/HySoP/hysop/operator/poisson.py
@@ -42,8 +42,6 @@ class Poisson(Operator):
## the same resolution.
self.resolutions = resolutions
- self.input = [self.vorticity]
- self.output = [self.velocity]
Operator.__init__(self, [velocity, vorticity], method, name="Poisson")
self.config = other_config
if method is None:
@@ -53,6 +51,8 @@ class Poisson(Operator):
assert self.resolution == self.resolutions[self.vorticity],\
'Poisson error : for fftw, all variables must have\
the same global resolution.'
+ self.input = [self.vorticity]
+ self.output = [self.velocity]
@debug
def setUp(self):
diff --git a/HySoP/hysop/problem/problem.py b/HySoP/hysop/problem/problem.py
index 3b87aa76f..a1c30c329 100644
--- a/HySoP/hysop/problem/problem.py
+++ b/HySoP/hysop/problem/problem.py
@@ -79,7 +79,7 @@ class Problem(object):
else:
self.name = name
## Default file name prefix for dump.
- self.filename = str(name)
+ self.filename = str(self.name)
self._filedump = self.filename + '_rk_' + str(main_rank)
@debug
@@ -92,11 +92,6 @@ class Problem(object):
if not isinstance(op, Monitoring):
if not isinstance(op, Redistribute):
op.setUp()
- for op in self.operators:
- if isinstance(op, Monitoring):
- op.setUp()
- if isinstance(op, Redistribute):
- op.setUp()
if __VERBOSE__:
print "==== Variables initialization ===="
@@ -116,6 +111,12 @@ class Problem(object):
for v in self.input:
v.initialize()
+ for op in self.operators:
+ if isinstance(op, Monitoring):
+ op.setUp()
+ if isinstance(op, Redistribute):
+ op.setUp()
+
if __VERBOSE__:
print "===="
for op in self.operators:
@@ -138,9 +139,6 @@ class Problem(object):
Displays timings at simulation end.
"""
print "\n\n Start solving ..."
- for op in self.operators:
- if isinstance(op, Monitoring):
- op.apply(self.simulation)
try:
## Pass the main loop to the OpenGL viewer
if not self.glRenderer is None:
@@ -203,6 +201,8 @@ class Problem(object):
db = NumPyDB_cPickle(self._filedump, mode='store')
db.dump(self.simulation, 'simulation')
for v in self.input:
+ print 'dump v ...'
+ print v
v.dump(self.filename, mode='append')
def restart(self, filename=None):
@@ -221,8 +221,15 @@ class Problem(object):
self.simulation = db.load('simulation')[0]
self.simulation.reset()
for v in self.input:
+ print "load ...", self.filename
v.load(self.filename)
+ for op in self.operators:
+ if isinstance(op, Monitoring):
+ op.setUp()
+ if isinstance(op, Redistribute):
+ op.setUp()
+
def setDumpFreq(self, freq):
"""
set rate of problem.dump call (every 'rate' iteration)
diff --git a/HySoP/hysop/problem/simulation.py b/HySoP/hysop/problem/simulation.py
index ae8590bd6..2d484fd91 100644
--- a/HySoP/hysop/problem/simulation.py
+++ b/HySoP/hysop/problem/simulation.py
@@ -28,7 +28,7 @@ class Simulation(object):
## Is simulation is terminated
self.isOver = False
## Iteration counter
- self.currentIteration = 0
+ self.currentIteration = 1
## Simulation time step
self.timeStep = timeStep
## Maximum number of iterations
@@ -38,18 +38,20 @@ class Simulation(object):
"""
Proceed to next time
"""
- if self.currentIteration < self.iterMax and self.time < self.end:
+ if self.currentIteration < self.iterMax:
self.currentIteration += 1
self.time += self.timeStep
else:
self.isOver = True
+ if self.time >= self.end:
+ self.isOver = True
def printState(self):
"""
print current state
"""
if main_rank == 0:
- print "\n==== Iteration : {0:3d} t={1:6.3f} ====".format(
+ print "==== Iteration : {0:3d}, start from t ={1:6.3f} ====".format(
self.currentIteration, self.time)
def reset(self):
@@ -59,7 +61,7 @@ class Simulation(object):
"""
self.start = self.time
self.isOver = False
- self.currentIteration = 0
+ self.currentIteration = 1
def __str__(self):
s = "Simulation parameters : "
diff --git a/HySoP/hysop/problem/transport.py b/HySoP/hysop/problem/transport.py
index 39ddd844f..2360ee801 100644
--- a/HySoP/hysop/problem/transport.py
+++ b/HySoP/hysop/problem/transport.py
@@ -10,9 +10,10 @@ class TransportProblem(Problem):
"""
Transport problem description.
"""
- def __init__(self, operators, simulation, monitors=[]):
+ def __init__(self, operators, simulation, monitors=[],
+ dumpFreq=100, name=None):
Problem.__init__(self, operators, simulation, monitors,
- name="Transport Problem")
+ dumpFreq, name)
self.advection, self.velocity = None, None
for op in self.operators:
if isinstance(op, Advection):
--
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