From c2d1d5fc51d2fa68fa2c5cbfbc1a64383b549efd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Fri, 24 May 2013 12:23:55 +0000
Subject: [PATCH] Add methods to serialize the problem and restart a simulation
from a file
---
HySoP/hysop/fields/continuous.py | 18 +++++++++++---
HySoP/hysop/fields/discrete.py | 16 ++++++++++---
HySoP/hysop/fields/scalar.py | 3 +++
HySoP/hysop/fields/vector.py | 4 ++++
HySoP/hysop/operator/monitors/printer.py | 12 +++++++---
HySoP/hysop/problem/problem.py | 30 ++++++++++++++++++++++++
HySoP/hysop/problem/simulation.py | 30 ++++++++++++++++--------
7 files changed, 94 insertions(+), 19 deletions(-)
diff --git a/HySoP/hysop/fields/continuous.py b/HySoP/hysop/fields/continuous.py
index 0fd1e9c64..427399cf8 100644
--- a/HySoP/hysop/fields/continuous.py
+++ b/HySoP/hysop/fields/continuous.py
@@ -169,20 +169,21 @@ class Field(object):
"""
self.extraParameters = args
- def dump(self, filename, topo=None):
+ def dump(self, filename, topo=None, mode=None):
"""
Dump (serialize) the data of the field into filename.
serialization process.
@param filename : name of the file in which data are serialized
@param topo : topology that identify a discrete field to be saved.
+ @param mode : set mode='append' to add data to an existing file.
if None, the first discrete field in the list will be saved.
"""
if topo is not None:
assert topo in self.discreteFields.keys()
- self.discreteFields[topo].dump(filename)
+ self.discreteFields[topo].dump(filename, mode)
else:
# dump all discr or only the first one?
- self.discreteFields.values()[0].dump(filename)
+ self.discreteFields.values()[0].dump(filename, mode)
def load(self, filename, topo=None):
"""
@@ -199,6 +200,17 @@ class Field(object):
# dump all discr or only the first one?
self.discreteFields.values()[0].load(filename)
+ def zero(self, topo=None):
+ """
+ reset to 0.0 all components of this field.
+ @param topo : if given, only discreteFields[topo] is
+ set to zero
+ """
+ if topo is not None:
+ self.discreteFields[topo].zero()
+ else:
+ for dfield in self.discreteFields.values():
+ dfield.zero()
if __name__ == "__main__":
print __doc__
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
index 12ff4c1a5..da71fd982 100644
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -100,7 +100,6 @@ class DiscreteField(object):
self.isVector = None
## Field data numpy array.
self.data = None
- ## An id (optional) used to identify the field for
@abstractmethod
def __getitem__(self, i):
@@ -118,14 +117,21 @@ class DiscreteField(object):
def get_data_method(self):
pass
- def dump(self, filename):
+ def dump(self, filename, mode=None):
"""
Dump (serialize) the data of the field into filename.
@param filename : name of the file in which data are serialized
+ @param mode : set mode='append' to add data to an existing file
"""
filename += '_rk_'
filename += str(main_rank)
- db = NumPyDB_cPickle(filename, mode='store')
+ # create a new db
+ if mode is None:
+ db = NumPyDB_cPickle(filename, mode='store')
+ elif mode is 'append':
+ # use an existing db
+ db = NumPyDB_cPickle(filename, mode='load')
+
#for dim in xrange(self.dimension):
# idd = self.name + '_' + str(dim)
db.dump(self.data, self.name)
@@ -145,6 +151,10 @@ class DiscreteField(object):
else:
self.data = db.load(self.name)[0]
+ @abstractmethod
+ def zero(self):
+ """ set all components to zero"""
+
if __name__ == "__main__":
print __doc__
print "- Provided class : Domain (abstract)."
diff --git a/HySoP/hysop/fields/scalar.py b/HySoP/hysop/fields/scalar.py
index be92d02e3..6b894baf3 100644
--- a/HySoP/hysop/fields/scalar.py
+++ b/HySoP/hysop/fields/scalar.py
@@ -102,6 +102,9 @@ class ScalarField(DiscreteField):
s = str(self.data.shape) + "."
return s + "\n"
+ def zero(self):
+ self.data[...] = 0.0
+
if __name__ == "__main__":
print __doc__
print "- Provided class : Scalar"
diff --git a/HySoP/hysop/fields/vector.py b/HySoP/hysop/fields/vector.py
index aa0087f73..70a0bf0bd 100644
--- a/HySoP/hysop/fields/vector.py
+++ b/HySoP/hysop/fields/vector.py
@@ -144,6 +144,10 @@ class VectorField(DiscreteField):
s = str(self.data[0].shape) + "."
return s + "\n"
+ def zero(self):
+ for dim in xrange(self.dimension):
+ self.data[dim][...] = 0.0
+
if __name__ == "__main__":
print __doc__
print "- Provided class : VectorField"
diff --git a/HySoP/hysop/operator/monitors/printer.py b/HySoP/hysop/operator/monitors/printer.py
index 1ca7e7f75..c0c94b6ce 100644
--- a/HySoP/hysop/operator/monitors/printer.py
+++ b/HySoP/hysop/operator/monitors/printer.py
@@ -16,7 +16,7 @@ class Printer(Monitoring):
Performs outputs in VTK images.
"""
- def __init__(self, frequency=0, fields=[], prefix='./out_', ext='.vtk'):
+ def __init__(self, frequency=0, fields=[], prefix=None, ext=None):
"""
Create a results printer for given fields, filename
prefix (relative path) and an output frequency.
@@ -28,9 +28,15 @@ class Printer(Monitoring):
"""
Monitoring.__init__(self, fields, frequency)
## output file name prefix
- self.prefix = prefix + str(main_rank)
+ if prefix is None:
+ self.prefix = './out_' + str(main_rank)
+ else:
+ self.prefix = prefix + str(main_rank)
## Extension for filename
- self.ext = ext
+ if ext is None:
+ self.ext = '.vtk'
+ else:
+ self.ext = ext
## Method to collect data in case of distributed data
self.get_data_method = None
if self.freq != 0:
diff --git a/HySoP/hysop/problem/problem.py b/HySoP/hysop/problem/problem.py
index 758bcbdda..2d7e841ac 100644
--- a/HySoP/hysop/problem/problem.py
+++ b/HySoP/hysop/problem/problem.py
@@ -7,6 +7,8 @@ from parmepy.constants import debug
from parmepy import __VERBOSE__
from parmepy.operator.monitors.monitoring import Monitoring
from parmepy.operator.redistribute import Redistribute
+from parmepy.mpi import main_rank
+from scitools.NumPyDB import NumPyDB_cPickle
class Problem(object):
@@ -156,6 +158,34 @@ class Problem(object):
return s
+ def dump(self, filename):
+ """
+ Serialize some data of the problem to file
+ (only data required for a proper restart, namely fields in self.input
+ and simulation).
+ @param filename : prefix for output file. Real name = filename_rk_N,
+ N being current process number.
+ """
+ filedump = filename + '_rk_' + str(main_rank)
+ db = NumPyDB_cPickle(filedump, mode='store')
+ db.dump(self.simulation, 'simulation')
+ for v in self.input:
+ v.dump(filename, mode='append')
+
+ def restart(self, filename):
+ """
+ Load serialized data to restart from a previous state.
+ self.input variables and simulation are loaded.
+ @param filename : prefix for downloaded file.
+ Real name = filename_rk_N, N being current process number.
+ """
+ filedump = filename + '_rk_' + str(main_rank)
+ db = NumPyDB_cPickle(filedump, mode='load')
+ self.simulation = db.load('simulation')[0]
+ self.simulation.reset()
+ for v in self.input:
+ v.load(filename)
+
if __name__ == "__main__":
print __doc__
print "- Provided class : problem"
diff --git a/HySoP/hysop/problem/simulation.py b/HySoP/hysop/problem/simulation.py
index 80b55bb2f..9b3d48483 100644
--- a/HySoP/hysop/problem/simulation.py
+++ b/HySoP/hysop/problem/simulation.py
@@ -11,12 +11,12 @@ class Simulation(object):
Setup for simulation parameters.
"""
- def __init__(self, tinit=0.0, tend=1.0, nbiter=10):
+ def __init__(self, tinit=0.0, tend=1.0, timeStep=0.01, iterMax=100):
"""
Creates a Timer.
@param t_end : Simulation final time.
- @param dt : Time step.
+ @param timeStep : Time step.
@param t_init : Simulation starting time.
"""
## Simulation final time
@@ -29,16 +29,16 @@ class Simulation(object):
self.isOver = False
## Iteration counter
self.currentIteration = 0
- ## Number of iteration
- self.nbiter = nbiter
## Simulation time step
- self.timeStep = (self.end - self.start) / float(self.nbiter)
+ self.timeStep = timeStep
+ ## Maximum number of iterations
+ self.iterMax = iterMax
def advance(self):
"""
Proceed to next time
"""
- if self.currentIteration < self.nbiter:
+ if self.currentIteration < self.iterMax and self.time < self.end:
self.currentIteration += 1
self.time += self.timeStep
else:
@@ -52,10 +52,20 @@ class Simulation(object):
print "==== Iteration : {0:3d} t={1:6.3f} ====".format(
self.currentIteration, self.time)
+ def reset(self):
+ """
+ set initial time to current and reset iteration counter.
+ Used to initialize simulation after a restart.
+ """
+ self.start = self.time
+ self.isOver = False
+ self.currentIteration = 0
+
def __str__(self):
s = "Simulation parameters : "
- s += "start from " + str(self.start) + ' to ' + str(self.end)
- s += ', time step = ' + str(self.timeStep)
- s += ', current time : ' + str(self.time) + ' iteration number :'
- s += str(self.currentIteration)
+ s += "from " + str(self.start) + ' to ' + str(self.end)
+ s += ', time step : ' + str(self.timeStep)
+ s += ', current time : ' + str(self.time) + ', iteration number : '
+ s += str(self.currentIteration) + ', max number of iterations : '
+ s += str(self.iterMax)
return s
--
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