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Message #14570
[Bug 1813550] [NEW] FlowEngine memory leak - 600 Mb/hr
Public bug reported:
Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
tracking RAM usage, I find we have a memory leak of 600 Mb/hr.
examples/oedometer.py with num_spheres=8000:
# -*- coding: utf-8 -*-
from yade import pack
num_spheres=8000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
sp.toSimulation(material='spheres')
triax=TriaxialStressController(
maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
thickness = 0,
stressMask = 7,
max_vel = 0.005,
internalCompaction=True, # If true the confining pressure is generated by growing particles
)
newton=NewtonIntegrator(damping=0.2)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
),
FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
newton
]
triax.goal1=triax.goal2=triax.goal3=-10000
while 1:
O.run(1000, True)
unb=unbalancedForce()
if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
break
setContactFriction(radians(finalFricDegree))
## ______________ Oedometer section _________________
#A. Check bulk modulus of the dry material from load/unload cycles
triax.stressMask=2
triax.goal1=triax.goal3=0
triax.internalCompaction=False
triax.wall_bottom_activated=False
#load
triax.goal2=-11000; O.run(2000,1)
#unload
triax.goal2=-10000; O.run(2000,1)
#load
triax.goal2=-11000; O.run(2000,1)
e22=triax.strain[1]
#unload
triax.goal2=-10000; O.run(2000,1)
e22=e22-triax.strain[1]
modulus = 1000./abs(e22)
#B. Activate flow engine and set boundary conditions in order to get permeability
flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.desiredPorosity=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.bndCondIsPressure=[0,0,1,1,0,0]
flow.bndCondValue=[0,0,1,0,0,0]
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
O.dt=0.1e-3
O.dynDt=False
O.run(1,1)
Qin = flow.getBoundaryFlux(2)
Qout = flow.getBoundaryFlux(3)
permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
print "Qin=",Qin," Qout=",Qout," permeability=",permeability
#C. now the oedometer test, drained at the top, impermeable at the bottom plate
flow.bndCondIsPressure=[0,0,0,1,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.updateTriangulation=True #force remeshing to reflect new BC immediately
newton.damping=0
#we want the theoretical value from Terzaghi's solution
#keep in mind that we are not in an homogeneous material and the small strain
#assumption is not verified => we don't expect perfect match
#there can be also an overshoot of pressure in the very beginning due to dynamic effects
Cv=permeability*modulus/1e4
zeroTime=O.time
zeroe22 = - triax.strain[1]
dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
drye22 = 1000/modulus*dryFraction
wetHeight=1*(1-dryFraction)
def consolidation(Tv): #see your soil mechanics handbook...
U=1
for k in range(50):
M=pi/2*(2*k+1)
U=U-2/M**2*exp(-M**2*Tv)
return U
triax.goal2=-11000
from yade import plot
## a function saving variables
def history():
plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
#plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
##make nice animations:
#O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]
from yade import plot
plot.plots={'t':('e22','e22_theory',None,'s22','p')}
plot.plot()
O.saveTmp()
O.timingEnabled=1
from yade import timing
print "starting oedometer simulation"
O.run(200,1)
timing.stats()
## Make more steps to see the convergence to the stationnary solution
** Affects: yade
Importance: High
Assignee: Robert Caulk (rcaulk)
Status: Fix Committed
** Description changed:
Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
tracking RAM usage, I find we have a memory leak of 600 Mb/hr.
examples/oedometer.py with num_spheres=8000:
# -*- coding: utf-8 -*-
from yade import pack
num_spheres=8000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
sp.toSimulation(material='spheres')
triax=TriaxialStressController(
- maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
- finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
- thickness = 0,
- stressMask = 7,
- max_vel = 0.005,
- internalCompaction=True, # If true the confining pressure is generated by growing particles
+ maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
+ finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
+ thickness = 0,
+ stressMask = 7,
+ max_vel = 0.005,
+ internalCompaction=True, # If true the confining pressure is generated by growing particles
)
newton=NewtonIntegrator(damping=0.2)
O.engines=[
- ForceResetter(),
- InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
- InteractionLoop(
- [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
- [Ip2_FrictMat_FrictMat_FrictPhys()],
- [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
- ),
- FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
- GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
- triax,
- newton
+ ForceResetter(),
+ InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
+ InteractionLoop(
+ [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
+ [Ip2_FrictMat_FrictMat_FrictPhys()],
+ [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
+ ),
+ FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
+ GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
+ triax,
+ newton
]
triax.goal1=triax.goal2=triax.goal3=-10000
while 1:
- O.run(1000, True)
- unb=unbalancedForce()
- if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
- break
+ O.run(1000, True)
+ unb=unbalancedForce()
+ if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
+ break
setContactFriction(radians(finalFricDegree))
## ______________ Oedometer section _________________
#A. Check bulk modulus of the dry material from load/unload cycles
triax.stressMask=2
triax.goal1=triax.goal3=0
triax.internalCompaction=False
triax.wall_bottom_activated=False
#load
triax.goal2=-11000; O.run(2000,1)
#unload
triax.goal2=-10000; O.run(2000,1)
#load
triax.goal2=-11000; O.run(2000,1)
e22=triax.strain[1]
#unload
triax.goal2=-10000; O.run(2000,1)
e22=e22-triax.strain[1]
modulus = 1000./abs(e22)
#B. Activate flow engine and set boundary conditions in order to get permeability
flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.desiredPorosity=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.bndCondIsPressure=[0,0,1,1,0,0]
flow.bndCondValue=[0,0,1,0,0,0]
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
O.dt=0.1e-3
O.dynDt=False
O.run(1,1)
Qin = flow.getBoundaryFlux(2)
Qout = flow.getBoundaryFlux(3)
permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
print "Qin=",Qin," Qout=",Qout," permeability=",permeability
#C. now the oedometer test, drained at the top, impermeable at the bottom plate
flow.bndCondIsPressure=[0,0,0,1,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.updateTriangulation=True #force remeshing to reflect new BC immediately
newton.damping=0
#we want the theoretical value from Terzaghi's solution
#keep in mind that we are not in an homogeneous material and the small strain
#assumption is not verified => we don't expect perfect match
#there can be also an overshoot of pressure in the very beginning due to dynamic effects
Cv=permeability*modulus/1e4
zeroTime=O.time
zeroe22 = - triax.strain[1]
dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
drye22 = 1000/modulus*dryFraction
wetHeight=1*(1-dryFraction)
def consolidation(Tv): #see your soil mechanics handbook...
- U=1
- for k in range(50):
- M=pi/2*(2*k+1)
- U=U-2/M**2*exp(-M**2*Tv)
- return U
+ U=1
+ for k in range(50):
+ M=pi/2*(2*k+1)
+ U=U-2/M**2*exp(-M**2*Tv)
+ return U
triax.goal2=-11000
-
from yade import plot
## a function saving variables
def history():
- plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
- #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
+ plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
+ #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
##make nice animations:
#O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]
from yade import plot
plot.plots={'t':('e22','e22_theory',None,'s22','p')}
plot.plot()
O.saveTmp()
O.timingEnabled=1
from yade import timing
print "starting oedometer simulation"
O.run(200,1)
timing.stats()
## Make more steps to see the convergence to the stationnary solution
** Changed in: yade
Importance: Undecided => High
** Changed in: yade
Status: New => Fix Committed
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https://bugs.launchpad.net/bugs/1813550
Title:
FlowEngine memory leak - 600 Mb/hr
Status in Yade:
Fix Committed
Bug description:
Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
tracking RAM usage, I find we have a memory leak of 600 Mb/hr.
examples/oedometer.py with num_spheres=8000:
# -*- coding: utf-8 -*-
from yade import pack
num_spheres=8000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
sp.toSimulation(material='spheres')
triax=TriaxialStressController(
maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
thickness = 0,
stressMask = 7,
max_vel = 0.005,
internalCompaction=True, # If true the confining pressure is generated by growing particles
)
newton=NewtonIntegrator(damping=0.2)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
),
FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
newton
]
triax.goal1=triax.goal2=triax.goal3=-10000
while 1:
O.run(1000, True)
unb=unbalancedForce()
if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
break
setContactFriction(radians(finalFricDegree))
## ______________ Oedometer section _________________
#A. Check bulk modulus of the dry material from load/unload cycles
triax.stressMask=2
triax.goal1=triax.goal3=0
triax.internalCompaction=False
triax.wall_bottom_activated=False
#load
triax.goal2=-11000; O.run(2000,1)
#unload
triax.goal2=-10000; O.run(2000,1)
#load
triax.goal2=-11000; O.run(2000,1)
e22=triax.strain[1]
#unload
triax.goal2=-10000; O.run(2000,1)
e22=e22-triax.strain[1]
modulus = 1000./abs(e22)
#B. Activate flow engine and set boundary conditions in order to get permeability
flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.desiredPorosity=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.bndCondIsPressure=[0,0,1,1,0,0]
flow.bndCondValue=[0,0,1,0,0,0]
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
O.dt=0.1e-3
O.dynDt=False
O.run(1,1)
Qin = flow.getBoundaryFlux(2)
Qout = flow.getBoundaryFlux(3)
permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
print "Qin=",Qin," Qout=",Qout," permeability=",permeability
#C. now the oedometer test, drained at the top, impermeable at the bottom plate
flow.bndCondIsPressure=[0,0,0,1,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.updateTriangulation=True #force remeshing to reflect new BC immediately
newton.damping=0
#we want the theoretical value from Terzaghi's solution
#keep in mind that we are not in an homogeneous material and the small strain
#assumption is not verified => we don't expect perfect match
#there can be also an overshoot of pressure in the very beginning due to dynamic effects
Cv=permeability*modulus/1e4
zeroTime=O.time
zeroe22 = - triax.strain[1]
dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
drye22 = 1000/modulus*dryFraction
wetHeight=1*(1-dryFraction)
def consolidation(Tv): #see your soil mechanics handbook...
U=1
for k in range(50):
M=pi/2*(2*k+1)
U=U-2/M**2*exp(-M**2*Tv)
return U
triax.goal2=-11000
from yade import plot
## a function saving variables
def history():
plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
#plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
##make nice animations:
#O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]
from yade import plot
plot.plots={'t':('e22','e22_theory',None,'s22','p')}
plot.plot()
O.saveTmp()
O.timingEnabled=1
from yade import timing
print "starting oedometer simulation"
O.run(200,1)
timing.stats()
## Make more steps to see the convergence to the stationnary solution
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