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[Luis Barbosa <question700611@xxxxxxxxxxxxxxxxxxxxx>]

New question #700611 on Yade:
https://answers.launchpad.net/yade/+question/700611

Hi all,

I am running the script [1] in OpenMpi with increased domain and smaller particles.
[1] https://gitlab.com/yade-dev/trunk/-/blob/master/examples/FluidCouplingPFV/drainage-2PFV-Yuan_and_Chareyre_2017.py


The pack is filled with 680 particles of radius 5e-4, 1520 particles of radius 3e-4 and 3590 particles of radius 2e-4.

This pack (matrix_vtest.txt) was inported to the drainage simulation 2PFV [1] and each particle was substituted by agglomarate of particles as:
particle size 5e-4 were substituted by agglomerates of particles of radius5e-5 (agg5e4_5e5.txt)
particle size 3e-4 were substituted by agglomerates of particles of radius 3e-5 (agg3e4_3e5.txt)
particle size 2e-4 were substituted by agglomerates of particles of radius 2e-5 (agg2e4_2e5.txt)

When I run the drainage simulation 2PFV [1] without substituting the pack by agglomerate (just to check its functionality) it works.
But, when I substitute the particles by the agglomerates I get the following error when the drainage starts:

double free or corruption (!prev)
[node030:278860] *** Process received signal ***
[node030:278860] Signal: Aborted (6)
[node030:278860] Signal code:  (-6)
[node030:278860] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x138e0)[0x2ae56996a8e0]
[node030:278860] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x141)[0x2ae5699b6e71]
[node030:278860] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x112)[0x2ae5699a0536]
[node030:278860] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7e2b8)[0x2ae5699f82b8]
[node030:278860] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x85d0a)[0x2ae5699ffd0a]
[node030:278860] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x8757c)[0x2ae569a0157c]
[node030:278860] [ 6] /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN4yade3CGT7NetworkINS0_12_TesselationINS0_18TriangulationTypesINS_18TwoPhaseVertexInfoENS_16TwoPhaseCellInfoEEEEEE19defineFictiousCellsEv+0x1c5)[0x2ae56d60ae55]
[node030:278860] [ 7] /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN4yade38TemplateFlowEngine_TwoPhaseFlowEngineTINS_16TwoPhaseCellInfoENS_18TwoPhaseVertexInfoENS_3CGT12_TesselationINS3_18TriangulationTypesIS2_S1_EEEENS3_25FlowBoundingSphereLinSolvIS7_NS3_18FlowBoundingSphereIS7_EEEEE18buildTriangulationEdRSB_+0xa18)[0x2ae56d6341b8]
[node030:278860] [ 8] /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN4yade18TwoPhaseFlowEngine14initializationEv+0x4f)[0x2ae56d5a4e8f]
[node030:278860] [ 9] /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIMN4yade18TwoPhaseFlowEngineEFvvENS0_21default_call_policiesENS_3mpl7vector2IvRS6_EEEEEclEP7_objectSH_+0x43)[0x2ae56d5aff03]
[node030:278860] [10] /usr/lib/x86_64-linux-gnu/libboost_python39.so.1.74.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x2bb)[0x2ae56e8596db]
[node030:278860] [11] /usr/lib/x86_64-linux-gnu/libboost_python39.so.1.74.0(+0x20968)[0x2ae56e859968]
[node030:278860] [12] /usr/lib/x86_64-linux-gnu/libboost_python39.so.1.74.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x2ae56e85e893]
[node030:278860] [13] /usr/lib/x86_64-linux-gnu/libboost_python39.so.1.74.0(+0x1e0c2)[0x2ae56e8570c2]
[node030:278860] [14] /usr/bin/python3.9(_PyObject_MakeTpCall+0x39b)[0x51df8b]
[node030:278860] [15] /usr/bin/python3.9[0x53c575]
[node030:278860] [16] /usr/bin/python3.9(_PyEval_EvalFrameDefault+0x5418)[0x517508]
[node030:278860] [17] /usr/bin/python3.9[0x510d5d]
[node030:278860] [18] /usr/bin/python3.9(_PyEval_EvalCodeWithName+0x47)[0x510b07]
[node030:278860] [19] /usr/bin/python3.9(PyEval_EvalCode+0x23)[0x5f38b3]
[node030:278860] [20] /usr/bin/python3.9[0x5f8540]
[node030:278860] [21] /usr/bin/python3.9[0x529ee4]
[node030:278860] [22] /usr/bin/python3.9(_PyEval_EvalFrameDefault+0x52b)[0x51261b]
[node030:278860] [23] /usr/bin/python3.9[0x510d5d]
[node030:278860] [24] /usr/bin/python3.9(_PyFunction_Vectorcall+0x342)[0x529362]
[node030:278860] [25] /usr/bin/python3.9(_PyEval_EvalFrameDefault+0x52b)[0x51261b]
[node030:278860] [26] /usr/bin/python3.9[0x511657]
[node030:278860] [27] /usr/bin/python3.9(_PyFunction_Vectorcall+0x342)[0x529362]
[node030:278860] [28] /usr/bin/python3.9(_PyEval_EvalFrameDefault+0x52b)[0x51261b]
[node030:278860] [29] /usr/bin/python3.9[0x511657]
[node030:278860] *** End of error message ***


I wounder if it has to do with Numpy/Scipy not supporting such a large number of in the sparce matrix and if would have a work around. Or if it is something else.

Below is the script I modified to import the pack and agglomerates (.txt). I did not provide an external link to these txt files, but I can do that if necessary.


#!/usr/bin/python
# -*- encoding=utf-8 -*-

import os
from yade import mpy as mp
from yade import pack
from yade import bodiesHandling
from yade import export
from yade import utils
from yade import ymport
#import math

############################################
###   DEFINING VARIABLES AND MATERIALS   ###
############################################

# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
    num_spheres=3000,# number of spheres
    compFricDegree = 1, # contact friction during the confining phase
    key='_triax_base_', # put you simulation's name here
    unknownOk=True
)
from yade.params import table

num_spheres=table.num_spheres# number of spheres
key=table.key

targetPorosity = 0.40 #the porosity we want for the packing
compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
finalFricDegree = 30 # contact friction during the deviatoric loading
rate=0 # loading rate (strain rate)
damp=0.8 # damping coefficient
stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
#2e4+70e4medio 1e4+70e4bom 1e4+60e4bom 3e4+90e4+w3,1,-1-the best
young=20e5 # contact stiffness200e4
young2=20e5
youngcoat=20e5
bondstr=0.3e3
bondstr2=0.3e3
bondstrcoat=1e3


## create materials for spheres and plates
mat=O.materials.append(JCFpmMat(type=1,young=young,poisson=0.3,frictionAngle=radians(compFricDegree),density=2000,tensileStrength=bondstr,cohesion=bondstr,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=bondstr,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='spheres'))
O.materials.append(JCFpmMat(type=1,young=20e7,poisson=0.3,frictionAngle=radians(0),density=2600,tensileStrength=0,cohesion=0,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=0,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='walls'))
O.materials.append(JCFpmMat(type=1,young=youngcoat,poisson=0.3,frictionAngle=radians(1),density=1500,tensileStrength=bondstrcoat,cohesion=bondstrcoat,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=bondstrcoat,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='spherescoat'))

## create walls around the packing

mn,mx=Vector3(0,0,0),Vector3(0.01005,0.01005,0.01005)
mnbox,mxbox=Vector3(-0.0001,-0.0001,-0.0001),Vector3(0.01005,0.0115,0.01005)
walls=aabbWalls([mnbox,mxbox],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

O.bodies.append(ymport.textExt("matrix_vtest.txt", format='x_y_z_r', shift=Vector3(0,0,0), scale=1.0,material='spherescoat',color=(0,1,1)))


################Particle substitution by large aggregate######################################################################

bodid=[]
a=[]
for b in O.bodies:
	if b and isinstance(b.shape,Sphere):
#		print (b.shape.radius)
		if b.shape.radius==0.0005:
			bodid.append(b.id)
			a.append(b.state.pos)

i=0
for p in bodid:
	t=a[i]
	f1=O.bodies.append(ymport.textExt("agg5e4_5e5.txt", format='x_y_z_r', shift=t-Vector3(0,0,0), scale=1.0,material='spheres',color=(0,1,1)))
	O.bodies.erase(bodid[i])
	i=i+1


bodidd=[]
aa=[]
for bb in O.bodies:# in sp:
	if bb and isinstance(bb.shape,Sphere):
#		print (bb.shape.radius)
		if bb.shape.radius==0.0003:
			bodidd.append(bb.id)
			aa.append(bb.state.pos)

ii=0
for pp in bodidd:
	tt=aa[ii]
	f2=O.bodies.append(ymport.textExt("agg3e4_3e5.txt", format='x_y_z_r', shift=tt-Vector3(0,0,0), scale=1.0,material='spheres',color=(0,1,1)))
	O.bodies.erase(bodidd[ii])
	ii=ii+1



bodiddd=[]
aaa=[]
for bbb in O.bodies:# in sp:
	if bbb and isinstance(bbb.shape,Sphere):
		print (bbb.shape.radius)
		if bbb.shape.radius==0.0002:
			bodiddd.append(bbb.id)
			aaa.append(bbb.state.pos)

iii=0
for ppp in bodiddd:
	ttt=aaa[iii]
	f3=O.bodies.append(ymport.textExt("agg2e4_2e5.txt", format='x_y_z_r', shift=ttt-Vector3(0,0,0), scale=1.0,material='spheres',color=(0,1,1)))
	O.bodies.erase(bodiddd[iii])
	iii=iii+1


##############################################################################################################################

#======================================================================================================

triax=TriaxialStressController(
    stressMask = 0,
    internalCompaction=False, # If true the confining pressure is generated by growing particles
    wall_front_activated=True,
    wall_back_activated=True,
    wall_top_activated=True,
    wall_bottom_activated=True,
    wall_left_activated=True,
    wall_right_activated=True,
    goal1=-5,
    goal2=-15,
    goal3=-5,
)

newton=NewtonIntegrator(damping=damp)

O.engines=[

	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=-1,label='Physicspheres')],#,xSectionWeibullShapeParameter=1.5, xSectionWeibullScaleParameter=1
		[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=False)]
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.3),
	triax,
	newton


]


###################################################
###   REACHING A SPECIFIED POROSITY PRECISELY   ###
###################################################


while triax.porosity>targetPorosity:
    setContactFriction(radians(compFricDegree))
    print ("\r Friction: ",compFricDegree," porosity:",triax.porosity)
    # porosity will decrease
    O.run(100,1)

print ("###    Compacted state saved      ###")
print(triax.stress(3)[1])


# Change contact friction (remember that decreasing it would generate instantaneous instabilities)
setContactFriction(radians(finalFricDegree))


#=======================================

#set stress control on x and z, we will impose strain rate on y
triax.stressMask = 2
triax.wall_bottom_activated=0
#now goal2 is the target strain rate
triax.goal1=rate#triax.stress(1)[0]
triax.goal3=rate#triax.stress(5)[2]
triax.goal2=triax.stress(3)[1]

#####################################################
###    Example of how to record and plot data     ###
#####################################################

#from yade import plot
from yade import plot
O.run(100,True)

#strain is logarithmic strain or true strain which is ls=(ln1+e) where e=dl/L (strain) 
ei0=-triax.strain[0];ei1=-triax.strain[1];ei2=-triax.strain[2]
si0=-triax.stress(0)[0];si1=-triax.stress(2)[1];si2=-triax.stress(4)[2]

## a function saving variables
def history():
    plot.addData(e11=-triax.strain[0]-ei0, e22=-triax.strain[1]-ei1, e33=-triax.strain[2]-ei2,
            ev=-triax.strain[0]-triax.strain[1]-triax.strain[2],
            s11=-triax.stress(triax.wall_right_id)[0]-si0,
            s22=-triax.stress(triax.wall_top_id)[1]-si1,
            s33=-triax.stress(triax.wall_front_id)[2]-si2,
            e=math.exp(-triax.strain[1]-ei1)-1,
            pc=-unsat.bndCondValue[2],
            sw=unsat.getSaturation(False),
            z1=O.bodies[3].state.pos[1],
            i=O.iter)


O.engines=O.engines+[PyRunner(iterPeriod=1000,command='history()',label='recorder')]

#######################################################
##     Drainage Test under oedometer conditions     ###
#######################################################
##Instantiate a two-phase engine
unsat=TwoPhaseFlowEngine()

##set boundary conditions, the drainage is controlled by decreasing W-phase pressure and keeping NW-phase pressure constant
unsat.bndCondIsPressure=[0,0,1,1,0,0]
unsat.bndCondIsWaterReservoir=[0,0,1,0,0,0]
unsat.bndCondValue=[0,0,-1e8,0,0,0]
unsat.isPhaseTrapped=True #the W-phase can be disconnected from its reservoir
unsat.initialization()
unsat.surfaceTension = 0.0728

#start invasion, the data of normalized pc-sw-strain will be written into pcSwStrain.txt

f5=open('SwPc5.txt',"w")

ts=O.dt
pgstep= 4500000*ts #30Pa/s
print (pgstep)
pgmax= 3000#9316 #Pa

for pg in arange(1.0e-8,pgmax,pgstep):
  unsat.bndCondValue=[0,0,(-1.0)*pg,0,0,0]
  unsat.invasion()
  unsat.computeCapillaryForce()
  unsat.meshUpdateInterval=500
  unsat.defTolerance=-1
  unsat.updateTriangulation=True
  print(unsat.getSaturation(False),pg,-triax.strain[1])

  for b in O.bodies:
    O.forces.setPermF(b.id, unsat.fluidForce(b.id))

  while 1:
    O.run(100,True)
    unb=unbalancedForce()
    if unb<0.05:
      break
  f5.write(str(pg)+" "+str(unsat.getSaturation(False))+" "+str(triax.strain[1])+"\n")
f5.close()

mp.DOMAIN_DECOMPOSITION= True   #automatic splitting/domain decomposition
mp.mpirun(1)              #passive mode run

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