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[Nima Goudarzi <question698388@xxxxxxxxxxxxxxxxxxxxx>]

Question #698388 on Yade changed:
https://answers.launchpad.net/yade/+question/698388

    Status: Expired => Open

Nima Goudarzi is still having a problem:
Hi all,

I have tried a lot to run a simulation with MPI with grains as a mixture
of Clump and Spherical particles. Unwantedly (the procedure for grain
generation is complex, and I have to run it in a separate script), The
grains are imported to the scene. Therefore, they are not generated in
the simulation. My analysis consists of the penetration of an excavator
bucket into a medium dense bed (n=0.44) and then rotation about a zero
point that excavates the bed. I, therefore, used the
CombinedKinematicEngine to handle both motions of the excavator. I have
used many MPI customizations for this simulation with little success,
which casts the doubt if MPI (with its automatic splitting) is
appropriate for grains other than perfect spheres. My simulation crashes
after a few hundred of iterations, and this is what I receive:

malloc(): invalid size (unsorted)
[ubuntu-office:998639] *** Process received signal ***
[ubuntu-office:998639] Signal: Aborted (6)
[ubuntu-office:998639] Signal code:  (-6)
[ubuntu-office:998639] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fcb6eebf210]
[ubuntu-office:998639] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7fcb6eebf18b]
[ubuntu-office:998639] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7fcb6ee9e859]
[ubuntu-office:998639] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x903ee)[0x7fcb6ef093ee]
[ubuntu-office:998639] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x9847c)[0x7fcb6ef1147c]
[ubuntu-office:998639] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x9b234)[0x7fcb6ef14234]
[ubuntu-office:998639] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x1b9)[0x7fcb6ef16419]
[ubuntu-office:998639] [ 7] /usr/bin/python3.8(PyBytes_FromStringAndSize+0x231)[0x5f7b11]
[ubuntu-office:998639] [ 8] /usr/lib/python3/dist-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x724d5)[0x7fcb53e6f4d5]
[ubuntu-office:998639] [ 9] /usr/lib/python3/dist-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x91642)[0x7fcb53e8e642]
[ubuntu-office:998639] [10] /usr/bin/python3.8(PyCFunction_Call+0x59)[0x5f2cc9]
[ubuntu-office:998639] [11] /usr/bin/python3.8(_PyObject_MakeTpCall+0x23f)[0x5f30ff]
[ubuntu-office:998639] [12] /usr/bin/python3.8(_PyEval_EvalFrameDefault+0x6246)[0x5705f6]
[ubuntu-office:998639] [13] /usr/bin/python3.8(_PyFunction_Vectorcall+0x1b6)[0x5f5956]
[ubuntu-office:998639] [14] /usr/bin/python3.8(_PyEval_EvalFrameDefault+0x72f)[0x56aadf]
[ubuntu-office:998639] [15] /usr/bin/python3.8(_PyFunction_Vectorcall+0x1b6)[0x5f5956]
[ubuntu-office:998639] [16] /usr/bin/python3.8(_PyEval_EvalFrameDefault+0x72f)[0x56aadf]
[ubuntu-office:998639] [17] /usr/bin/python3.8(_PyFunction_Vectorcall+0x1b6)[0x5f5956]
[ubuntu-office:998639] [18] /usr/bin/python3.8(_PyEval_EvalFrameDefault+0x57d7)[0x56fb87]
[ubuntu-office:998639] [19] /usr/bin/python3.8(_PyEval_EvalCodeWithName+0x26a)[0x568d9a]
[ubuntu-office:998639] [20] /usr/bin/python3.8(PyEval_EvalCode+0x27)[0x68cdc7]
[ubuntu-office:998639] [21] /usr/bin/python3.8[0x67e161]
[ubuntu-office:998639] [22] /usr/bin/python3.8[0x67e1df]
[ubuntu-office:998639] [23] /usr/bin/python3.8(PyRun_StringFlags+0x7f)[0x67e32f]
[ubuntu-office:998639] [24] /usr/bin/python3.8(PyRun_SimpleStringFlags+0x3f)[0x67e38f]
[ubuntu-office:998639] [25] /home/ngoudarzi/Desktop/My Own YADE/install/lib/x86_64-linux-gnu/yade-2020.01a/libyade.so(_Z11pyRunStringRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1c)[0x7fcb6d40622c]
[ubuntu-office:998639] [26] /home/ngoudarzi/Desktop/My Own YADE/install/lib/x86_64-linux-gnu/yade-2020.01a/libyade.so(_ZN4yade5Scene18moveToNextTimeStepEv+0x132)[0x7fcb6c397922]
[ubuntu-office:998639] [27] /home/ngoudarzi/Desktop/My Own YADE/install/lib/x86_64-linux-gnu/yade-2020.01a/libyade.so(_ZN4yade14SimulationFlow12singleActionEv+0x78)[0x7fcb6c3b5d58]
[ubuntu-office:998639] [28] /home/ngoudarzi/Desktop/My Own YADE/install/lib/x86_64-linux-gnu/yade-2020.01a/libyade.so(_ZN4yade12ThreadWorker16callSingleActionEv+0x14)[0x7fcb6c3d60f4]
[ubuntu-office:998639] [29] /home/ngoudarzi/Desktop/My Own YADE/install/lib/x86_64-linux-gnu/yade-2020.01a/libyade.so(_ZN4yade12ThreadRunner4callEv+0x3f)[0x7fcb6c3d3fdf]
[ubuntu-office:998639] *** End of error message ***
--------------------------------------------------------------------------
Child job 2 terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------

I think I am missing some important adjustments for the simulation but
need to know first that MPI works with imported clumps or it has only
been designed for spherical particles.

This is my last script for the simulation. My target, for now, is
understanding if there is a significant issue in the structure of the
input and therefore, all inputs (Stl, clumps) and outputs are empty:

from yade import pack
from yade import plot
from yade import ymport
from yade import export
import os
from yade import mpy as mp
############################################
###           INPUT PARAMETERS           ###
############################################
NSTEPS=1000 #turn it >0 to see time iterations, else only initilization
numThreads = 9 # number of threads to be spawned, (in interactive mode).
velocity=10 #m/s THAT SHOULD BE 0.01 m/s
angularVelocity=10 #RAD/S
gravityAcc=-9.81
atRestFricDegree = 40 # INITIAL CONTACT FRICTION FOR SAMPLE PREPARATION
normalDamp=0.3 # NUMERICAL DAMPING
shearDamp=0.3
youngSoil=0.7e8# CONTACT STIFFNESS FOR SOIL
youngContainer=210e9 # CONTACT STIFFNESS FOR CONTAINER
poissonSoil=0.3 # POISSION'S RATIO FOR SOIL
poissionContainer=0.25 # POISSION'S RATIO FOR CONTAINER
densSoil=2650 # DENSITY FOR SOIL
densContainer=7850 # DENSITY FOR CONTAINER
numDamp=0.4
InitialPeneterationofExcavator=0.7e-3

O.materials.append(FrictMat(young=youngContainer,poisson=poissionContainer,frictionAngle=radians(0),density=densContainer,label='excavator'))
O.materials.append(FrictMat(young=youngSoil,poisson=poissonSoil,frictionAngle=radians(atRestFricDegree),density=densSoil,label='Soil'))

ymport.textClumps("EMPTY",material='Soil')

mn,mx=aabbExtrema()
walls=aabbWalls([mn,mx],thickness=0.0001, oversizeFactor=1.0,material='excavator')
#for w in walls: w.shape.wire=False
O.bodies.append(walls[:3]+walls[4:]) #don't insert top wall


Excavator = O.bodies.append(ymport.stl('EMPTY',material='excavator',wire=True,color=Vector3(255,178,102)))
ExcavatorID = [b for b in O.bodies if isinstance(b.shape,Facet)] # list of facets in simulation


O.engines = [VTKRecorder(fileName='EMPTY' ,parallelMode=True, recorders=['all'],iterPeriod=50000),
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb()], label="collider"),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_MindlinPhys(betan=normalDamp,betas=shearDamp,label='ContactModel')],
		[Law2_ScGeom_MindlinPhys_Mindlin(label='Mindlin')]
	),

	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,parallelMode=True, timestepSafetyCoefficient=0.35),
	PyRunner(iterPeriod=1, command="penetration()" ,label='checker'),
	CombinedKinematicEngine(ids=Excavator,label='combEngine') + TranslationEngine(translationAxis=(0,-1,0),velocity=velocity) + RotationEngine(rotationAxis=(0,0,1), angularVelocity=0, rotateAroundZero=True, zeroPoint=(0.005851,0.009186,0.003200)),
	NewtonIntegrator(damping=numDamp,gravity=(0,gravityAcc,0)),
	PyRunner(iterPeriod=100,command='history()',label='recorder'),
]
#collider.verletDist = 0.0007
# collider.targetInterv=200
#O.dt=0.1*PWaveTimeStep()

# get TranslationEngine and RotationEngine from CombinedKinematicEngine
transEngine, rotEngine = combEngine.comb[0], combEngine.comb[1]
initialZeroPointVertical=rotEngine.zeroPoint[1]
print ("Zero Point Initial Vertical Position:",initialZeroPointVertical)


def penetration():
 transEngine.velocity = velocity
 print ("Zero Point Vertical Position:",rotEngine.zeroPoint[1])
 print ("Iteration:",O.iter)

 #rotEngine.angularVelocity = angularVelocity
 rotEngine.zeroPoint += Vector3(0,-1,0)*velocity*O.dt
 if rotEngine.zeroPoint[1]<=(initialZeroPointVertical-InitialPeneterationofExcavator):
 	checker.command='updateKinematicEngines()'

def updateKinematicEngines():
 transEngine.translationAxis=(0,0,1)	
 transEngine.velocity = 0
 print ("Zero Point Vertical Position:",rotEngine.zeroPoint[1])
 rotEngine.angularVelocity = angularVelocity
 #rotEngine.zeroPoint += Vector3(0,0,1)*velocity*O.dt

def history():
  global Fx,Fy,Fz
  Fx=0
  Fy=0
  Fz=0
  for b in ExcavatorID:
    Fx+=O.forces.f(b.id,sync=True)[0]
    Fy+=O.forces.f(b.id,sync=True)[1]
    Fz+=O.forces.f(b.id,sync=True)[2]
  yade.plot.addData({'i':O.iter,'Fx':Fx,'Fy':Fy,'Fz':Fz,})
  ## In that case we can still save the data to a text file at the the end of the simulation, with:
  plot.saveDataTxt('EMPTY')
  
## declare what is to plot. "None" is for separating y and y2 axis
plot.plots={'i':('Fx','Fy','Fz')}
plot.plot()

########  RUN  ##########
#customize mpy
mp.ACCUMULATE_FORCES=True
mp.ERASE_REMOTE_MASTER = True   #keep remote bodies in master?
mp.DOMAIN_DECOMPOSITION= True   #automatic splitting/domain decomposition
mp.OPTIMIZE_COM=True
#mp.mpirun(NSTEPS)              #passive mode run
mp.MERGE_W_INTERACTIONS = False
mp.mpirun(NSTEPS,numThreads,withMerge=True) # interactive run, numThreads is the number of workers to be initialized, see below for withMerge explanation.
mp.mergeScene()  #merge scene after run.
if mp.rank == 0: O.save('mergedScene.yade')

# #demonstrate getting stuff from workers, here we get kinetic energy from worker subdomains, notice that the master (mp.rank = 0), uses the sendCommand to tell workers to compute kineticEnergy.
# if mp.rank==0:
#         print("kinetic energy from workers: "+str(mp.sendCommand([1,2],"kineticEnergy()",True)))

Thanks so much

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