Question #215877 on Yade changed:
https://answers.launchpad.net/yade/+question/215877
Status: Answered => Open
Giulia Macaro is still having a problem:
Hello,
I have run more tx tests with only 5,000 spheres:
I've restarted the computer, launched the test, and I have not opened any other
program (not even a folder, firefox, mouse, or music).
After 3 hours of running with 4 out of 8 cores, the total memory usage
increased from 11.13 to 11.51% (compared with the previous 22 to 32% which I
had while running other programs).
At the end of the test, after 18 hours, the memory arrived up to 14.29%, which
is considerably less than before.
It not a sceintific way, but it gives an idea of what is happening. Some
observations:
- As soon as I start using the pc for other stuff, the memory used by Yade
starts increasing faster
- Have you noticed the same behaviour?
- It is good news, I assume, that the memory does not increase much if I don't
run anything else. But why, while I run other programs, does the memory used
by Yade increase?
I am now trying to do the same (not using the pc at all) with the large
simulation (which crashed with SIGKILL before). Can I decide how much
memory Yade can use? Is there any command similar to -j4 given for the
number of cores?
Here is the script of the large simulation. It took me 3 or 4 days only
to settle the packing, and other 4 days in debug mode until it crashed.
Thanks for any suggestion
Giulia
#!/usr/bin/python
# -*- coding: utf-8 -*-
from yade import pack,log,params,timing,plot
if utils.runningInBatch()==False: from yade import qt
import os,sys,matplotlib
import numpy as np
from math import *
from yade import *
quick=False
#-----------------------------------------------------------------------
# D I M E N S I O N S
passing = [0, 5.72, 24.26, 35.07, 45.38, 55.17, 70.10, 79.58,
90.19, 100.0]
diameters= [0.600, 0.632, 0.710, 0.770, 0.810, 0.850, 0.940, 1.000,
1.060, 1.200]
radii = []; PSDup = 4
for i in range(len(diameters)): radii.append(diameters[i]*0.5e-3*PSDup)
Rmin = 0.632*0.5e-3*PSDup
Rmax = 1.200*0.5e-3*PSDup
AvgRadius= .400e-3*PSDup
Dpipe = 50e-3 # (m) pipe
diameter
# Initial packing
dim0 = 5*2*AvgRadius
dim1 = 9*Dpipe
dim2 = 4*Dpipe
extra = 1*Dpipe # clearance
between the packing and the periodic cell
# way of roughly estimating the initial packing
poroi = 0.76
porof = 0.5
nSph = int((1-porof)*(dim0*dim1*dim2)/(4/3*pi*AvgRadius**3))# approximate
nSph to get the desired final packing
hi = nSph*(4/3*pi*AvgRadius**3)/((1-poroi)*dim0*dim1)
# initial height of the packing
# Periodic cell dimensions
cell0 = dim0
cell1 = dim1+2*extra
cell2 = hi+2*extra
# Corners of the initial packing (in sp.particleSD)
minCorner = (0,extra,extra)
maxCorner = (dim0,extra+dim1,extra+hi)
#-----------------------------------------------------------------------
maxUnbalancedForce = 0.05
dporoMax = 0.001
dhppMax = 0.001
Damping = 0.5
#-----------------------------------------------------------------------
# M A T E R I A L S
O.materials.append(
FrictMat(density=2650,young=70e10,poisson=0.3,frictionAngle=radians(0),
label='bottomFloorMat'))
O.materials.append(
FrictMat(density=2650,young=70e10,poisson=0.3,frictionAngle=radians(0),
label='rightWallMat'))
O.materials.append(
FrictMat(density=2650,young=70e10,poisson=0.3,frictionAngle=radians(0),
label='leftWallMat'))
O.materials.append(
FrictMat(density=2650,young=70e09,poisson=0.3,frictionAngle=radians(26),
label='sandMat'))
O.materials.append(
FrictMat(density=7850,young=20e10,poisson=0.3,frictionAngle=radians(26*2/3),label='pipeMat'))
#-----------------------------------------------------------------------
# G E O M E T R Y
n0 = 3; n1 = 5; n2 = 10
# lat direction 0; lat direction 1; vert direction 2
deltah0 = dim0/n0; deltah1 = dim1/n1; deltav = hi/n2
#"""
# ~~~ Periodic cell ~~~
O.periodic = True
O.cell.setBox(Vector3(cell0,cell1,cell2)) # set size of the cell (rectangular)
# ~~~ Wall ~~~
# bottom floor
si = 1./n1; sj = 1./n0
for i in range(0,n1):
for j in range(0,n0):
x1 = (j*sj*cell0,extra*1.0+i*si*(extra*0.0+dim1),extra);
x2 = (j*sj*cell0,extra*1.0+(i+1)*si*(extra*0.0+dim1),extra); x3 =
((j+1)*sj*cell0,extra*1.0+(i+1)*si*(extra*0.0+dim1),extra); x4 =
((j+1)*sj*cell0,extra*1.0+i*si*(extra*0.0+dim1),extra)
O.bodies.append([utils.facet([x1,x2,x3],wire=False,fixed=True,material='bottomFloorMat'),utils.facet([x1,x3,x4],wire=False,fixed=True,material='bottomFloorMat'),])
# right wall
si = 1./n2; sj = 1./n0
for i in range(0,n2):
for j in range(0,n0):
x1 = (j*sj*cell0,extra,extra+i*si*hi); x2 =
((j+1)*sj*cell0,extra,extra+i*si*hi); x3 =
((j+1)*sj*cell0,extra,extra+(i+1)*si*hi); x4 =
((j)*sj*cell0,extra,extra+(i+1)*si*hi)
O.bodies.append([utils.facet([x1,x2,x3],fixed=True,material='rightWallMat'),utils.facet([x1,x3,x4],fixed=True,material='rightWallMat'),])
# left wall
si=1./n2;sj=1./n0
for i in range(0,n2):
for j in range(0,n0):
x1 = (j*sj*cell0,extra+dim1,extra+i*si*hi); x2 =
((j+1)*sj*cell0,extra+dim1,extra+i*si*hi); x3 =
((j+1)*sj*cell0,extra+dim1,extra+(i+1)*si*hi); x4 =
((j)*sj*cell0,extra+dim1,extra+(i+1)*si*hi)
O.bodies.append([utils.facet([x1,x2,x3],fixed=True,material='leftWallMat'),utils.facet([x1,x3,x4],fixed=True,material='leftWallMat'),])
# ~~~ Particles ~~~
sp=pack.SpherePack()
sp.particleSD(minCorner,maxCorner,rMean=AvgRadius,periodic=False,name="",numSph=nSph,radii=radii,passing=passing)
packing = [utils.sphere(s[0],s[1],material='sandMat') for s in sp]
O.bodies.append(packing)
#"""
#-----------------------------------------------------------------------
# bodies ids
ids_bottomFloor=[]; ids_leftWall=[]; ids_rightWall=[]; ids_sand=[]
for b in O.bodies:
if b.material.label=='bottomFloorMat': ids_bottomFloor.append(b.id)
elif b.material.label=='leftWallMat': ids_leftWall.append(b.id)
elif b.material.label=='rightWallMat': ids_rightWall.append(b.id)
elif b.material.label=='sandMat': ids_sand.append(b.id)
#-----------------------------------------------------------------------
# E N G I N E S
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Box_Aabb(),Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),],allowBiggerThanPeriod=True),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),],
[Ip2_FrictMat_FrictMat_MindlinPhys
(gamma=0.0,betan=0,betas=0),],
[Law2_ScGeom_MindlinPhys_Mindlin
(includeAdhesion=False,preventGranularRatcheting=True,includeMoment=True,label='contactLaw'),]
),
TranslationEngine(velocity=0,translationAxis=[0,0,1],ids=[0],dead=True,label='tEng'),
GravityEngine (gravity= (0,0,0), label='gravEng'),
NewtonIntegrator (damping= Damping, label='newton'),
PyRunner(command='gravityfunction(-9.81)',iterPeriod=50000,
label='gravityfunc'),
PyRunner(command='deposition()', iterPeriod=1000,
dead=False, label='mainfunction'),
]
#-----------------------------------------------------------------------
flag = 1
O.dt=0.5*utils.PWaveTimeStep()
#-----------------------------------------------------------------------
# F U N C T I O N S
def deposition():
fName = sys._getframe().f_code.co_name
global flag
if quick==False:
if O.iter<1e7: return
if gravEng.gravity[2]!=-9.81: return
if 2*O.interactions.countReal()*1./len(O.bodies)<=1: return
mainfunction.command='waitForDeposition()'
poro_prev = poroi; poro_curr = poroi; dporo = poroi
def waitForDeposition():
fName = sys._getframe().f_code.co_name
global poro_prev,poro_curr,dporo
poro_prev = poro_curr
poro_curr = porosityfunction()
dporo = poro_prev-poro_curr
if utils.unbalancedForce()<maxUnbalancedForce and dporo<=dporoMax:
mainfunction.command = 'depositionEnd()'
def depositionEnd():
global flag
fName = sys._getframe().f_code.co_name
if flag==1:
flag=2
newton.damping = 0.0
mainfunction.command = 'waitForDeposition()'
return
if flag==2:
if utils.unbalancedForce()<maxUnbalancedForce and
dporo<=dporoMax:
flag=3
if flag==3:
generatePipe()
flag=5
if flag==4:
mainfunction.command='pipeDeposition()'
if flag==5:
O.engines[3].velocity=0
O.engines[3].ids = [pipe.id]
O.engines[3].dead = False
colorSpheres(htop()/20)
mainfunction.command = 'loading()'
def colorSpheres(beta):
for bi in ids_sand:
bzp=(O.bodies[bi].state.pos[2]-extra)//beta
if bzp%2==0:
O.bodies[bi].shape.color=Vector3(0/255.,250.0/255.,154.0/255.)
else:
O.bodies[bi].shape.color=Vector3(1.0,0.0,0.0)
loadVel=-0.05
def loading():
global flag, zpp0,wpp, flagInt,loadVel,normEmbedment, vStar,xpp0
fName = sys._getframe().f_code.co_name
if flag==5:
O.engines[3].velocity = loadVel; flag=6
flagInt=0
if flag==6:
for i in ids_sand:
if flagInt==0:
try:
int=O.interactions[i,pipe.id]
if int.isReal==True:
zpp0 = pipe.state.pos[2]
xpp0=0
flagInt = 1
flag = 7
except StandardError:
int=0
if flag==7:
wpp = zpp0-pipe.state.pos[2]
normEmbedment = -(zpp0-pipe.state.pos[2])/Dpipe,
if abs(wpp)/Dpipe>=0.5: O.pause()
#-----------------------------------------------------------------------
# P I P E
z_cyl=float('nan')
def generatePipe():
wasRunning=True if O.running==True else False
if wasRunning==True:O.pause()
fName = sys._getframe().f_code.co_name
global pipe, z_cyl, ids_pipe
radius_cyl = Dpipe/2
z_cyl = extra+htop()+radius_cyl
center_cyl = Vector3(dim0/2.0,extra+2.5*Dpipe,z_cyl)
length_cyl = dim0*2.
radius_sph = dim0/2*0.9
z_sph = extra+htop()+radius_sph
center_sph = Vector3(dim0/2.0,extra+dim1/2,z_sph)
pipe = utils.sphere(center=center_sph,
radius=radius_sph,material='pipeMat', fixed=False, color=(0,0,1))
pipe.state.blockedDOFs='xXYZ'
O.bodies.append(pipe)
pipe.dynamic= False
ids_pipe = pipe.id
if wasRunning==True:O.run()
def pipeInteractions():
global pipeInt
pipeInt=[]
for i in O.interactions:
if i.id2==pipe.id:
pipeInt.append(i.id1)
return pipeInt
def htop(): # height from the bottom floor
top=0
for itop in ids_sand:
if O.bodies[itop].state.pos[2]>top:
top=O.bodies[itop].state.pos[2]
return (top-extra)
def porosityfunction():
global currPoro
volPack=htop()*dim0*dim1
volSph=utils.getSpheresVolume()
currPoro=(volPack-volSph)/volPack
return currPoro
def gravityfunction(g0):
nSteps=100 if quick==False else 1
dg=g0*1.0/nSteps
temp=gravEng.gravity[2]
if temp<=g0:
gravEng.gravity=(0,0,-9.81)
else:
gravEng.gravity=(0,0,temp+dg)
#-----------------------------------------------------------------------
O.trackEnergy=True
O.timingEnabled=True # to enable timing services
O.saveTmp()
#-----------------------------------------------------------------------
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