Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-12 Thread Jan Stránský 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Needs information => Answered

Jan Stránský proposed the following answer:
Hi Mike,
using pure yade, it resulted in segmentation fault in my case.

However, I noticed that the polyhedrons are really "crazy", completely
intersecting each other. I think in this case the DEM itself is not valid
anyway.. Is this a script just to reproduced the problem, or are you using
the script in other situations?

cheers
Jan


2016-05-09 9:57 GMT+02:00 MikeZhao :

> Question #293445 on Yade changed:
> https://answers.launchpad.net/yade/+question/293445
>
> MikeZhao gave more information on the question:
> Hi, I have tried to reproduce this bug, and the script is as
> following:##
>
> from libyade import yade
> from yade import *
>
>
> mat = PolyhedraMat()
> mat.density = 2600 * 10e15 #kg/m^3
> mat.Ks = 1.5e8
> mat.Kn = 2E9   #Pa
> mat.frictionAngle = 0.5 #rad
> yade.O.materials.append(mat)
> coords = dict()
> coords[0] =
> [yade.Vector3(0.12506498908304559,0.004170586360067608,0.04718878419835185),
>
> yade.Vector3(0.07196917639353285,0.002130673955178613,0.04829019846239369),
>
> yade.Vector3(0.12452553414402667,0.05548698237982243,0.09674610334959563),
>
> yade.Vector3(0.10202107066713305,0.003501573781327025,0.09778836768091179)]
> coords[1] =
> [yade.Vector3(0.14295032259085494,-0.006505603044225198,0.10466693700014766),
>
> yade.Vector3(0.11566808726849623,0.0437318004347,0.10573503009510624),
>
> yade.Vector3(0.09295451012074624,-0.008001021823003239,0.10600124068861566),
>
> yade.Vector3(0.11621529452629992,-0.007042223507702154,0.05542740653091893)]
> coords[2] =
> [yade.Vector3(0.2130315465641754,0.09686131087477995,0.053289505254753),
>   yade.Vector3(0.164020561929353,0.04648070412681492,0.004219224080575502),
>   yade.Vector3(0.1862772963099485,0.09652671335229797,0.00417259537268409),
>
> yade.Vector3(0.16288263942085443,0.09471008739327443,0.055098349410302505)]
> coords[3] =
> [yade.Vector3(0.17228834709600793,0.10610590338541123,0.04456793567930975),
>
> yade.Vector3(0.17280626014182954,0.056807096563525575,-0.00527106604700384),
>
> yade.Vector3(0.19547690664041997,0.1064874328191193,-0.006528797650868522),
>
> yade.Vector3(0.1454828764592455,0.10501383881798207,-0.004532778418338768)]
> coords[4] =
> [yade.Vector3(0.12518512144479108,0.004202482634043023,0.047282108263384234),
>
> yade.Vector3(0.07215900355266172,0.0022067170630582396,0.048405189227085095),
>
> yade.Vector3(0.09927440181878336,0.002841487802841776,-0.0020490482509290323),
>
> yade.Vector3(0.12194553936223902,0.053900337377603164,-0.003137962336613641)]
> coords[5] =
> [yade.Vector3(0.1230094368221373,-0.01217837847454617,0.0385941766299165),
>
> yade.Vector3(0.09606163246660983,-0.009341849627069044,-0.010265958898953698),
>
> yade.Vector3(0.14605505129391785,-0.007892828978239817,-0.012758832943173034),
>
> yade.Vector3(0.1191666025858279,0.04146035772028468,-0.007885859751166355)]
> coords[6] =
> [yade.Vector3(0.11631337631682945,-0.0072190647263523505,0.05526504476519887),
>
> yade.Vector3(0.11546679195549954,0.04339612477093768,0.10546948815801681),
>
> yade.Vector3(0.16283607913807063,0.09468384437456645,0.054801725781359986),
>   yade.Vector3(0.1660494458383337,0.04445695707723045,0.10422688539183134)]
> coords[7] =
> [yade.Vector3(0.12517826549319078,0.004210666781740674,0.04713033641567168),
>
> yade.Vector3(0.12503175035775993,0.05566147427541226,0.09662450106256898),
>
> yade.Vector3(0.1218967526875405,0.054092789281228446,-0.0033114695372207723),
>   yade.Vector3(0.1723941910681486,0.10613783179410324,0.04465530410432424)]
> coords[8] =
> [yade.Vector3(0.16282407041415756,0.0946878041824045,0.054807634434872056),
>
> yade.Vector3(0.1660391862703065,0.044454782962754805,0.10419776714643575),
>
> yade.Vector3(0.1641981030564517,0.04610198242630093,0.004203199959939556),
>
> yade.Vector3(0.11627599902436038,-0.007311015046615452,0.05527225087207195)]
> coords[9] =
> [yade.Vector3(0.1255192872383347,0.004248839377251908,0.04705512287925926),
>
> yade.Vector3(0.12177640027256077,0.05401449241996102,-0.003310973765333125),
>
> yade.Vector3(0.17288309620166054,0.0567881426706257,-0.005251109507840107),
>
> yade.Vector3(0.17239800601486288,0.10615025111591658,0.04466410423643576)]
> coords[10] =
> [yade.Vector3(0.16586255674847272,0.04442314808389014,0.10431426071039843),
>
> yade.Vector3(0.16306972984454005,0.09458742037006168,0.05488233416872211),
>   yade.Vector3(0.13921142362682418,0.09338844867941465,0.1051850240520792),
>
> yade.Vector3(0.11532750614560142,0.043572756568788916,0.10524886894605867)]
> coords[11] =
> [yade.Vector3(0.12553762857591796,0.05564020559697192,0.09672553666297364),
>
> yade.Vector3(0.12188774949220496,0.10432230228089284,0.04742164646483482),
>
> yade.Vector3(0.1723696031234631,0.10635275656158034,0.044620790102675174),
>
>

Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-11 Thread Bruno Chareyre 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Open => Needs information

Bruno Chareyre requested more information:
Hi,
Thanks for the script but in fact it does not show the bug, since you add 
"After calling O.step() for several times, this bug will occur."
It may sound like a dumb question but can you really try to make the script 
hang by itself? The reason could be there.
Bruno

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-09 Thread MikeZhao 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

MikeZhao gave more information on the question:
Hi, I have tried to reproduce this bug, and the script is as
following:##

from libyade import yade
from yade import *


mat = PolyhedraMat()
mat.density = 2600 * 10e15 #kg/m^3 
mat.Ks = 1.5e8 
mat.Kn = 2E9   #Pa
mat.frictionAngle = 0.5 #rad
yade.O.materials.append(mat)
coords = dict()
coords[0] = 
[yade.Vector3(0.12506498908304559,0.004170586360067608,0.04718878419835185),
  yade.Vector3(0.07196917639353285,0.002130673955178613,0.04829019846239369),
  yade.Vector3(0.12452553414402667,0.05548698237982243,0.09674610334959563),
  yade.Vector3(0.10202107066713305,0.003501573781327025,0.09778836768091179)]
coords[1] = 
[yade.Vector3(0.14295032259085494,-0.006505603044225198,0.10466693700014766),
  yade.Vector3(0.11566808726849623,0.0437318004347,0.10573503009510624),
  yade.Vector3(0.09295451012074624,-0.008001021823003239,0.10600124068861566),
  yade.Vector3(0.11621529452629992,-0.007042223507702154,0.05542740653091893)]
coords[2] = 
[yade.Vector3(0.2130315465641754,0.09686131087477995,0.053289505254753),
  yade.Vector3(0.164020561929353,0.04648070412681492,0.004219224080575502),
  yade.Vector3(0.1862772963099485,0.09652671335229797,0.00417259537268409),
  yade.Vector3(0.16288263942085443,0.09471008739327443,0.055098349410302505)]
coords[3] = 
[yade.Vector3(0.17228834709600793,0.10610590338541123,0.04456793567930975),
  yade.Vector3(0.17280626014182954,0.056807096563525575,-0.00527106604700384),
  yade.Vector3(0.19547690664041997,0.1064874328191193,-0.006528797650868522),
  yade.Vector3(0.1454828764592455,0.10501383881798207,-0.004532778418338768)]
coords[4] = 
[yade.Vector3(0.12518512144479108,0.004202482634043023,0.047282108263384234),
  yade.Vector3(0.07215900355266172,0.0022067170630582396,0.048405189227085095),
  yade.Vector3(0.09927440181878336,0.002841487802841776,-0.0020490482509290323),
  yade.Vector3(0.12194553936223902,0.053900337377603164,-0.003137962336613641)]
coords[5] = 
[yade.Vector3(0.1230094368221373,-0.01217837847454617,0.0385941766299165),
  yade.Vector3(0.09606163246660983,-0.009341849627069044,-0.010265958898953698),
  yade.Vector3(0.14605505129391785,-0.007892828978239817,-0.012758832943173034),
  yade.Vector3(0.1191666025858279,0.04146035772028468,-0.007885859751166355)]
coords[6] = 
[yade.Vector3(0.11631337631682945,-0.0072190647263523505,0.05526504476519887),
  yade.Vector3(0.11546679195549954,0.04339612477093768,0.10546948815801681),
  yade.Vector3(0.16283607913807063,0.09468384437456645,0.054801725781359986),
  yade.Vector3(0.1660494458383337,0.04445695707723045,0.10422688539183134)]
coords[7] = 
[yade.Vector3(0.12517826549319078,0.004210666781740674,0.04713033641567168),
  yade.Vector3(0.12503175035775993,0.05566147427541226,0.09662450106256898),
  yade.Vector3(0.1218967526875405,0.054092789281228446,-0.0033114695372207723),
  yade.Vector3(0.1723941910681486,0.10613783179410324,0.04465530410432424)]
coords[8] = 
[yade.Vector3(0.16282407041415756,0.0946878041824045,0.054807634434872056),
  yade.Vector3(0.1660391862703065,0.044454782962754805,0.10419776714643575),
  yade.Vector3(0.1641981030564517,0.04610198242630093,0.004203199959939556),
  yade.Vector3(0.11627599902436038,-0.007311015046615452,0.05527225087207195)]
coords[9] = 
[yade.Vector3(0.1255192872383347,0.004248839377251908,0.04705512287925926),
  yade.Vector3(0.12177640027256077,0.05401449241996102,-0.003310973765333125),
  yade.Vector3(0.17288309620166054,0.0567881426706257,-0.005251109507840107),
  yade.Vector3(0.17239800601486288,0.10615025111591658,0.04466410423643576)]
coords[10] = 
[yade.Vector3(0.16586255674847272,0.04442314808389014,0.10431426071039843),
  yade.Vector3(0.16306972984454005,0.09458742037006168,0.05488233416872211),
  yade.Vector3(0.13921142362682418,0.09338844867941465,0.1051850240520792),
  yade.Vector3(0.11532750614560142,0.043572756568788916,0.10524886894605867)]
coords[11] = 
[yade.Vector3(0.12553762857591796,0.05564020559697192,0.09672553666297364),
  yade.Vector3(0.12188774949220496,0.10432230228089284,0.04742164646483482),
  yade.Vector3(0.1723696031234631,0.10635275656158034,0.044620790102675174),
  yade.Vector3(0.14933095821244555,0.10569338022640279,0.09538317504306985)]
coords[12] = 
[yade.Vector3(0.2173311133734367,-0.00291435614061983,0.050878549630080615),
  yade.Vector3(0.2640348114070128,0.049396955137835985,0.0007687422103086969),
  
yade.Vector3(0.23998126829150335,-0.0013654269667168015,0.0010097662543496304),
  yade.Vector3(0.26756518846385796,-0.0012810266002693128,0.0498993551659514)]
coords[13] = 
[yade.Vector3(0.21732797257016542,-0.002825738834439564,0.050857917624400034),
  yade.Vector3(0.2643104682138871,0.04965977725183429,0.0007946325029359932),
  yade.Vector3(0.21413337322661294,0.04673315137371154,0.002351451925924373),

Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-09 Thread MikeZhao 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

MikeZhao gave more information on the question:
I will try if I could provide an example.

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-09 Thread MikeZhao 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Answered => Open

MikeZhao is still having a problem:
Eh, it is hard for me to provide an example, since I was building a FE-
DE model, another FEM software OOFEM is included in my calculation.

But this bug did occur within Yade, as I have added several cout codes
to locate this bug. This bug did occur when yade.O.step() is called.

I want to trace back to the source of this bug, but it seems O.step()
has used several function in boost library, so it's hard for me to
understand what actions O.step() actually contain within yade.

So I hope maybe you could tell me what codes are called for O.step(),
and I could better locate this bug.

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-09 Thread Jan Stránský 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Open => Answered

Jan Stránský proposed the following answer:
Hi Mike,
could you please provide a complete script which does this problem?
Thanks
Jan


2016-05-09 7:52 GMT+02:00 MikeZhao :

> Question #293445 on Yade changed:
> https://answers.launchpad.net/yade/+question/293445
>
> MikeZhao gave more information on the question:
> The new engine is as following:
> O.engines = [
> ForceResetter(),
> InsertionSortCollider([Bo1_Polyhedra_Aabb()]),
> InteractionLoop(
> [Ig2_Polyhedra_Polyhedra_PolyhedraGeom()],
> [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
> [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
> ),
> NewtonIntegrator(damping=0),
> ]
>
> According to my test, this bug happens during Yade.O.step().
>
> I have added several cout codes at the begining and the end of several
> places. It turns out that this bug doesn't locate in
> Ig2_Polyhedra_Polyhedra_PolyhedraGeom::go,
> Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys::go or
> Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::go.
>
> Could anybody tell me where this bug possibly locate? Thanks a lot.
>
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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-08 Thread MikeZhao 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

MikeZhao gave more information on the question:
The new engine is as following:
O.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Polyhedra_Aabb()]),
InteractionLoop(
[Ig2_Polyhedra_Polyhedra_PolyhedraGeom()],
[Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
[Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
),
NewtonIntegrator(damping=0),
]

According to my test, this bug happens during Yade.O.step().

I have added several cout codes at the begining and the end of several
places. It turns out that this bug doesn't locate in
Ig2_Polyhedra_Polyhedra_PolyhedraGeom::go,
Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys::go or
Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::go.

Could anybody tell me where this bug possibly locate? Thanks a lot.

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-08 Thread MikeZhao 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Answered => Open

MikeZhao is still having a problem:
I have updated yade, using trunk-master. However, this problem still
exists:

The speed of my calculation is about 5 steps per second, however when it
comes to a certain step, it will hold there while the usage of CPU
remains 100%. I am pretty sure that this program encountered an infinite
loop when yade.O.step() is called..

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-08 Thread Anton Gladky 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Anton Gladky proposed the following answer:
You can try yadedaily which is updating permanently now
for most supported Debian-based distributions.

Best regards

Anton

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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-08 Thread Jan Stránský 
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Status: Open => Answered

Jan Stránský proposed the following answer:
Hi Mike,
according to PolyhedraVolumetricLaw (which was renamed to
Law2_PolyhedraGeom_PolyhedraPhys_Volumetric), it seems you have an older
version of Yade. Since then, there were some changes in polyhedra code. Is
it possible for you to try the script with some newer version?
cheers
Jan


2016-05-08 8:57 GMT+02:00 MikeZhao :

> New question #293445 on Yade:
> https://answers.launchpad.net/yade/+question/293445
>
> I have been working on building finite-discrete element model to simulate
> fracture generation, and polyhedra elements in yade are used for DEM.
>
> After several steps, it seems that an infinite loop occurs when
> yade.O.step() is called. I want to trace back to the source of this bug,
> but it seems O.step() has called several functions in boost library, and it
> is hard for me to understand what codes in Yade are involved for O.step().
>
> Could you please give me some advice on locating this bug? It will be very
> helpful if someone can tell my what codes in Yade are called for O.step().
>
> By the way, the engine I used is as following:
> O.engines = [
> ForceResetter(),
> InsertionSortCollider([Bo1_Polyhedra_Aabb()]),
> InteractionLoop(
> [Ig2_Polyhedra_Polyhedra_PolyhedraGeom()],
> [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
> [PolyhedraVolumetricLaw()]
> ),
> NewtonIntegrator(damping=0),
> ]
>
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[Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

2016-05-08 Thread MikeZhao 
New question #293445 on Yade:
https://answers.launchpad.net/yade/+question/293445

I have been working on building finite-discrete element model to simulate 
fracture generation, and polyhedra elements in yade are used for DEM. 

After several steps, it seems that an infinite loop occurs when yade.O.step() 
is called. I want to trace back to the source of this bug, but it seems 
O.step() has called several functions in boost library, and it is hard for me 
to understand what codes in Yade are involved for O.step().

Could you please give me some advice on locating this bug? It will be very 
helpful if someone can tell my what codes in Yade are called for O.step().

By the way, the engine I used is as following:
O.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Polyhedra_Aabb()]),
InteractionLoop(
[Ig2_Polyhedra_Polyhedra_PolyhedraGeom()],
[Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
[PolyhedraVolumetricLaw()]
),
NewtonIntegrator(damping=0),
]

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