Re: [Yade-users] [Question #294741]: Adding resulting pictures of 3D view and plot.plots on a video

[Marcus Moravia]

Question #294741 on Yade changed:
https://answers.launchpad.net/yade/+question/294741

Status: Answered => Open

Marcus Moravia is still having a problem:
Hi Klaus,

First of all I need to thank you for your generosity to help me. I
confess that I am still confused about how create images for each frame
of 2D plot (this is the key to me!). I tried to find something to help
me on matplotlib.org Web site but I got lost in the number of examples.
Could you show me an example or tell me a link where I can find it?

Cheers,

Marcus.

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Re: [Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Feng Chen]

Question #294790 on Yade changed:
https://answers.launchpad.net/yade/+question/294790

Status: Answered => Open

Feng Chen is still having a problem:
Hi, Anton, thanks for your quick reply, I attached here the debug info
for the run, it seems quite long, do you have any idea which part went
wrong?

[fchen14@host003 bin]$ ./yade-1.20.0 >err.log 2>&1
Segmentation fault

below is the err.log:
---
Welcome to Yade 1.20.0 
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.hpp:108 Omega: Constructing 
Omega.
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:212 loadPlugins: 
Loading plugin /project/fchen14/yade/install/lib64/yade-1.20.0/libyade.so
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:136 
buildDynlibDatabase: called with 234 plugins.
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin AxialGravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BicyclePedalEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Box_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_ChainedCylinder_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Cylinder_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Facet_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_GridConnection_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Sphere_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Tetra_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bo1_Wall_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Body
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Bound
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BoundDispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BoundFunctor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BoundaryController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Box
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BoxFactory
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BubbleMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin BubblePhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CapillaryPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CapillaryStressRecorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CapillaryTriaxialTest
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Cell
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CentralGravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin ChCylGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin ChainedCylinder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin ChainedState
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CircularFactory
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Clump
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CohFrictMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CohFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CohesiveFrictionalContactLaw
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CohesiveTriaxialTest
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin Collider
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 
buildDynlibDatabase: Factoring plugin CombinedKinematicEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.

Re: [Yade-users] [Question #293955]: How to generate dense packing of aggregates

[VG]

Question #293955 on Yade changed:
https://answers.launchpad.net/yade/+question/293955

Status: Open => Solved

VG confirmed that the question is solved:
Thanks Jan Stránský, that solved my question.

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[Yade-users] [Question #294792]: Stable and Dense Packing using TriaxialStressController

[VG]

New question #294792 on Yade:
https://answers.launchpad.net/yade/+question/294792

Hello everyone,

I am trying to generate a packing of agglomerates which should be both dense 
and stable. I am using the procedure described here: 
https://github.com/yade/trunk/tree/master/examples/agglomerate

The packing generated using TriaxialStressController in compress.py is not 
stable in the presence of gravity. In other words, when I load this packing in 
simulation.py and run the simulation only with gravitational forces, the 
particles move quite a bit. Is there a way to make this packing also stable in 
the presence of gravity ?

I am trying to follow the solution proposed by Bruno here, but not quite sure 
how it works: https://answers.launchpad.net/yade/+question/263739
In this case, should I just run it first for few iterations with gravity and no 
triax.goal and then set the triax.goal as suggested.

Also, in the compress.py, is it not necessary to get unbalancedForce() below 
some threshold value ? I tried to put a threshold, but with the given 
parameters of triax.goal = -1e-5, the unbalancedForce() does not come down. 
However, if I use, triax.goal = -1, then it comes down below 0.01 within 
few iterations.

Thanks
Varun


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Re: [Yade-users] [Question #293955]: How to generate dense packing of aggregates

[VG]

Question #293955 on Yade changed:
https://answers.launchpad.net/yade/+question/293955

VG posted a new comment:
Sure, Thanks Bruno. I have posted a new question for this packing related issue:
https://answers.launchpad.net/yade/+question/294792

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Re: [Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Anton Gladky]

Question #294790 on Yade changed:
https://answers.launchpad.net/yade/+question/294790

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

you need to compile Yade in debug-mode to get debugging symbols:
-DDEBUG=1 option on the cmake-step.

After that you start Yade and should get a lot of information during 
the crash, which can be useful to understand the source the problems. 

Regards

Anton

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[Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Feng Chen]

New question #294790 on Yade:
https://answers.launchpad.net/yade/+question/294790

Hi, All:

I am now trying to use YADE-1.20.0 on a cluster (Redhat Enterprise 6) compiled 
with Intel Compiler 15.0.0, I made some attempt yesterday and was successful in 
compiling YADE with the following cmake configure and make, I compiled loki, 
boost 1.54 (1.55 has a problem with shard_ptr), eigen and minieigen using the 
same intel compiler, 

#!/bin/bash
export CC=icc
export CXX=icpc
export BSTTARGET=/project/fchen14/yade/boost/boost_1_54_0/install/
cmake -DCMAKE_C_COMPILER="icc" \
-DCMAKE_CXX_COMPILER="icpc" \
-DBoost_NO_BOOST_CMAKE=TRUE \
-DBoost_NO_SYSTEM_PATHS=TRUE \
-DBOOST_ROOT:PATHNAME=$BSTTARGET \
-DBoost_LIBRARY_DIRS:FILEPATH=${BSTTARGET}/lib \
-DBoost_INCLUDE_DIRS=${BSTTARGET}/include \
-DENABLE_GTS=OFF \
-DENABLE_GL2PS=OFF -DENABLE_GTS=OFF \
-DPY_minieigen=/project/fchen14/yade/eigen/minieigen-0.5.3/install/ \

-DEIGEN3_INCLUDE_DIR=/project/fchen14/yade/eigen/eigen-3.2.8/install/include/eigen3
 \
-DLOKI_INCLUDE_DIR=/project/fchen14/yade/loki/loki-0.1.7/install/include \
-DLOKI_LIBRARY=/project/fchen14/yade/loki/loki-0.1.7/install/lib \
-DCMAKE_INSTALL_PREFIX=../install \
../trunk-1.20.0/ #/project/fchen14/yade/loki/loki-0.1.7/install/include

the libyade.so was generated successfully, however when I tried to launch 
yade-1.20.0 with the following command it resulted in a segmentation fault:

[fchen14@host001 bin]$ ./yade-1.20.0
Welcome to Yade 1.20.0
Segmentation fault

further exploring into the script ./yade-1.20.0 I located the segmentation 
fault happens at the line 129 in ./yade-1.20.0

129 import yade

So I am wondering 

1) does anyone have the experience of using YADE with intel compiler?

2) As this will be only using the cluster with batch job so I do not need any 
GUI and use as few dependencies as possible, I just want to run a very simple 
case like free fall/collision of a few thousand particles and then benchmark 
the run,  can I run yade without python interface? (If trying to diagnose the 
segmentation fault with python interface will take a long time?

Thanks for any suggestions!

Feng Chen




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Re: [Yade-users] [Question #293955]: How to generate dense packing of aggregates

[Bruno Chareyre]

Question #293955 on Yade changed:
https://answers.launchpad.net/yade/+question/293955

Bruno Chareyre posted a new comment:
Please, one question at a time. If this one is answered mark it closed.
If you have other questions open them as new questions.
Bruno

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Re: [Yade-users] [Question #293955]: How to generate dense packing of aggregates

[VG]

Question #293955 on Yade changed:
https://answers.launchpad.net/yade/+question/293955

Status: Answered => Open

VG is still having a problem:
Hello everyone,

I have another follow up question: The packing generated using
TriaxialStressController in compress.py
(https://github.com/yade/trunk/tree/master/examples/agglomerate) is not
stable in the presence of gravity. In other words, when I load this
packing in simulation.py and run the simulation only with gravitational
forces, the particles move quite a bit.  Is there a way to make this
packing also stable in the presence of gravity.

I am trying to follow the solution proposed by Bruno here, but not quite sure 
how it works: https://answers.launchpad.net/yade/+question/263739  
In this case, should I just run it first for few iterations with gravity and 
then set the triax.goal as suggested. 


Also, in the compress.py, is it not necessary to get unbalancedForce() below 
some threshold value ? I tried to put a threshold, but with the given 
parameters of triax.goal = -1e-5, the unbalancedForce() does not come down. 
However, if I use, triax.goal = -1, then it comes down below 0.01 within 
few iterations.


Thanks
Varun

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Re: [Yade-users] [Question #294657]: Cpm model problem in Yade 1.20.0-151-0ecfcd0~trusty

[mohsen]

Question #294657 on Yade changed:
https://answers.launchpad.net/yade/+question/294657

Status: Answered => Solved

mohsen confirmed that the question is solved:
Thanks Jan Stránský, that solved my question.

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Re: [Yade-users] [Question #294657]: Cpm model problem in Yade 1.20.0-151-0ecfcd0~trusty

[mohsen]

Question #294657 on Yade changed:
https://answers.launchpad.net/yade/+question/294657

mohsen posted a new comment:
Hi Jan
>it should be fixed now. Could you please use the newest version and confirm
it?

I installed Yade 1.20.0-166-3cd917a_trusty

Now it is working right!
thanks Jan!!
(Jan also i have a another question that will be emailed to you! Not relevant 
to this topic)

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