"FATAL" error in https://gitlab.com/yade-dev/trunk/blob/master/doc/sphinx/tutorial/06-periodic-triaxial-test.py

Asked by Rong Zhao on 2019-11-07

When I try to run the script of tutorial example for periodic triaxial test from[1], the following error message pops up:

==================================================================================================
FATAL /build/yade-fDuCoe/yade-2018.02b/pkg/common/InsertionSortCollider.cpp:495 spatialOverlapPeri: Body #669 spans over half of the cell size 0.167282 (axis=2, see flag allowBiggerThanPeriod)

FATAL /build/yade-fDuCoe/yade-2018.02b/core/ThreadRunner.cpp:30 run: Exception occured:
/build/yade-fDuCoe/yade-2018.02b/pkg/common/InsertionSortCollider.cpp: Body larger than half of the cell size encountered.
=====================================================================================================

By the way, The version of Yade I installed is the 2018.02b. I hope someone can advise me on how to solve this problem.
Thanks in advance!

[1]https://gitlab.com/yade-dev/trunk/blob/master/doc/sphinx/tutorial/06-periodic-triaxial-test.py

Question information

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Solved by:
Rong Zhao
Solved:
2019-11-11
Last query:
2019-11-11
Last reply:
2019-11-08
Jérôme Duriez (jduriez) said : #1

Hi,

I'm sorry, I can not confirm:

jerome.duriez@AXP17003:~$ yade 06-periodic-triaxial-test.py # script just donwloaded from your [1]
Welcome to Yade 2018.02b
TCP python prompt on localhost:9000, auth cookie `yassud'
XMLRPC info provider on http://localhost:21000
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed
Running script 06-periodic-triaxial-test.py
yade.plot: creating fake plot, since there are no y-data yet
WARNING:matplotlib.legend:No handles with labels found to put in legend.
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view (use h-key for showing help), F10 both, F9 generator, F8 plot. ]]

In [1]:

Note that the error you mentions is "normal" in cases where "Body larger than half of the cell size" are present in YADE periodic simulations.
There are workarounds such as InsertionSortCollider.allowBiggerThanPeriod [*] but, as the doc says, they may require some good understanding of YADE periodic boundaries.

[*] https://yade-dem.org/doc/yade.wrapper.html?highlight=insertionsortcollider#yade.wrapper.InsertionSortCollider.allowBiggerThanPeriod

Hi,
Please note that example scripts should _never_ be taken directly from gitlab.com unless you really know what you doing.
If you are using Yade ver. 2018.02b then you should use the example scripts from the yade-doc package of that same version.
Regards
Bruno

Rong Zhao (zhaorong) said : #3

Thanks very much, Bruno Chareyre. You solved my question.