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Re: [Question #678494]: Segmentation fault (core dumped) O.bodies.append

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Janek Kozicki <question678494@xxxxxxxxxxxxxxxxxxxxx>
Date: Tue, 12 Feb 2019 20:22:51 -0000
Reply-to: question678494@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
Question #678494 on Yade changed:
https://answers.launchpad.net/yade/+question/678494

Janek Kozicki proposed the following answer:
In short: try using SpatialQuickSortCollider

Also, to have a useful backtrace from yade which you didn't compile
yourself but installed it from debian distribution, you have to
install this package:

  libyade-dbgsym python-yade-dbgsym

however a special repository with debug symbols must be enabled:

  deb     http://debug.mirrors.debian.org/debian-debug/  stretch-debug
main non-free-contrib

Instead of "stretch" put your distribution name. It also works with
devuan, because devuan mirrors most of debian packages.

Janek


Janek Kozicki said:     (by the date of Tue, 12 Feb 2019 19:22:35 -0000)

> Question #678494 on Yade changed:
> https://answers.launchpad.net/yade/+question/678494
> 
>     Status: Open => Answered
> 
> Janek Kozicki proposed the following answer:
> To obtain a useful Backtrace please make sure that you have compiled
> yade with -DDEBUG=1, otherwise the backtrace will be useless.
> 
> Also on newer linux kernels you might need to run a command:
>   echo 0 > /proc/sys/kernel/yama/ptrace_scope ## debug ON
> 
> Backtrace:
> 
> Successfully delete periodic box!
> Successfully generate shear box!
> DEBUG yade/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 400 to 424, will std::sort.
> python: yade/pkg/common/InsertionSortCollider.cpp:223: virtual void InsertionSortCollider::action(): Assertion `(size_t)BB[0].size==2*scene->bodies->size()' failed.
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> 0x00007fa8ccece67d in poll () at ../sysdeps/unix/syscall-template.S:84
> 84      ../sysdeps/unix/syscall-template.S: No such file or directory.
> Invalid thread ID: info
> 
> Thread 24 (Thread 0x7fa878f0a700 (LWP 11503)):
> #0  0x00007fa8ccea704a in __GI___waitpid (pid=11509, stat_loc=stat_loc@entry=0x7fa878f091f0, options=options@entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
> #1  0x00007fa8cce2e0ab in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148
> #2  0x00007fa8cc5e2a1e in crashHandler (sig=6) at yade/core/main/pyboot.cpp:13
> #3  <signal handler called>
> #4  __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51
> #5  0x00007fa8cce2342a in __GI_abort () at abort.c:89
> #6  0x00007fa8cce1ae67 in __assert_fail_base (fmt=<optimized out>, assertion=assertion@entry=0x7fa8cb4e9478 "(size_t)BB[0].size==2*scene->bodies->size()", file=file@entry=0x7fa8cb4e90c8 "yade/pkg/common/InsertionSortCollider.cpp", line=line@entry=223, function=function@entry=0x7fa8cb4f22e0 <InsertionSortCollider::action()::__PRETTY_FUNCTION__> "virtual void InsertionSortCollider::action()") at assert.c:92
> #7  0x00007fa8cce1af12 in __GI___assert_fail (assertion=assertion@entry=0x7fa8cb4e9478 "(size_t)BB[0].size==2*scene->bodies->size()", file=file@entry=0x7fa8cb4e90c8 "yade/pkg/common/InsertionSortCollider.cpp", line=line@entry=223, function=function@entry=0x7fa8cb4f22e0 <InsertionSortCollider::action()::__PRETTY_FUNCTION__> "virtual void InsertionSortCollider::action()") at assert.c:101
> #8  0x00007fa8ca92e675 in InsertionSortCollider::action (this=0x556bcc023b10) at yade/pkg/common/InsertionSortCollider.cpp:223
> #9  0x00007fa8ca458a42 in Scene::moveToNextTimeStep (this=this@entry=0x556bca0c9d30) at yade/core/Scene.cpp:97
> #10 0x00007fa8ca45bf47 in SimulationFlow::singleAction (this=0x556bca0c9b10) at yade/core/SimulationFlow.cpp:24
> #11 0x00007fa8ca45fa67 in ThreadWorker::callSingleAction (this=0x556bca0c9b10) at yade/core/ThreadWorker.cpp:71
> #12 0x00007fa8ca45cb37 in ThreadRunner::call (this=this@entry=0x556bca1c2d30) at yade/core/ThreadRunner.cpp:52
> #13 0x00007fa8ca45ce78 in ThreadRunner::run (this=0x556bca1c2d30) at yade/core/ThreadRunner.cpp:26
> #14 0x00007fa8ca45eed2 in boost::function0<void>::operator() (this=<optimized out>) at /usr/include/boost/function/function_template.hpp:771
> #15 boost::detail::thread_data<boost::function0<void> >::run (this=<optimized out>) at /usr/include/boost/thread/detail/thread.hpp:116
> #16 0x00007fa8c7320116 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.62.0
> #17 0x00007fa8cdaba494 in start_thread (arg=0x7fa878f0a700) at pthread_create.c:333
> #18 0x00007fa8cced7acf in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:97
> 
> 
> We can see that the problem is in InsertionSortCollider with Assertion `(size_t)BB[0].size==2*scene->bodies->size()'
> 
> You might want to try a different collider
> https://yade-dev.gitlab.io/trunk/user.html#bo1-functors
> https://yade-dev.gitlab.io/trunk/yade.wrapper.html#collider
> 
> https://yade-
> dev.gitlab.io/trunk/yade.wrapper.html#yade.wrapper.SpatialQuickSortCollider
> 
> is suppose to be the safest one.
> 
> OTOH, it looks like maybe there is a bug in InsertionSortCollider
> because following lines are in contradiction with each other:
> 
>  long nBodies=(long)scene->bodies->size();
>  ...
>  if(BB[0].size!=2*nBodies){
>  ... // fix the BB[0].size
>  }
>  assert((size_t)BB[0].size==2*scene->bodies->size()); // Crash here.
> 
> best regards
> Janek
> 
> 
> Jan Stránský said:     (by the date of Tue, 12 Feb 2019 16:32:29 -0000)
> 
> > Question #678494 on Yade changed:
> > https://answers.launchpad.net/yade/+question/678494
> > 
> > Jan Stránský posted a new comment:
> > Hello,
> > no idea.. for others, output of catchsegv (it seems the problem is around InsertionSortCollider::action)
> > Jan
> > 
> > Backtrace:
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(+0x1f0227b)[0x7f1d31ff627b]
> > /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f1d294a7ecf]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN21InsertionSortCollider6actionEv+0x3e4)[0x7f1d31ff98a4]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN5Scene18moveToNextTimeStepEv+0x4b2)[0x7f1d31dba882]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN14SimulationFlow12singleActionEv+0x33)[0x7f1d31dbdd83]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN12ThreadWorker16callSingleActionEv+0x4f)[0x7f1d31dc179f]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN12ThreadRunner4callEv+0x47)[0x7f1d31dbe9b7]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN12ThreadRunner3runEv+0x50)[0x7f1d31dbec90]
> > /usr/lib/x86_64-linux-gnu/yade/libyade.so(_ZN5boost6detail11thread_dataINS_9function0IvEEE3runEv+0x32)[0x7f1d31dc0d52]
> > /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.65.1(+0x11bcd)[0x7f1d2ef7dbcd]
> > /lib/x86_64-linux-gnu/libpthread.so.0(+0x76db)[0x7f1d352c56db]
> > /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f1d355fe88f]
> > 
> > -- 
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> > 
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> 
> 
> -- 
> Janek Kozicki                               http://janek.kozicki.pl/  |
> 
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-- 
Janek Kozicki                               http://janek.kozicki.pl/  |

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