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] > > > > -- > > You received this question notification because your team > > yade-users is an answer contact for Yade. > > > > _______________________________________________ > > Mailing list: https://launchpad.net/~yade-users > > Post to : [email protected] > > Unsubscribe : https://launchpad.net/~yade-users > > More help : https://help.launchpad.net/ListHelp > > > -- > Janek Kozicki http://janek.kozicki.pl/ | > > You received this question notification because your team yade-users is > an answer contact for Yade. > > _______________________________________________ > Mailing list: https://launchpad.net/~yade-users > Post to : [email protected] > Unsubscribe : https://launchpad.net/~yade-users > More help : https://help.launchpad.net/ListHelp -- Janek Kozicki http://janek.kozicki.pl/ | You received this question notification because your team yade-users is an answer contact for Yade. _______________________________________________ Mailing list: https://launchpad.net/~yade-users Post to : [email protected] Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
