yade-users team mailing list archive

[chiara modenese <c.modenese@xxxxxxxxx>]

Hi Luc,

have a look at this thread, it might be related to your problem. I had a
similar problem when I was trying to reload simulations from the triaxial
test. (
http://www.mail-archive.com/yade-dev@xxxxxxxxxxxxxxxxxxx/msg04708.html)

Chiara


On 26 November 2010 10:11, Luc Sibille <luc.sibille@xxxxxxxxxxxxxx> wrote:

> Hi Nejib thank you for your reply.
>
> I don't make any modification of the xml. I just run a simulation, stop it
> and save the xml file. Then reload the xml file and it is there that Yade
> can't iterate with this reloaded xml file. I checked the xml file, it is
> complete with the good lines at the end, at the beginning and so on. Of
> course the xml is quite big: about 250 MB but it should not be a problem. I
> verified this problem on several computers with different configurations
> (Ubuntu, fedora ...) and I get it each time.
>
> There are several things like that quite strange when you save and reload a
> xml file. As long as you don't reload a xml file the simulation works fine.
> But when you reload a xml file, you can have as I explained memory problems,
> or previous contact normal with one of the component being nan whereas none
> of the current contact normal has a nan ...
>
> Luc
>
> Nejib Hadda a écrit :
>
>  Hi Luc,
>>
>> I think you have a memory problem when loading the xml file, I don't
>> know why yade developpers changed the craft in the xml file so that evry
>> almost evry word takes one line. At first (when generating) your file
>> can be loaded, but since interactions take place the xml file will
>> increase in lines and system can not load it easily anymore.
>>
>> Another thing is that may be you made change on the xml file, but you
>> did not wait untill it is fully loaded, then you saved a corrupted file,
>> but I think it's not the because yade will crash.
>>
>> May be you can try something, launch YADE and then Go to the system
>> monitor (equivalent to task manager on windows), click on the processus
>> tab, and then right clik on yade and click on change priority, take a
>> small value (hight priority), and click ok.
>>
>> load your file, once loaded, before running reset the priority to normal
>> and then run your simulation.
>>
>> Hope this would be helpful !
>>
>>
>> Le jeudi 25 novembre 2010 à 18:52 +0100, Luc Sibille a écrit :
>>
>>> Hi everyone,
>>>
>>> After some Yade iterations (more than about 600 000) I save a xml. Then
>>> when I reload this xml all is fine, but when I run the simulation, Yade is
>>> not able to iterates: the ram memory used increases until having the
>>> following message:
>>>
>>> Yade [1]: O.load('on_va_voir.xml')
>>> Yade [2]: O.run()
>>> Yade [3]: 117953 FATAL yade.ThreadRunner
>>> /home/luc/Sim_DEM2/YADE_lbm/yade-0.50-lbm-dev_mainrepo/core/ThreadRunner.cpp:31
>>> run: Exception occured:
>>> std::bad_alloc
>>>
>>>
>>> I use Yade 0.50, I tried to run Yade throught Valgrind and here is the
>>> result below. Have you got an idea where to look for to solve this problem?
>>>
>>> Thank you in advance,
>>>
>>> Luc
>>>
>>>
>>> Yade [6]: O.run()
>>> Yade [7]: **8588** new/new[] failed and should throw an exception, but
>>> Valgrind
>>> ==8588==    at 0x402513F: VALGRIND_PRINTF_BACKTRACE (valgrind.h:4214)
>>> ==8588==    by 0x40256CC: operator new(unsigned int)
>>> (vg_replace_malloc.c:255)
>>> ==8588==    by 0xC4F9325:
>>> boost::shared_ptr<Interaction>::shared_ptr<Interaction>(Interaction*)
>>> (shared_count.hpp:87)
>>> ==8588==    by 0xC4D7B20:
>>> InsertionSortCollider::handleBoundInversion(int, int, InteractionContainer*,
>>> Scene*) (InsertionSortCollider.cpp:45)
>>> ==8588==    by 0xC4DD9B8: InsertionSortCollider::action()
>>> (InsertionSortCollider.cpp:282)
>>> ==8588==    by 0x5E93276: Scene::moveToNextTimeStep() (Scene.cpp:87)
>>> ==8588==    by 0x5E958D6: SimulationFlow::singleAction()
>>> (SimulationFlow.cpp:18)
>>> ==8588==    by 0x5E8ABCB: ThreadWorker::callSingleAction()
>>> (ThreadWorker.cpp:71)
>>> ==8588==    by 0x5E8E2DC: ThreadRunner::call() (ThreadRunner.cpp:53)
>>> ==8588==    by 0x5E92FB5: ThreadRunner::run() (ThreadRunner.cpp:27)
>>> ==8588==    by 0x5E9C41C:
>>> boost::detail::function::void_function_obj_invoker0<boost::_bi::bind_t<void,
>>> boost::_mfi::mf0<void, ThreadRunner>,
>>> boost::_bi::list1<boost::_bi::value<ThreadRunner*> > >,
>>> void>::invoke(boost::detail::function::function_buffer&)
>>> (mem_fn_template.hpp:49)
>>> ==8588==    by 0x5EEAD65:
>>> boost::detail::thread_data<boost::function0<void> >::run()
>>> (function_template.hpp:1013)
>>> **8588**    cannot throw exceptions and so is aborting instead.  Sorry.
>>> ==8588==    at 0x402513F: VALGRIND_PRINTF_BACKTRACE (valgrind.h:4214)
>>> ==8588==    by 0x40256DA: operator new(unsigned int)
>>> (vg_replace_malloc.c:255)
>>> ==8588==    by 0xC4F9325:
>>> boost::shared_ptr<Interaction>::shared_ptr<Interaction>(Interaction*)
>>> (shared_count.hpp:87)
>>> ==8588==    by 0xC4D7B20:
>>> InsertionSortCollider::handleBoundInversion(int, int, InteractionContainer*,
>>> Scene*) (InsertionSortCollider.cpp:45)
>>> ==8588==    by 0xC4DD9B8: InsertionSortCollider::action()
>>> (InsertionSortCollider.cpp:282)
>>> ==8588==    by 0x5E93276: Scene::moveToNextTimeStep() (Scene.cpp:87)
>>> ==8588==    by 0x5E958D6: SimulationFlow::singleAction()
>>> (SimulationFlow.cpp:18)
>>> ==8588==    by 0x5E8ABCB: ThreadWorker::callSingleAction()
>>> (ThreadWorker.cpp:71)
>>> ==8588==    by 0x5E8E2DC: ThreadRunner::call() (ThreadRunner.cpp:53)
>>> ==8588==    by 0x5E92FB5: ThreadRunner::run() (ThreadRunner.cpp:27)
>>> ==8588==    by 0x5E9C41C:
>>> boost::detail::function::void_function_obj_invoker0<boost::_bi::bind_t<void,
>>> boost::_mfi::mf0<void, ThreadRunner>,
>>> boost::_bi::list1<boost::_bi::value<ThreadRunner*> > >,
>>> void>::invoke(boost::detail::function::function_buffer&)
>>> (mem_fn_template.hpp:49)
>>> ==8588==    by 0x5EEAD65:
>>> boost::detail::thread_data<boost::function0<void> >::run()
>>> (function_template.hpp:1013)
>>> ==8588==
>>> ==8588== HEAP SUMMARY:
>>> ==8588==     in use at exit: 761,091,121 bytes in 14,178,786 blocks
>>> ==8588==   total heap usage: 139,013,366 allocs, 124,834,577 frees,
>>> 5,365,970,720 bytes allocated
>>> ==8588==
>>> ==8588==
>>> ==8588==     Valgrind's memory management: out of memory:
>>> ==8588==        newSuperblock's request for 56717312 bytes failed.
>>> ==8588==        2883981312 bytes have already been allocated.
>>> ==8588==     Valgrind cannot continue.  Sorry.
>>> ==8588==
>>> ==8588==     There are several possible reasons for this.
>>> ==8588==     - You have some kind of memory limit in place.  Look at the
>>> ==8588==       output of 'ulimit -a'.  Is there a limit on the size of
>>> ==8588==       virtual memory or address space?
>>> ==8588==     - You have run out of swap space.
>>> ==8588==     - Valgrind has a bug.  If you think this is the case or you
>>> are
>>> ==8588==     not sure, please let us know and we'll try to fix it.
>>> ==8588==     Please note that programs can take substantially more memory
>>> than
>>> ==8588==     normal when running under Valgrind tools, eg. up to twice or
>>> ==8588==     more, depending on the tool.  On a 64-bit machine, Valgrind
>>> ==8588==     should be able to make use of up 32GB memory.  On a 32-bit
>>> ==8588==     machine, Valgrind should be able to use all the memory
>>> available
>>> ==8588==     to a single process, up to 4GB if that's how you have your
>>> ==8588==     kernel configured.  Most 32-bit Linux setups allow a maximum
>>> of
>>> ==8588==     3GB per process.
>>> ==8588==
>>> ==8588==     Whatever the reason, Valgrind cannot continue.  Sorry.
>>> luc@pc-calc-luc2:~$
>>>
>>>
>>>
>>
>>
> --
> Luc Sibille
>
> Université de Nantes - Laboratoire GeM UMR CNRS
>
> IUT de Saint Nazaire
> 58, rue Michel-Ange - BP 420
> 44606 Saint-Nazaire Cedex, France
>
> Tel: +33 (0)2 40 17 81 78
>
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