Re: Seg fault after 2 days of simulation

[Ginger Booth]

Hi, Jan,
    It could be running out of memory. Looks like the bacillus data structures
are being recycled, but a new Quad is being allocated for each new bacillus.
If instead myquad were also reused, might fix. An idea.

Best,
    Ginger

Jan Kreft wrote:

> Dear all,
>
> I've been making many long simulations during the last weeks and some
> of them crashed with a seg fault after a long time. Since I have to
> wait two days to reach the same time again in the sim, I'd like to
> know what I should do to track this error down.
>
> I'm really clueless as to what causes this crash, the same messages
> have been called in the program thousands of times before. Why does it
> go wrong after 56884 steps when it worked all the time before?
>
> Here is the last line of sim output with the output from gdb:
>
> diffusion at 56884 made 13 diffSteps totalling 5368215 steps
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x404134d8 in chunk_free (ar_ptr=0x4046d300, p=0x9c7bf90) at malloc.c:2942
> malloc.c:2942: No such file or directory.
> Current language:  auto; currently c
> (gdb) bt
> #0  0x404134d8 in chunk_free (ar_ptr=0x4046d300, p=0x9c7bf90) at malloc.c:2942
> #1  0x40412c3e in malloc_extend_top (ar_ptr=0x4046d300, nb=72) at 
> malloc.c:2464
> #2  0x40413253 in chunk_alloc (ar_ptr=0x4046d300, nb=72) at malloc.c:2793
> #3  0x40412d15 in __libc_malloc (bytes=64) at malloc.c:2561
> #4  0x4019f672 in xmalloc (size=64) at xmalloc.c:13
> #5  0x4018b409 in -[Zone(c) _allocIVars:] (self=0x81dc470, _cmd=0x40197c10, 
> aClass=0x817d800) at Zone.m:28
> #6  0x4017ddaa in +[CreateDrop(s) _createBegin:] (self=0x817d800, 
> _cmd=0x817d840, aZone=0x81dc470) at Create.m:32
> #7  0x80523aa in +[Mcr create] (self=0x817d800, _cmd=0x817d898) at Mcr.m:16
> #8  0x8052d5a in -[Mcr intersectMcr:] (self=0x8282d98, _cmd=0x817d398, 
> m=0x90c71c0) at Mcr.m:169
> #9  0x8050e58 in -[Quad growMcr] (self=0x90c7188, _cmd=0x817d2e8) at 
> Quad.m:325
> #10 0x805066c in -[Quad addNode:] (self=0x8282d60, _cmd=0x818ac70, 
> p=0x90c7188) at Quad.m:142
> #11 0x809d94f in -[Bacillus reproduce] (self=0x9af8cc0, _cmd=0x818ac20) at 
> Bacillus.m:756
> #12 0x809d088 in -[Bacillus checkVolume] (self=0x9af8cc0, _cmd=0x818acb0) at 
> Bacillus.m:662
> #13 0x809dad8 in -[Bacillus step] (self=0x9af8cc0, _cmd=0x817d558) at 
> Bacillus.m:780
> #14 0x80521f5 in -[Quad substep] (self=0x96ccfb0, _cmd=0x817d568) at 
> Quad.m:650
> #15 0x8052257 in -[Quad substep] (self=0x9984580, _cmd=0x817d568) at 
> Quad.m:655
> #16 0x8052257 in -[Quad substep] (self=0x9396d18, _cmd=0x817d568) at 
> Quad.m:655
> #17 0x8052257 in -[Quad substep] (self=0x94c1320, _cmd=0x817d568) at 
> Quad.m:655
> #18 0x8052257 in -[Quad substep] (self=0x963c8d0, _cmd=0x817d568) at 
> Quad.m:655
> #19 0x8052257 in -[Quad substep] (self=0x97797e8, _cmd=0x817d570) at 
> Quad.m:655
> #20 0x80522b3 in -[Quad step] (self=0x8282d60, _cmd=0x817d580) at Quad.m:665
> #21 0x805231f in -[Quad stepOn:] (self=0x8282d60, _cmd=0x818beb8, roundth=1) 
> at Quad.m:672
> #22 0x401817ac in -[Object(s) _perform:with:] (self=0x8282d60, 
> _cmd=0x400b8070, aSel=0x818beb8, anObject1=0x1) at DefObject.m:521
> #23 0x400a86e7 in -[ActionTo(1) __performAction::] (self=0x845fde0, 
> _cmd=0x400bbb28, anActivity=0x9bb82a0) at Action.m:277
> #24 0x400af75b in -[Activity(c) __run:] (self=0x9bb82a0, _cmd=0x400bbb10) at 
> XActivity.m:185
> #25 0x400af65d in -[Activity(c) __run:] (self=0x84625c8, _cmd=0x400bbb10) at 
> XActivity.m:143
> #26 0x400af65d in -[Activity(c) __run:] (self=0x8461bf0, _cmd=0x400bbb10) at 
> XActivity.m:143
> #27 0x400af65d in -[Activity(c) __run:] (self=0x8461000, _cmd=0x400bbaf8) at 
> XActivity.m:143
> #28 0x400af539 in -[Activity(c) _run] (self=0x8461000, _cmd=0x8183910) at 
> XActivity.m:72
> #29 0x80792a5 in -[GeckoControlSwarm go] (self=0x8259b08, _cmd=0x817ced8) at 
> GeckoControlSwarm.m:315
> #30 0x805013f in main (argc=4, argv=0xbffff7c4) at main.m:42
> (gdb)
>
> And here is the relevant code:
>
> #import <limits.h>
> #import <math.h>
> #import "Mcr.h"
> #import "Stat.h"
>
> // Defining the methods for an Mcr.
> @implementation Mcr
>
> //creating a null Mcr.
> +create
> {
>     id result;
>     result = [[Mcr createBegin: globalZone] createEnd];
>     [result setNullMcr];
>     return result;
> }
>
> -(void) drop
> {
>     [super drop];
> }
>
> -setNullMcr
> {
>     lx = INT_MAX;
>     ux = INT_MIN;
>     ly = INT_MAX;
>     uy = INT_MIN;
>     lz = INT_MAX;
>     uz = INT_MIN;
>     return self;
> }
>
> ...........
>
> What should I do to track this down further?
>
> Many thanks, Jan.
>
>                   ==================================
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                  ==================================
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   to day usage of Swarm.  For list administration needs (esp.
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   with "help" in the body of the message.