Re: [Denovoassembler-devel] segmentation fault

[Sébastien B. <seb...@ul...>]

Hello Carlos,

I hope everything goes fine for you.

Regarding the segmentation fault, I don't understand why the memory
usage would be 3315548 KiB *before* loading any sequence.

In /rap/nne-790-ac/Cray/2048-2013-01-10-1-Seg-Fault/ray_n2048.o470670
(on Colosse):

Rank 1992 has 0 sequence reads
Rank 1992: assembler memory usage: 3315548 KiB


>From a 512-rank job on the same dataset on Colosse:
 ( log HiSeq-2500-NA12878-demo-2x150-2012-12-18-1.stdout ):

Rank 258 has 0 sequence reads
Rank 258: assembler memory usage: 210692 KiB


Are you able to reproduce the segmentation fault with 2048 MPI ranks ?

I downloaded the core files, but they are binary so I can not do
anything with them I think.

Ticket: https://github.com/sebhtml/ray/issues/134


(I CC'ed this to denovoassembler-devel to have some sort of archive)

On Tue, Jan 08, 2013 at 03:53:53PM -0500, Carlos P. Sosa wrote:
> This on hera from last night 2048 MPI tasks:  (from stderr)
> 
>  
> 
> Stack walkback for Rank 1992 starting:
> 
>   _start@start.S:113
> 
>   __libc_start_main@0x2aaab0d74c35
> 
>   main@ray_main.cpp:32
> 
>   RankProcess<Machine>::run()@RankProcess.h:214
> 
>   RankProcess<Machine>::startMiniRank()@RankProcess.h:294
> 
>   Machine::run()@stl_construct.h:83
> 
>   Machine::start()@stl_construct.h:83
> 
>   ComputeCore::run()@stl_iterator.h:858
> 
>   ComputeCore::runVanilla()@stl_iterator.h:858
> 
>   ComputeCore::processData()@stl_iterator.h:858
> 
>   SlaveModeExecutor::callHandler(int)@stl_iterator.h:858
> 
>   Adapter_RAY_SLAVE_MODE_ADD_EDGES::call()@stl_algobase.h:217
> 
>   VerticesExtractor::call_RAY_SLAVE_MODE_ADD_EDGES()@stl_algobase.h:217
> 
>   Read::getSeq(char*, bool, bool) const@stl_algobase.h:217
> 
> Stack walkback for Rank 1992 done
> 
> Process died with signal 11: 'Segmentation fault'
> 
> Forcing core dumps of ranks 1992, 61, 218, 267, 271, 361, 510, 86, 1258, 8,
> 126, 293, 106, 373, 688, 59, 129, 145, 208, 17
> 
>  
> 
> Carlos P Sosa   
> 
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