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
>
> 380 Jackson Street, Suite 210 | Saint Paul, MN 55101 | cp...@cr... |
> www.cray.com
>
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