Thank you for your reply
addr2line command gives the following output:
??:0
??:0
??:0
??:0
??:0
??:?
/home/programs/assembly/Ray-2.3.1/code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.cpp:889
(discriminator 1)
??:?
??:?
/home/programs/assembly/Ray-2.3.1/code/application_core/Machine.cpp:571
/home/programs/assembly/Ray-2.3.1/RayPlatform/RayPlatform/core/RankProcess.h:318
/home/programs/assembly/Ray-2.3.1/RayPlatform/RayPlatform/core/RankProcess.h:61
??:0
??:?
On 14 October 2014 18:57, Boisvert, Sebastien <boisv...@anl.gov> wrote:
> > From: Bart Nijsse [bart.nij...@wur.nl]
> > Sent: Thursday, October 09, 2014 9:42 AM
> > To: denovoassembler-users@lists.sourceforge.net
> > Subject: [Denovoassembler-users] Critical exception... memory exceeds
> the CHUNK_SIZE
> >
> >
> >
> >
> > Dear Ray developers,
> >
> > I am trying to do a denovo assembly using Ray with 300bp paired end
> reads. But I am receiving an error halfway of the run with the following
> command:
> >
> > mpiexec -n 28 /home/programs/assembly/Ray-2.3.1/Ray -k 101 -p
> read1.fastq read2.fastq -o k_101
> >
> >
> > Using different k-mers doesn't help.
> >
> > Critical exception: The length of the requested memory exceeds the
> CHUNK_SIZE: 63958792 > 33554432
> > Ray: RayPlatform/memory/MyAllocator.cpp:97: void*
> MyAllocator::allocate(int): Assertion `false' failed.
> > [ssb5:01427] *** Process received signal ***
> > [ssb5:01427] Signal: Aborted (6)
> > [ssb5:01427] Signal code: (-6)
> > [ssb5:01427] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340)
> [0x7fd9ebb00340]
> > [ssb5:01427] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39)
> [0x7fd9eb75ebb9]
> > [ssb5:01427] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148)
> [0x7fd9eb761fc8]
> > [ssb5:01427] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fa76)
> [0x7fd9eb757a76]
> > [ssb5:01427] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fb22)
> [0x7fd9eb757b22]
> > [ssb5:01427] [ 5] /home/programs/assembly/Ray-2.3.1/Ray() [0x544ece]
> > [ssb5:01427] [ 6] /home/programs/assembly/Ray-2.3.1/Ray() [0x4ff79f]
> > [ssb5:01427] [ 7] /home/programs/assembly/Ray-2.3.1/Ray() [0x567d20]
> > [ssb5:01427] [ 8] /home/programs/assembly/Ray-2.3.1/Ray() [0x56b29c]
> > [ssb5:01427] [ 9] /home/programs/assembly/Ray-2.3.1/Ray() [0x412936]
> > [ssb5:01427] [10] /home/programs/assembly/Ray-2.3.1/Ray() [0x40febc]
> > [ssb5:01427] [11] /home/programs/assembly/Ray-2.3.1/Ray() [0x40b902]
> > [ssb5:01427] [12]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fd9eb749ec5]
> > [ssb5:01427] [13] /home/programs/assembly/Ray-2.3.1/Ray() [0x40d41f]
> > [ssb5:01427] *** End of error message ***
> >
> >
> > Any idea what might be causing the problem?
>
> I never got that error before.
>
> Can you put the following lines (these are the addresses from your
> message) in a file named "Addresses.txt":
>
> 0x7fd9ebb00340
> 0x7fd9eb75ebb9
> 0x7fd9eb761fc8
> 0x7fd9eb757a76
> 0x7fd9eb757b22
> 0x544ece
> 0x4ff79f
> 0x567d20
> 0x56b29c
> 0x412936
> 0x40febc
> 0x40b902
> 0x7fd9eb749ec5
> 0x40d41f
>
>
> and then can you run this command:
>
>
> addr2line -e /home/programs/assembly/Ray-2.3.1/Ray < Addresses.txt
>
>
> This will tell us where this memory allocation is taking place.
>
> >
> >
> > Thanks in advance,
> > Bart Nijsse
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
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