Hi,
> Hi All
>
> Having some problems with set faults-- have tried 1.6.1-rc2 and a bleeding
> edge version pulled from github yesterday.. I've tried as many as 1024 cores
> with same results. Network latency is ~500microseconds. I have 384Gb fastq
> files and genome size of ~1Gb. This only happens when kmer is < 40.
>
So this is happenning with MAXKMERLENGTH=64 and -k 39, but not with
MAXKMERLENGTH=64 and -k 41 ? Strange.
Can you compile with ASSERT=y to see if something is picked up by run-time
assertions ?
Seems to be one of the 4 calls to printf in Scaffolder::writeScaffolds.
Thanks.
> System details per Ray:
> Rank 0: Ray version: 1.6.2-devel
> Rank 0 MAXKMERLENGTH: 64 (KMER_U64_ARRAY_SIZE: 2)
> Rank 0: GNU system (__GNUC__): yes
> Rank 0: Operating System: Linux (__linux__) POSIX (OS_POSIX)
> Rank 0: real-time Operating System (HAVE_CLOCK_GETTIME): no
> Rank 0: Message-Passing Interface implementation: Open-MPI (OMPI_MPI_H) 1.4.2
> Rank 0: Message-Passing Interface standard version: 2.1
> Rank 0: GZIP (HAVE_LIBZ): no
> Rank 0: BZIP2 (HAVE_LIBBZ2): no
> Rank 0: GNU/Linux (__linux__): yes
> Rank 0: assertions (ASSERT): no
> Rank 0: maximum size of a message (MAXIMUM_MESSAGE_SIZE_IN_BYTES): 4000 bytes
> Rank 0: don't align addresses on 8 bytes (FORCE_PACKING): no
>
>
> Number of MPI ranks: 512
> Ray master MPI rank: 0
> Ray slave MPI ranks: 0-511
>
>
>
> The error message:
> ..
> Rank 12: gathering scaffold links [2714/2719] [2298/2298] (completed)
> Rank 12: gathering scaffold links [2715/2719] [1/3291]
> Rank 12: gathering scaffold links [2715/2719] [3291/3291] (completed)
> Rank 12: gathering scaffold links [2716/2719] [1/3127]
> Rank 12: gathering scaffold links [2716/2719] [3127/3127] (completed)
> Rank 12: gathering scaffold links [2717/2719] [1/2312]
> Rank 12: gathering scaffold links [2717/2719] [2312/2312] (completed)
> Rank 12: gathering scaffold links [2718/2719] [1/2765]
> Rank 12: gathering scaffold links [2718/2719] [2765/2765] (completed)
> Rank 12: gathering scaffold links [2719/2719] [1/2384]
> Rank 12: gathering scaffold links [2719/2719] [2384/2384] (completed)
> [i101-410:31156] *** Process received signal ***
> [i101-410:31156] Signal: Segmentation fault (11)
> [i101-410:31156] Signal code: Address not mapped (1)
> [i101-410:31156] Failing at address: 0xc0
> [i101-410:31156] [ 0] /lib64/tls/libpthread.so.0 [0x323f40c4f0]
> [i101-410:31156] [ 1] /lib64/tls/libc.so.6(_IO_vfprintf+0x25) [0x323e73f6e5]
> [i101-410:31156] [ 2] /lib64/tls/libc.so.6(fprintf+0x86) [0x323e748276]
> [i101-410:31156] [ 3]
> /work/01301/mmacmane/ray.new/code/Ray(_ZN10Scaffolder14writeScaffoldsEv+0x3d9)
> [0x4656e9]
> [i101-410:31156] [ 4]
> /work/01301/mmacmane/ray.new/code/Ray(_ZN7Machine10runVanillaEv+0x46)
> [0x441a76]
> [i101-410:31156] [ 5]
> /work/01301/mmacmane/ray.new/code/Ray(_ZN7Machine5startEv+0xd56) [0x443536]
> [i101-410:31156] [ 6] /work/01301/mmacmane/ray.new/code/Ray(main+0x3a)
> [0x48f89a]
> [i101-410:31156] [ 7] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
> [0x323e71c3fb]
> [i101-410:31156] [ 8]
> /work/01301/mmacmane/ray.new/code/Ray(__gxx_personality_v0+0x1d2) [0x422b7a]
> [i101-410:31156] *** End of error message ***
>
>
> Thanks, Matt
Sébastien Boisvert
http://github.com/sebhtml/ray
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