to e clear, k40 works, k35 does not, nor does k30.
Same result:
Rank 13: gathering scaffold links [2547/2550] [2271/2271] (completed)
Rank 13: gathering scaffold links [2548/2550] [1/2059]
Rank 13: gathering scaffold links [2548/2550] [2059/2059] (completed)
Rank 13: gathering scaffold links [2549/2550] [1/2095]
Rank 13: gathering scaffold links [2549/2550] [2095/2095] (completed)
Rank 13: gathering scaffold links [2550/2550] [1/2319]
Rank 13: gathering scaffold links [2550/2550] [2319/2319] (completed)
[i167-403:11005] *** Process received signal ***
[i167-403:11005] Signal: Segmentation fault (11)
[i167-403:11005] Signal code: Address not mapped (1)
[i167-403:11005] Failing at address: 0xc0
[i167-403:11005] [ 0] /lib64/tls/libpthread.so.0 [0x312240c4f0]
[i167-403:11005] [ 1] /lib64/tls/libc.so.6(_IO_vfprintf+0x25) [0x312173f6e5]
[i167-403:11005] [ 2] /lib64/tls/libc.so.6(fprintf+0x86) [0x3121748276]
[i167-403:11005] [ 3]
/work/01301/mmacmane/ray.new/code/Ray(_ZN10Scaffolder14writeScaffoldsEv+0x47c)
[0x46c92c]
[i167-403:11005] [ 4]
/work/01301/mmacmane/ray.new/code/Ray(_ZN7Machine10runVanillaEv+0x36) [0x4459c6]
[i167-403:11005] [ 5]
/work/01301/mmacmane/ray.new/code/Ray(_ZN7Machine5startEv+0xd56) [0x446cc6]
[i167-403:11005] [ 6] /work/01301/mmacmane/ray.new/code/Ray(main+0x3a)
[0x49a6fa]
[i167-403:11005] [ 7] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
[0x312171c3fb]
[i167-403:11005] [ 8]
/work/01301/mmacmane/ray.new/code/Ray(__gxx_personality_v0+0x1ca) [0x42338a]
[i167-403:11005] *** End of error message ***
On Jul 25, 2011, at 9:25 AM, Sébastien Boisvert wrote:
> 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
____________________________________________
Matthew MacManes
University of California- Berkeley
Museum of Vertebrate Zoology
Phone: 510-495-5833
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://macmanes.com/
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