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.
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
------------------------------------------------------------------------------
Magic Quadrant for Content-Aware Data Loss Prevention
Research study explores the data loss prevention market. Includes in-depth
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http://www.accelacomm.com/jaw/sfnl/114/51385063/
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