Any core files generated ? Thank you !
> ________________________________________ > De : Matthew MacManes [[email protected]] > Date d'envoi : 26 juillet 2011 20:10 > À : Sébastien Boisvert > Cc : Ray Mailing List > Objet : Re: [Denovoassembler-users] seg fault issues when kmer < 40 > > 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/ > > Sébastien Boisvert http://github.com/sebhtml/ray ------------------------------------------------------------------------------ BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. 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