Hi all,
We're seeing this seg fault occur in Vertex.cpp, it seems, using Ray 2.3.0 on
x86 launched via Slurm:
[jtan@barcoo-m barcoo]$ grep 27960 slurm-349755.out
Rank 233: Rank= 233 Size= 512 ProcessIdentifier= 27960
[barcoo050:27960] *** Process received signal ***
[barcoo050:27960] Signal: Segmentation fault (11)
[barcoo050:27960] Signal code: Address not mapped (1)
[barcoo050:27960] Failing at address: 0x18
[barcoo050:27960] [ 0] /lib64/libpthread.so.0(+0xf500) [0x2b076d782500]
[barcoo050:27960] [ 1]
/usr/local/Ray/2.3.0-gcc/Ray(_ZN6Vertex7addReadEP4KmerP14ReadAnnotation+0xe)
[0x5d18ee]
[barcoo050:27960] [ 2]
/usr/local/Ray/2.3.0-gcc/Ray(_ZN33Adapter_RAY_MPI_TAG_START_SEEDING4callEP7Message+0x481)
[0x4cdf11]
[barcoo050:27960] [ 3]
/usr/local/Ray/2.3.0-gcc/Ray(_ZN18MessageTagExecutor11callHandlerEiP7Message+0x22)
[0x62cca2]
[barcoo050:27960] [ 4]
/usr/local/Ray/2.3.0-gcc/Ray(_ZN11ComputeCore15runWithProfilerEv+0x1105)
[0x60fb75]
[barcoo050:27960] [ 5]
/usr/local/Ray/2.3.0-gcc/Ray(_ZN11ComputeCore3runEv+0x28e) [0x60d33e]
[barcoo050:27960] [ 6] /usr/local/Ray/2.3.0-gcc/Ray(_ZN7Machine5startEv+0x2024)
[0x475544]
[barcoo050:27960] [ 7] /usr/local/Ray/2.3.0-gcc/Ray(_ZN7Machine3runEv+0x6)
[0x473516]
[barcoo050:27960] [ 8] /usr/local/Ray/2.3.0-gcc/Ray(main+0x2d7) [0x470c47]
[barcoo050:27960] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd) [0x2b076d9aecdd]
[barcoo050:27960] [10] /usr/local/Ray/2.3.0-gcc/Ray() [0x4708a9]
[jtan@barcoo-m barcoo]$ gdb -d ~/src/Ray-2.3.0 -c core.27960 `which Ray`
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6_4.1)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/Ray/2.3.0-gcc/Ray...done.
....
Core was generated by `/usr/local/Ray/2.3.0-gcc/Ray BarcooRay31.conf'.
Program terminated with signal 11, Segmentation fault.
#0 0x00000000005d18ee in Vertex::addRead (this=0x2b079cfae040,
vertex=0x7fffadade1b0, e=0x2b079cfae040)
at code/VerticesExtractor/Vertex.cpp:176
176 e->setNext(m_readsStartingHere);
...
with the source code in ~/src/Ray-2.3.0.
and I find:
(gdb) where full
#0 0x00000000005d18ee in Vertex::addRead (this=0x2b079cfae040,
vertex=0x7fffadade1b0, e=0x2b079cfae040)
at code/VerticesExtractor/Vertex.cpp:176
...
(gdb) print m_readsStartingHere
$1 = (ReadAnnotation *) 0x0
With the user's permission, I have attached the configuration file, but not the
800MB core dump. :-)
Does anyone have any experience with this sort of problem? Maybe suggestions on
how to debug this further?
Regards
Jeff Tan
High Performance Computing Specialist
IBM Research Collaboratory for Life Sciences, Melbourne
-k 31
-p Female_PE10_read1_sequence_trim.fastq Female_PE10_read2_sequence_trim.fastq
-p Female_PE11_read1_sequence_trim.fastq Female_PE11_read2_sequence_trim.fastq
-p Female_PE12_read1_sequence_trim.fastq Female_PE12_read2_sequence_trim.fastq
-p Female_PE13_read1_sequence_trim.fastq Female_PE13_read2_sequence_trim.fastq
-p Female_PE14_read1_sequence_trim.fastq Female_PE14_read2_sequence_trim.fastq
-p Female_PE15_read1_sequence_trim.fastq Female_PE15_read2_sequence_trim.fastq
-p Female_PE1_read1_sequence_trim.fastq Female_PE1_read2_sequence_trim.fastq
-p Female_PE2_read1_sequence_trim.fastq Female_PE2_read2_sequence_trim.fastq
-p Female_PE3_read1_sequence_trim.fastq Female_PE3_read2_sequence_trim.fastq
-p Female_PE4_read1_sequence_trim.fastq Female_PE4_read2_sequence_trim.fastq
-p Female_PE5_read1_sequence_trim.fastq Female_PE5_read2_sequence_trim.fastq
-p Female_PE6_read1_sequence_trim.fastq Female_PE6_read2_sequence_trim.fastq
-p Female_PE7_read1_sequence_trim.fastq Female_PE7_read2_sequence_trim.fastq
-p Female_PE8_read1_sequence_trim.fastq Female_PE8_read2_sequence_trim.fastq
-p Female_PE9_read1_sequence_trim.fastq Female_PE9_read2_sequence_trim.fastq
-p GM_260-280_2_1_sequence_trim.fastq GM_260-280_2_2_sequence_trim.fastq
-p GM_260-280_3_1_sequence_trim.fastq GM_260-280_3_2_sequence_trim.fastq
-p GM_260-280_4_1_sequence_trim.fastq GM_260-280_4_2_sequence_trim.fastq
-p GM_260-280_5_1_sequence_trim.fastq GM_260-280_5_2_sequence_trim.fastq
-p Set23GB_GM_260-280_2_1_sequence_trim.fastq
Set23GB_GM_260-280_2_2_sequence_trim.fastq
-p Set23GB_GM_260-280_3_1_sequence_trim.fastq
Set23GB_GM_260-280_3_2_sequence_trim.fastq
-p Set23GB_GM_260-280_4_1_sequence_trim.fastq
Set23GB_GM_260-280_4_2_sequence_trim.fastq
-p Set23GB_GM_260-280_5_1_sequence_trim.fastq
Set23GB_GM_260-280_5_2_sequence_trim.fastq
-p Set2_GM_260-280_2_1_sequence_trim.fastq
Set2_GM_260-280_2_2_sequence_trim.fastq
-p Set2_GM_260-280_3_1_sequence_trim.fastq
Set2_GM_260-280_3_2_sequence_trim.fastq
-p Set2_GM_260-280_4_1_sequence_trim.fastq
Set2_GM_260-280_4_2_sequence_trim.fastq
-p Set2_GM_260-280_5_1_sequence_trim.fastq
Set2_GM_260-280_5_2_sequence_trim.fastq
-p Set2_GM_260-280_6_1_sequence_trim.fastq
Set2_GM_260-280_6_2_sequence_trim.fastq
-p Set2_GM_260-280_7_1_sequence_trim.fastq
Set2_GM_260-280_7_2_sequence_trim.fastq
-p Set2_GM_260-280_8_1_sequence_trim.fastq
Set2_GM_260-280_8_2_sequence_trim.fastq
-p Male-PE-1_read1_sequence_trim.fastq Male-PE-1_read2_sequence_trim.fastq
-p Male-PE-2_read1_sequence_trim.fastq Male-PE-2_read2_sequence_trim.fastq
-p Male-PE-3_read1_sequence_trim.fastq Male-PE-3_read2_sequence_trim.fastq
-p Male-PE-4_read1_sequence_trim.fastq Male-PE-4_read2_sequence_trim.fastq
-p Male-PE-5_read1_sequence_trim.fastq Male-PE-5_read2_sequence_trim.fastq
-p Male-PE-6_read1_sequence_trim.fastq Male-PE-6_read2_sequence_trim.fastq
-p Male-PE-7_read1_sequence_trim.fastq Male-PE-7_read2_sequence_trim.fastq
-p Male-PE-8_read1_sequence_trim.fastq Male-PE-8_read2_sequence_trim.fastq
-p Male-PE-9_read1_sequence_trim.fastq Male-PE-9_read2_sequence_trim.fastq
-p PE1_500_read1_sequence_trim.fastq PE1_500_read2_sequence_trim.fastq
-p PE2_500_read1_sequence_trim.fastq PE2_500_read2_sequence_trim.fastq
-p PE3_500_read1_sequence_trim.fastq PE3_500_read2_sequence_trim.fastq
-p PE1_800_read1_sequence_trim.fastq PE1_800_read2_sequence_trim.fastq
-p PE2_800_read1_sequence_trim.fastq PE2_800_read2_sequence_trim.fastq
-p PE3_800_read1_sequence_trim.fastq PE3_800_read2_sequence_trim.fastq
-p PE4_800_read1_sequence_trim.fastq PE4_800_read2_sequence_trim.fastq
-p PE5_800_read1_sequence_trim.fastq PE5_800_read2_sequence_trim.fastq
-p PE6_800_read1_sequence_trim.fastq PE6_800_read2_sequence_trim.fastq
-p PE7_800_read1_sequence_trim.fastq PE7_800_read2_sequence_trim.fastq
-p PE8_800_read1_sequence_trim.fastq PE8_800_read2_sequence_trim.fastq
-p PE9_800_read1_sequence_trim.fastq PE9_800_read2_sequence_trim.fastq
-p MP1_2kb_read1_sequence_trim.fastq MP1_2kb_read2_sequence_trim.fastq 2000 112
-p MP2_2kb_read1_sequence_trim.fastq MP2_2kb_read2_sequence_trim.fastq 2000 197
-p MP3_2kb_read1_sequence_trim.fastq MP3_2kb_read2_sequence_trim.fastq 2000 196
-p Male-4kb-1_read1_sequence_trim.fastq Male-4kb-1_read2_sequence_trim.fastq
4000 112
-p Male-4kb-2_read1_sequence_trim.fastq Male-4kb-2_read2_sequence_trim.fastq
4000 111
-p Male-4kb-3_read1_sequence_trim.fastq Male-4kb-3_read2_sequence_trim.fastq
4000 110
-p Male-4kb-4_read1_sequence_trim.fastq Male-4kb-4_read2_sequence_trim.fastq
4000 110
-p Male-4kb-5_read1_sequence_trim.fastq Male-4kb-5_read2_sequence_trim.fastq
4000 111
-p MP1_4kb_read1_sequence_trim.fastq MP1_4kb_read2_sequence_trim.fastq 4000 96
-p MP2_4kb_read1_sequence_trim.fastq MP2_4kb_read2_sequence_trim.fastq 4000 107
-p MP3_4kb_read1_sequence_trim.fastq MP3_4kb_read2_sequence_trim.fastq 4000 91
-p MP4_4kb_read1_sequence_trim.fastq MP4_4kb_read2_sequence_trim.fastq 4000 136
-p MP5_4kb_read1_sequence_trim.fastq MP5_4kb_read2_sequence_trim.fastq 4000 138
-p MP6_4kb_read1_sequence_trim.fastq MP6_4kb_read2_sequence_trim.fastq 4000 133
-p MP7_4kb_read1_sequence_trim.fastq MP7_4kb_read2_sequence_trim.fastq 4000 133
-p MP8_4kb_read1_sequence_trim.fastq MP8_4kb_read2_sequence_trim.fastq 4000 133
-p MP1_10kb_read1_sequence_trim.fastq MP1_10kb_read2_sequence_trim.fastq 10000
99
-p MP2_10kb_read1_sequence_trim.fastq MP2_10kb_read2_sequence_trim.fastq 10000
97
-p MP3_10kb_read1_sequence_trim.fastq MP3_10kb_read2_sequence_trim.fastq 10000
98
-p MP4_10kb_read1_sequence_trim.fastq MP4_10kb_read2_sequence_trim.fastq 10000
98
-p MP5_10kb_read1_sequence_trim.fastq MP5_10kb_read2_sequence_trim.fastq 10000
98
-p MP6_10kb_read1_sequence_trim.fastq MP6_10kb_read2_sequence_trim.fastq 10000
98
-p MP7_10kb_read1_sequence_trim.fastq MP7_10kb_read2_sequence_trim.fastq 10000
97
-p MP8_10kb_read1_sequence_trim.fastq MP8_10kb_read2_sequence_trim.fastq 10000
97
-p Female-P1_85-90perc_trim.fastq Female-P2_85-90perc_trim.fastq 12500 2500
-p Male-P1_109-90perc_trim.fastq Male-P2_109-90perc_trim.fastq 6000 2000
-p Male-P1_86-90perc_trim.fastq Male-P2_86-90perc_trim.fastq 6000 2000
-p SP6_trim_Match.fastq T7_trim_Match.fastq 150000 1500
-s s_1_sequence_trim.fasta
-s s_2_sequence_trim.fasta
-s s_3_sequence_trim.fasta
-s s_4_sequence_trim.fasta
-s s_6_sequence_trim.fasta
-s s_7_sequence_trim.fasta
-s s_8_sequence_trim.fasta
-s PacSet1_F1_trim.fasta
-s PacSet1_F2_trim.fasta
-s PacSet1_F3_trim.fasta
-s PacSet1_F4_trim.fasta
-s F1_s1s2ccs_trim.fasta
-s F2_s1s2ccs_trim.fasta
-s F3_s1s2ccs_trim.fasta
-s F4_s1s2ccs_trim.fasta
-s F32JLNA01_trim.fasta
-s F32JLNA02_trim.fasta
-s F32JLNA03_trim.fasta
-s F32JLNA04_trim.fasta
-s F3EG98R01_trim.fasta
-s F3EG98R02_trim.fasta
-s F5V4F3A01_trim.fasta
-s F5V4F3A02_trim.fasta
-s F5ZTILC01_trim.fasta
-s F7JDG4X01_trim.fasta
-s F7JDG4X02_trim.fasta
-s All-Unigene.fa
-s Result_Novel_Brain.fasta
-s Result_Novel_Skin.fasta
-o /vlsci/VR0002/shared/canetoad/trimfiles/RayOutK31_barcooov2
-disable-recycling
-read-write-checkpoints BarcooRaycheck31
-minimum-contig-length 100
-enable-neighbourhoods
-write-read-markers
-write-extensions
-write-contig-paths
-write-marker-summary
-show-memory-usage
-show-memory-allocations
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