Does this segfault happen right after section of optimal reads?
Matt
_____________________________________
Matthew MacManes, Ph.D.
University of New Hampshire I Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH 03824<x-apple-data-detectors://2/0>
Phone: 603-862-4052<tel:603-862-4052> I Twitter:
@PeroMHC<https://twitter.com/PeroMHC>
Web: genomebio.org<http://genomebio.org/>
Office: 189 Rudman Hall
Laboratory: 145 Rudman Hall
On Dec 6, 2013, at 12:09, "Sébastien Boisvert"
<sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>> wrote:
On 02/12/13 07:32 PM, Jeff Tan wrote:
Hi all,
We're seeing this seg fault occur in Vertex.cpp, it seems, using Ray 2.3.0 on
x86 launched via Slurm:
Do you have a tail of stdout. Maybe it is related to what Matthew MacManes is
seeing too.
[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
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