Hi,
On 07/12/24 4:25 pm, Étienne Mollier wrote:
Hi Nilesh,
Nilesh Patra, on 2024-12-07:
Thanks for debugging this. The error to me appears to be here:
https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L140
and consequently at
https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L144
It is then trying to access matchList[m] and m is matchList.size() in the
first iteration which is undefined behavior.
It should start from matchList.size() - 1. I've pushed a fix -- do blasr
autopkgtest pass now?
Thanks for taking the time to diagnose the error, I have pulled
your changes for pbseqlib, rebuilt it, then built blasr against
the fresh pbseqlib. I still hit a core dump though. The back
trace looks like:
#0 __pthread_kill_implementation (threadid=<optimized out>,
signo=signo@entry=6, no_tid=no_tid@entry=0) at
./nptl/pthread_kill.c:44
#1 0x00007ffff71e4cef in __pthread_kill_internal (threadid=<optimized
out>,
signo=6) at ./nptl/pthread_kill.c:78
#2 0x00007ffff7190c42 in __GI_raise (sig=sig@entry=6)
at ../sysdeps/posix/raise.c:26
#3 0x00007ffff71794f0 in __GI_abort () at ./stdlib/abort.c:79
#4 0x00007ffff7530f9e in std::__glibcxx_assert_fail(char const*, int,
char const*, char const*) () from /lib/x86_64-linux-gnu/libstdc++.so.6
#5 0x00005555555bacd0 in std::vector<ChainedMatchPos, std::allocator<ChainedMatchPos>
>::operator[] (this=<optimized out>, __n=<optimized out>)
at /usr/include/c++/14/bits/stl_vector.h:1128
#6 std::vector<ChainedMatchPos, std::allocator<ChainedMatchPos>
>::operator[]
(this=<optimized out>, __n=<optimized out>)
at /usr/include/c++/14/bits/stl_vector.h:1128
#7 RemoveOverlappingAnchors<std::vector<ChainedMatchPos,
std::allocator<ChainedMatchPos> > > (matchList=std::vector of length 34, capacity 64
= {...})
at
/usr/include/pbseq/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp:144
#8 0x00005555555cd01f in MapRead<SMRTSequence, FASTASequence, SuffixArray<unsigned char,
std::vector<int, std::allocator<int> >, DefaultCompareStrings<unsigned char>, DNATuple>,
TupleCountTable<FASTASequence, DNATuple> > (read=...,
readRC=..., genome=..., sarray=..., bwt=..., seqBoundary=...,
ct=...,
seqdb=..., params=..., metrics=..., alignmentPtrs=...,
mappingBuffers=...,
mapData=<optimized out>, semaphores=...)
at ../iblasr/BlasrAlignImpl.hpp:149
#9 0x0000555555591364 in MapReadsNonCCS (
mapData=mapData@entry=0x555555691f38, mappingBuffers=...,
smrtRead=...,
smrtReadRC=..., subreads=std::vector of length 0, capacity 0,
params=...,
associatedRandInt=@0x7fffffffa73c: 813429720, allReadAlignments=...,
threadOut=...) at ../Blasr.cpp:347
#10 0x0000555555595119 in MapReads
(mapData=mapData@entry=0x555555691f38)
at ../Blasr.cpp:763
#11 0x000055555556c77f in main (argc=<optimized out>, argv=<optimized
out>)
at ../Blasr.cpp:1376
Hmmm. Weird, it does pass on my environment :S
I will maybe try this in a fresh chroot.
There does not seem to have been much changes. Maybe the error
is somewhere else? I hope I ran the test properly, it was a bit
intricate.
Your earlier reply to the bug report had this trace:
/usr/include/c++/14/bits/stl_vector.h:1130:
std::vector<_Tp, _Alloc>::reference
std::vector<_Tp, _Alloc>::operator[](size_type)
[
with _Tp = ChainedMatchPos;
_Alloc = std::allocator<ChainedMatchPos>;
reference = ChainedMatchPos&;
size_type = long unsigned int
]: Assertion '__n < this->size()' failed.
/tmp/autopkgtest.WdOt0L/build.sPS/src/debian/tests/run-unit-
The Assertion failure "'__n < this->size()' failed." indicates that the
index is going out of bounds in the vector. (upper bound)
Do you still see this trace? If so, maybe the versions are not tested
correctly?
-n
