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membranepotential avatar membranepotential commented on September 3, 2024

For -s 21 I get the same segfault for another k-mer:

kmer: GGCTCACGAATTGTAACACA int: 1039706809617 hash: 872651690707

Thread 2 "squeakr-count" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffae0ce700 (LWP 29009)]
0x000000000043f60a in shift_remainders (qf=0x7fffffffbd00, start_index=1677734,
    empty_index=2112650) at threadsafe-gqf/gqf.c:716

(gdb) bt
#0  0x000000000043f60a in shift_remainders (qf=0x7fffffffbd00, start_index=1677734,
    empty_index=2112650) at threadsafe-gqf/gqf.c:716
#1  0x0000000000440f26 in insert1(QF *, __int128 unsigned, bool, bool) (
    qf=0x7fffffffbd00, hash=872651690707, lock=true, spin=false)
    at threadsafe-gqf/gqf.c:1362
#2  0x0000000000442378 in qf_insert (qf=0x7fffffffbd00, key=872651690707, value=0,
    count=1, lock=true, spin=false) at threadsafe-gqf/gqf.c:1816
#3  0x0000000000409821 in reads_to_kmers (c=..., obj=0x66e270) at main.cc:338
#4  0x0000000000409b1d in fastq_to_uint64kmers_prod (obj=0x66e270) at main.cc:379
...

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membranepotential avatar membranepotential commented on September 3, 2024

Finally I tried to compile with #define BITS_PER_SLOT 64 to force using the other shift_remainders implementation.

Again it segfaulted:

gdb --args squeakr-count -f -k 20 -s 20 -t 1 -o cqfs/ raw/SRR1660308.fastq
...
kmer: GGATGTCTGTGTGTTCTATT int: 1060369262746 hash: 674258092905

Thread 2 "squeakr-count" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffadd3d700 (LWP 30643)]
0x00007fffae8ac947 in memmove () from /lib64/libc.so.6
(gdb) bt
#0  0x00007fffae8ac947 in memmove () from /lib64/libc.so.6
#1  0x000000000043f3cc in shift_remainders (qf=0x7fffffffbd00, start_index=650765,
    empty_index=1058979) at threadsafe-gqf/gqf.c:689
#2  0x0000000000440ca0 in insert1(QF *, __int128 unsigned, bool, bool) (
    qf=0x7fffffffbd00, hash=674258092905, lock=true, spin=false)
    at threadsafe-gqf/gqf.c:1362
#3  0x00000000004420ed in qf_insert (qf=0x7fffffffbd00, key=674258092905, value=0,
    count=1, lock=true, spin=false) at threadsafe-gqf/gqf.c:1816
#4  0x0000000000409821 in reads_to_kmers (c=..., obj=0x66d270) at main.cc:338
#5  0x0000000000409b1d in fastq_to_uint64kmers_prod (obj=0x66d270) at main.cc:379
...

I suppose shift_remainders should be called with an empty_index < 2^log_n_slots?

Cheers

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membranepotential avatar membranepotential commented on September 3, 2024

I browsed the other issues and I think I understand that this is related to setting log_n_slots too small. I will try with the method you described in #17 and report back.

Cheers

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ttriche avatar ttriche commented on September 3, 2024

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membranepotential avatar membranepotential commented on September 3, 2024

With sufficently high log n_slots setting it runs without segfaulting.

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