Segmentation fault for specific sequence

[LotusIodid]

Minimal example:

import pyopal
import archspec
print(archspec.cpu.host())

db = pyopal.Database([
   'MSKPPPKPAKPGQVKVYRALFTFDPRTPDELYFEEGDILYISDTSDSNWWKGTCRGRTGLIPSNYVAEQAESIDNPMHEAAKRGNLSWLRECLDNKVGINGLDKAGNTSLYWACHGGHKDVVEILLSQPNCELNQQNKLGDTPLHAAAWKGYSDIVEMLLNKNARTDVVNNEKKTALDMATNAQCASLLKRKLGGVILRTHSNAEEYLDDEDSD'
   'MSKPPPKPAKPGQVKVFRALFTFDPRTPDELYFEEGDILYISDTSDTNWWKGTCRGRTGLIPSNYVAEQAETIDHPMHEAAKRGNLSWLRECVENKVGINGLDKAGNTALYWACHGGHKDVVELLLNQPSVELNQQNKLGDTVLHAAAWKGYSDIVEMLLDKNARTDIRNNENKLALEMATNAQCASLLKRKQGTNVTRTLSNAEEYLDDDDSD',
   'MSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDILYIADMSDTNWWKGTCKGKTGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLENRVGVNGLDKAGSTALYWGCHGGHKDVVDMLLAQPNIELNQQNKLGDTALHAAAWKGYADIVELLLVKGARTDLRNNEKKLALDMATNAQCASLLKKKQAQGIVRTSSNADEYLDDEDSD',
   ])
seq = 'MAAEGSEVLKPSPKPIKPGQVKVFRALYTFELRTPEELYFEEADIIYITDMSDTSWWKGTCKGQTGLIPSNYVAEQAESIDNPLHEACLDNPVGVDGRDKAGSTALHWACHGGRKDTVEAPFTRPNTELNQQNKLGDAALHAAAWKGCADIVQLLLAKDARTDLNNEKKLALDMATNAAGASLLKKKRGADAVQTLSNTEDYLFFFFFFF';
print(db.search(seq, mode="full", algorithm="nw"))

Output:

broadwell
Segmentation fault (core dumped)

Stacktrace:

                Found module /root/micromamba/envs/tmp/bin/python3.11 without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/lib-dynload/select.cpython-311-x86_64-linux-gnu.so without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal_avx2.cpython-311-x86_64-linux-gnu.so with build-id: a841203005b553c0ce68bb9a84386fadb171eea3
                Found module /root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal_sse4.cpython-311-x86_64-linux-gnu.so with build-id: 3fb75bcf716affa84d20a4e00e13343108a7d305
                Found module /root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal_sse2.cpython-311-x86_64-linux-gnu.so with build-id: d4b5c00ab2dd9282a1c87572615f0605a0b807e0
                Found module /root/micromamba/envs/tmp/lib/libgcc_s.so.1 without build-id.
                Found module /root/micromamba/envs/tmp/lib/libstdc++.so.6.0.31 without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/lib-dynload/_posixsubprocess.cpython-311-x86_64-linux-gnu.so without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/lib-dynload/_json.cpython-311-x86_64-linux-gnu.so without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/lib-dynload/fcntl.cpython-311-x86_64-linux-gnu.so without build-id.
                Found module /root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal.cpython-311-x86_64-linux-gnu.so with build-id: 0db7d37356d05183777036bbe151e63d83383e3d
                Found module linux-vdso.so.1 with build-id: 99df10e56dd5eafb5d4529f48a70e4bd75b2c2b0
                Found module ld-linux-x86-64.so.2 with build-id: 61ef896a699bb1c2e4e231642b2e1688b2f1a61e
                Found module librt.so.1 with build-id: 1030be4690f8aa93b63acd9180b3037d99a974bf
                Found module libc.so.6 with build-id: 69389d485a9793dbe873f0ea2c93e02efaa9aa3d
                Found module libm.so.6 with build-id: 27e82301dba6c3f644404d504e1bb1c97894b433
                Found module libutil.so.1 with build-id: 2bac9e4cf30824d56388dc43b83a2ad87d1bd33d
                Found module libdl.so.2 with build-id: 952123c3bdce7c3370553717942b4878d1fad797
                Found module libpthread.so.0 with build-id: e62798b68557abb4bc5548aba2640cd5ab948f36
                Stack trace of thread 95318:
                #0  0x00007fe5fdea9fa1 n/a (/root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal_avx2.cpython-311-x86_64-linux-gnu.so + 0x17fa1)
                #1  0x00007fe5fe88e91b n/a (/root/micromamba/envs/tmp/lib/python3.11/site-packages/pyopal/_opal.cpython-311-x86_64-linux-gnu.so + 0x5991b)
                #2  0x00005623717b636a n/a (/root/micromamba/envs/tmp/bin/python3.11 + 0x22636a)

The bug depends on the sequences. It has not occurred on the same machine, same config, and same binary for multiple hundreds of other sequences.

#lscpu
Architecture:            x86_64
  CPU op-mode(s):        32-bit, 64-bit
  Address sizes:         46 bits physical, 48 bits virtual
  Byte Order:            Little Endian
CPU(s):                  16
  On-line CPU(s) list:   0-15
Vendor ID:               GenuineIntel
  Model name:            Intel(R) Xeon(R) CPU E5-2686 v4 @ 2.30GHz
    CPU family:          6
    Model:               79
    Thread(s) per core:  2
    Core(s) per socket:  8
    Socket(s):           1
    Stepping:            1
    CPU max MHz:         3000.0000
    CPU min MHz:         1200.0000
    BogoMIPS:            4600.01
    Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid s
                         se4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single pti fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm rdseed adx xsaveopt
Virtualization features: 
  Hypervisor vendor:     Xen
  Virtualization type:   full
Caches (sum of all):     
  L1d:                   256 KiB (8 instances)
  L1i:                   256 KiB (8 instances)
  L2:                    2 MiB (8 instances)
  L3:                    45 MiB (1 instance)
NUMA:                    
  NUMA node(s):          1
  NUMA node0 CPU(s):     0-15
Vulnerabilities:         
  Gather data sampling:  Not affected
  Itlb multihit:         KVM: Mitigation: VMX unsupported
  L1tf:                  Mitigation; PTE Inversion
  Mds:                   Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown
  Meltdown:              Mitigation; PTI
  Mmio stale data:       Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown
  Retbleed:              Not affected
  Spec store bypass:     Vulnerable
  Spectre v1:            Mitigation; usercopy/swapgs barriers and __user pointer sanitization
  Spectre v2:            Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
  Srbds:                 Not affected
  Tsx async abort:       Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown

[althonos]

Hi @LotusIodid , was able to confirm the bug and trace it back in the Opal source code. Please install v0.4.2, it should work properly now that I have applied a patch.