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bwa-mem2 / mm2-fast

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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Segmentation fault (core dumped) Intel(R) oneAPI DPC++/C++ Compiler 2023.0.0 (2023.0.0.20221201) #11

Open fo40225 opened 9 months ago

fo40225 commented 9 months ago

If -xCORE-AVX512 or -march=x86-64-v4 is used, it crashes. However, when using -xCOMMON-AVX512 or -march=common-avx512, it runs normally.

The minimum reproducible input file has been attached for your reference.

mm2_bug.fastq.gz

$ objdump -s --section .comment minimap2

minimap2:     file format elf64-x86-64

Contents of section .comment:
 0000 496e7465 6c285229 206f6e65 41504920  Intel(R) oneAPI
 0010 4450432b 2b2f432b 2b20436f 6d70696c  DPC++/C++ Compil
 0020 65722032 3032332e 302e3020 28323032  er 2023.0.0 (202
 0030 332e302e 302e3230 32323131 31362900  3.0.0.20221116).
 0040 496e7465 6c285229 206f6e65 41504920  Intel(R) oneAPI
 0050 4450432b 2b2f432b 2b20436f 6d70696c  DPC++/C++ Compil
 0060 65722032 3032332e 302e3020 28323032  er 2023.0.0 (202
 0070 332e302e 302e3230 32323132 30312900  3.0.0.20221201).
 0080 00474343 3a202855 62756e74 7520352e  .GCC: (Ubuntu 5.
 0090 342e302d 36756275 6e747531 7e31362e  4.0-6ubuntu1~16.
 00a0 30342e31 32292035 2e342e30 20323031  04.12) 5.4.0 201
 00b0 36303630 39004c69 6e6b6572 3a204c4c  60609.Linker: LL
 00c0 44203136 2e302e30 00                 D 16.0.0.
$ lscpu
Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
CPU(s):              80
On-line CPU(s) list: 0-79
Thread(s) per core:  2
Core(s) per socket:  20
Socket(s):           2
NUMA node(s):        2
Vendor ID:           GenuineIntel
CPU family:          6
Model:               85
Model name:          Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping:            4
CPU MHz:             1000.439
CPU max MHz:         3700.0000
CPU min MHz:         1000.0000
BogoMIPS:            4800.00
Virtualization:      VT-x
L1d cache:           32K
L1i cache:           32K
L2 cache:            1024K
L3 cache:            28160K
NUMA node0 CPU(s):   0-19,40-59
NUMA node1 CPU(s):   20-39,60-79
Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities
sanchit-misra commented 9 months ago

Thank you for bringing this to our attention. Will look into it.