Open fo40225 opened 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.
-xCORE-AVX512
-march=x86-64-v4
-xCOMMON-AVX512
-march=common-avx512
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
Thank you for bringing this to our attention. Will look into it.
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