fix intel compiler build break

[fo40225]

build environment

Ubuntu 18.04.6 LTS
gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
Intel(R) oneAPI DPC++/C++ Compiler 2022.2.0 (2022.2.0.20220730)
boost 1.58

run environment

hardware

2x Intel Xeon Gold 6342
2TB RAM (16x 128GB DDR4-3200)
4x 4TB PCI-E 4.0 NVME SSD RAID 0 (ref and input here)

system

Ubuntu 22.04.1 LTS

common options

--ref-load-hash-bin 1 --mmap-reference 1

data

board institute gatk bundle hg38 + using alt-masked bed file
inhouse wes 200x coverage 150bp paied-end

MAPPING/ALIGNING SUMMARY,,Total input reads,142688722,100.00
MAPPING/ALIGNING SUMMARY,,Number of duplicate marked reads,0,0.00
MAPPING/ALIGNING SUMMARY,,Number of duplicate marked and mate reads removed,0,0.00
MAPPING/ALIGNING SUMMARY,,Number of unique reads (excl. duplicate marked reads),142688722,100.00
MAPPING/ALIGNING SUMMARY,,Reads with mate sequenced,142688722,100.00
MAPPING/ALIGNING SUMMARY,,Reads without mate sequenced,0,0.00
MAPPING/ALIGNING SUMMARY,,QC-failed reads,0,0.00
MAPPING/ALIGNING SUMMARY,,Mapped reads,142533774,99.89
MAPPING/ALIGNING SUMMARY,,Mapped reads adjusted for filtered mapping,142533774,99.89
MAPPING/ALIGNING SUMMARY,,Mapped reads R1,71304146,99.94
MAPPING/ALIGNING SUMMARY,,Mapped reads R2,71229628,99.84
MAPPING/ALIGNING SUMMARY,,Number of unique & mapped reads (excl. duplicate marked reads),142533774,99.89
MAPPING/ALIGNING SUMMARY,,Unmapped reads,154948,0.11
MAPPING/ALIGNING SUMMARY,,Unmapped reads adjusted for filtered mapping,154948,0.11
MAPPING/ALIGNING SUMMARY,,Adjustment of reads matching non-reference decoys,0,0.00
MAPPING/ALIGNING SUMMARY,,Singleton reads (itself mapped; mate unmapped),110302,0.08
MAPPING/ALIGNING SUMMARY,,Paired reads (itself & mate mapped),142423472,99.81
MAPPING/ALIGNING SUMMARY,,Properly paired reads,141084044,98.88
MAPPING/ALIGNING SUMMARY,,Not properly paired reads (discordant),1339428,0.94
MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes,142423472,100.00
MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes (MAPQ>=10),133005934,93.39
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [40:inf),124162867,87.02
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [30:40),2394718,1.68
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [20:30),3708424,2.60
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [10:20),2812611,1.97
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [ 0:10),9455154,6.63
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ NA (Unmapped reads),154948,0.11
MAPPING/ALIGNING SUMMARY,,Reads with indel R1,857524,1.20
MAPPING/ALIGNING SUMMARY,,Reads with indel R2,871870,1.22
MAPPING/ALIGNING SUMMARY,,Total bases,21545997022
MAPPING/ALIGNING SUMMARY,,Total bases R1,10772998511
MAPPING/ALIGNING SUMMARY,,Total bases R2,10772998511
MAPPING/ALIGNING SUMMARY,,Mapped bases R1,10766926046
MAPPING/ALIGNING SUMMARY,,Mapped bases R2,10755673828
MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R1,773694088,7.19
MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R2,802316036,7.46
MAPPING/ALIGNING SUMMARY,,Mismatched bases R1,26865434,0.25
MAPPING/ALIGNING SUMMARY,,Mismatched bases R2,35386201,0.33
MAPPING/ALIGNING SUMMARY,,Mismatched bases R1 (excl. indels),24746504,0.23
MAPPING/ALIGNING SUMMARY,,Mismatched bases R2 (excl. indels),33232164,0.31
MAPPING/ALIGNING SUMMARY,,Q30 bases,19997458379,92.81
MAPPING/ALIGNING SUMMARY,,Q30 bases R1,10094153115,93.70
MAPPING/ALIGNING SUMMARY,,Q30 bases R2,9903305264,91.93
MAPPING/ALIGNING SUMMARY,,Total alignments,144115736
MAPPING/ALIGNING SUMMARY,,Secondary alignments,0
MAPPING/ALIGNING SUMMARY,,Supplementary (chimeric) alignments,1581962
MAPPING/ALIGNING SUMMARY,,Estimated read length,151.00

original 1.3.0

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],330.71
        User time (seconds): 32616.91
        System time (seconds): 132.32
        Percent of CPU this job got: 7580%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 7:12.02
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55974088
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 364
        Minor (reclaiming a frame) page faults: 58609499
        Voluntary context switches: 792066
        Involuntary context switches: 87493
        Swaps: 0
        File system inputs: 72
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

changed gcc opt options (sse2 only)

CPPFLAGS += -march=x86-64 -O3 -ftree-vectorize -fvect-cost-model=cheap 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],305.52
        User time (seconds): 37615.52
        System time (seconds): 126.13
        Percent of CPU this job got: 8078%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 7:47.21
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55965548
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 272
        Minor (reclaiming a frame) page faults: 57129594
        Voluntary context switches: 752958
        Involuntary context switches: 129579
        Swaps: 0
        File system inputs: 1064
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

icc skylake-avx512

CPPFLAGS += -xSKYLAKE-AVX512 -O3 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],356.07
        User time (seconds): 20044.17
        System time (seconds): 99.55
        Percent of CPU this job got: 5020%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 6:41.21
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55977116
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 462
        Minor (reclaiming a frame) page faults: 61073017
        Voluntary context switches: 1047728
        Involuntary context switches: 41240
        Swaps: 0
        File system inputs: 0
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

icc icelake-server

CPPFLAGS += -xICELAKE-SERVER -O3 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],353.45
        User time (seconds): 20134.72
        System time (seconds): 102.66
        Percent of CPU this job got: 5009%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 6:43.96
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55977712
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 202
        Minor (reclaiming a frame) page faults: 60891037
        Voluntary context switches: 1044493
        Involuntary context switches: 40804
        Swaps: 0
        File system inputs: 0
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0