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Thread: Internal Threads Error - pigz

  1. #1

    Internal Threads Error - pigz

    Hey,

    I am expeting a very strange behavior on an HP ProLiant DL380 Gen10. I'm not sure if it is hardware or software related.

    When I use pigz (SLES default package) and specify the number of threads (4 in this example)

    Code:
    zcat AmP1_R1.fastq.gz | pigz -p 4 > out.fastq.gz
    I get this error (5 out of 10 times):
    Code:
    pigz: abort: internal threads error

    Strace says:

    write(1, "T\nTCACCGTGCCAGACTAGAGTCAAGCTCAAC"..., 32644) = 32644
    read(10, "\254Ml@\344\300\351;\216%\356\v\253Ce\26Q\306\250 \324\265\f\350\312\362\301 #F\353\313\341"..., 32768) = 32768
    pigz: abort: internal threads error
    write(1, "@NB551369:35:H3VGYBGX9:2:21304:1"..., 32768) = 32768
    write(1, "ATGCCTCGTCATCTAATTAGTGACGCGCATGA"..., 32638) = 32638
    write(1, "@NB551369:35:H3VGYBGX9:2:21304:1"..., 32768) = -1 EPIPE (Broken pipe)
    --- SIGPIPE {si_signo=SIGPIPE, si_code=SI_USER, si_pid=67738, si_uid=1030} ---
    rt_sigprocmask(SIG_BLOCK, [HUP INT PIPE TERM XCPU XFSZ], [HUP INT PIPE TERM XCPU XFSZ], 8) = 0
    rt_sigprocmask(SIG_SETMASK, [HUP INT PIPE TERM XCPU XFSZ], NULL, 8) = 0
    rt_sigaction(SIGPIPE, {sa_handler=SIG_DFL, sa_mask=[PIPE], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fb5a0713160}, {sa_handler=0x55bc0c4beb2c, sa_mask=[HUP INT PIPE TERM XCPU XFSZ], sa_flags=SA_RESTORER, sa_restorer=0x7fb5a0713160}, 8) = 0
    rt_sigprocmask(SIG_BLOCK, ~[RTMIN RT_1], [HUP INT PIPE TERM XCPU XFSZ], 8) = 0
    getpid() = 67738
    gettid() = 67738
    tgkill(67738, 67738, SIGPIPE) = 0
    rt_sigprocmask(SIG_SETMASK, [HUP INT PIPE TERM XCPU XFSZ], NULL, 8) = 0
    rt_sigreturn({mask=[]}) = -1 EPIPE (Broken pipe)
    --- SIGPIPE {si_signo=SIGPIPE, si_code=SI_TKILL, si_pid=67738, si_uid=1030} ---
    +++ killed by SIGPIPE +++

    If I dont specify the number of threads, it runs like a charm.
    Also a different zip-tool like pbzip2 doesn't have any problem at all.
    Prime95 runs without any problems for 24h, no bad sector detected, ram has been tested and is okay.

    Also, on another server (same Software and OS - different hardware), there is no problem at all.

    Anyone has a clue about this issue?

    I also opend an issue for this problem at Github itself:

    https://github.com/madler/pigz/issues/68

    Thanks

  2. #2

    Re: Internal Threads Error - pigz

    Wrong forum, its an SLES installation @mod could you please move the thread?

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