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Mithras
02-Apr-2019, 08:45
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)


zcat AmP1_R1.fastq.gz | pigz -p 4 > out.fastq.gz

I get this error (5 out of 10 times):

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

Mithras
02-Apr-2019, 08:58
Wrong forum, its an SLES installation @mod could you please move the thread?