Thank you all for your answers. I am starting to believe more and more that this is somehow openVZ related. Maybe the hoster has implemented some CPU or RAM limits, since it was working for years before.
The problem is not related with some file, it happens with different directories, I tested that. in the index folder at the repo (new repo, no finished backup by now) is just one file with 6MB…
A run with strace ends like this:
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 2264378868
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=31478469}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=31510199}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=39790781}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=39823538}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=39857971}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=39888580}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=39929996}) = 0
ioctl(1, TIOCGWINSZ, {ws_row=51, ws_col=209, ws_xpixel=0, ws_ypixel=0}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=40013993}) = 0
ioctl(1, TIOCGPGRP, [26859]) = 0
getpgid(0) = 26859
[0:34] 9.72% 20980 files 4.896 GiB, total 456618 files 50.395 GiB, 0 errors ETA 5:21
) = 91
/home/mysql/mysql-bin.000013
) = 9
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=40247684}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=40278782}) = 0
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=42242818}) = 0
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 824672807784
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=61672326}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=61703598}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=77189311}) = 0 errors ETA 5:21
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=77224105}) = 0
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=94649638}) = 0
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=94761013}) = 0
NULL) = 074% 20980 files 4.909 GiB, total 456618 files 50.395 GiB, 0 errors ETA 5:21
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=98374199}) = 0
futex(0xc000200148, FUTEX_WAKE_PRIVATE, 1) = 1
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 824759794536
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=112170038}) = 0
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=112279719}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=112333121}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=112369207}) = 0
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---rs ETA 5:21
rt_sigreturn({mask=[]}) = 824759794536
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=127403710}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=127431483}) = 0
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 824759794536
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=146641822}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=146669763}) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=150385316}) = 0errors ETA 5:21
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=150414123}) = 0
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=159320107}) = 0
nanosleep({tv_sec=0, tv_nsec=3000}, NULL) = 0
--- SIGURG {si_signo=SIGURG, si_code=SI_TKILL, si_pid=26861, si_uid=0} ---
rt_sigreturn({mask=[]}) = 824637303656
clock_gettime(CLOCK_MONOTONIC, {tv_sec=159761, tv_nsec=174982104}) = 0errors ETA 5:21
futex(0x15a3ce8, FUTEX_WAIT_PRIVATE, 0, NULL) = ?
+++ killed by SIGKILL +++015
Killed
But who sends this SIGKILL? Can be only the OpenVZ host, no?
I will also ask the hoster if they updated something or implemented some limits.