В чём может быть причина:
root@host-88 ~ # service nginx reload
Error: Too many open files
root@host-88 /etc/nginx # nginx -v
nginx version: nginx/1.12.1
root@host-88 ~ # ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 256928
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 131070
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 256928
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
root@host-88 ~ # sysctl fs.file-nr
fs.file-nr = 26112 0 6562344
root@host-88 ~ # lsof | wc -l
149451