Several times a day, all sites on the server freeze. Only init 6 helps. What could be the problem?

Question

linux

Good afternoon. For several days now, a strange problem has been manifesting on the server - all sites freeze completely and only init 6 saves. In htop, the processor load drops to almost 0. iotop also shows almost zero. iftop - similar.

nothing in apache logs. in nginx logs:
In nginx 229892 upstream timed out (110: Connection timed out) while connecting to upstream, client

Everything works in the apache + nginx bundle.

Apache and nginx restart does not help. after their restart, only 1-2 seconds the pages open, then everything freezes again.

The system is Ubuntu 16.04.
Apache/2.4.18 (Ubuntu)
nginx version: nginx/1.12.2

A couple of days ago, some kind of Monero miner virus started up. was launched from the /tmp directory and loaded the percent by 100%. I don’t know if this is related to this or not, but I saw the virus only twice. and sites fall off every 5 hours.

whence the virus is started - too did not find out.

Answer 1

reinstall the server from scratch
if you do not know how and where the virus came from, there is no point in looking for malfunctions in Apache, your system is already completely compromised

Answer 2

You have a completely compromised server, you need to demolish everything and install from scratch

Answer 3

Look at outgoing connections, maybe they are blocking connections to Apache (netstat -anp|grep tcp|grep apache2)
The fact that something was launched in the / tmp folder does not mean at all that the server was hacked (a separate CMS or script could be hacked) , sense to rearrange the server - is not present.
It is better to turn to groping people (especially at the time of the manifestation of the problem), such errors are quickly fixed with sufficient experience.