It was not manually renamed.
The table name hstgrp was there.
I ran
rename table zabbix.hstgrp to groups;
and started the server again, now the database was correctly upgraded.
Old zabbix-server logs from when the upgrade went through:
22606:20180623:210318.055 Got signal [signal:15(SIGTERM),sender_pid:21699,sender_uid:0,reason:0]. Exiting ...
22606:20180623:210320.059 syncing history data...
22606:20180623:210320.077 syncing history data done
22606:20180623:210320.077 syncing trend data...
22606:20180623:210321.128 syncing trend data done
22606:20180623:210321.128 Zabbix Server stopped. Zabbix 4.0.0alpha6 (revision 80305).
21704:20180623:210321.194 Starting Zabbix Server. Zabbix 4.0.0alpha8 (revision 81985).
21704:20180623:210321.194 ****** Enabled features ******
21704:20180623:210321.194 SNMP monitoring: YES
21704:20180623:210321.194 IPMI monitoring: YES
21704:20180623:210321.194 Web monitoring: YES
21704:20180623:210321.194 VMware monitoring: YES
21704:20180623:210321.194 SMTP authentication: YES
21704:20180623:210321.194 Jabber notifications: YES
21704:20180623:210321.194 Ez Texting notifications: YES
21704:20180623:210321.194 ODBC: YES
21704:20180623:210321.194 SSH2 support: YES
21704:20180623:210321.194 IPv6 support: YES
21704:20180623:210321.194 TLS support: YES
21704:20180623:210321.194 ******************************
21704:20180623:210321.194 using configuration file: /etc/zabbix/zabbix_server.conf
21704:20180623:210321.238 current database version (mandatory/optional): 03050068/03050068
21704:20180623:210321.239 required mandatory version: 03050120
21704:20180623:210321.239 starting automatic database upgrade
21704:20180623:210321.242 completed 1% of database upgrade
21704:20180623:210321.254 completed 3% of database upgrade
21704:20180623:210321.256 completed 5% of database upgrade
21704:20180623:210321.259 completed 7% of database upgrade
21704:20180623:210321.262 completed 9% of database upgrade
21704:20180623:210321.268 completed 11% of database upgrade
21704:20180623:210321.287 completed 13% of database upgrade
21704:20180623:210321.290 completed 15% of database upgrade
21704:20180623:210321.297 completed 17% of database upgrade
21704:20180623:210321.299 completed 19% of database upgrade
21704:20180623:210321.301 completed 21% of database upgrade
21704:20180623:210321.302 completed 23% of database upgrade
21704:20180623:210321.305 completed 25% of database upgrade
21704:20180623:210321.401 [Z3005] query failed: [2002] Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2 "No such file or directory") [update dbversion set mandatory=3050082,optional=3050082]
21704:20180623:210321.401 [Z3001] connection to database 'zabbix' failed: [2002] Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2 "No such file or directory")
21704:20180623:210321.401 database is down: reconnecting in 10 seconds
21704:20180623:210331.405 database connection re-established
21704:20180623:210331.405 database upgrade failed
23397:20180623:210341.568 Starting Zabbix Server. Zabbix 4.0.0alpha8 (revision 81985).
23397:20180623:210341.568 ****** Enabled features ******
23397:20180623:210341.568 SNMP monitoring: YES
23397:20180623:210341.568 IPMI monitoring: YES
23397:20180623:210341.568 Web monitoring: YES
23397:20180623:210341.568 VMware monitoring: YES
23397:20180623:210341.568 SMTP authentication: YES
23397:20180623:210341.568 Jabber notifications: YES
23397:20180623:210341.568 Ez Texting notifications: YES
23397:20180623:210341.568 ODBC: YES
23397:20180623:210341.568 SSH2 support: YES
23397:20180623:210341.568 IPv6 support: YES
23397:20180623:210341.569 TLS support: YES
23397:20180623:210341.569 ******************************
23397:20180623:210341.569 using configuration file: /etc/zabbix/zabbix_server.conf
23397:20180623:210341.606 current database version (mandatory/optional): 03050081/03050081
23397:20180623:210341.607 required mandatory version: 03050120
23397:20180623:210341.607 starting automatic database upgrade
23397:20180623:210341.607 [Z3005] query failed: [1146] Table 'zabbix.groups' doesn't exist [alter table `groups` rename to `hstgrp`]
23397:20180623:210341.607 database upgrade failed
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