2014/12/06 12:27:13 [error] 12579#0: *513670 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 126.96.36.199, server: translatewiki.net, request: "GET /wiki/Special:AncientPages HTTP/1.1", upstream: "fastcgi://unix:/run/php5-fpm.sock", host: "translatewiki.net"
I have nginx upstream timeout set to 15 seconds. Curiously enough it does not show up as PHP fatal error. Looking with mytop the query takes about 50 seconds. The query should be faster or not enabled by default.