It seems to be https://tools.wmflabs.org/locator-tool/ but that is not to blame. A single application should not overload the databases- last time that happened, on wikidata, it brought down all wikis.
{
"_index": "logstash-2018.06.06",
"_type": "mediawiki",
"_id": "AWPUJyIoVAdyMbafYwpw",
"_version": 1,
"_score": null,
"_source": {
"server": "commons.wikimedia.org",
"db_server": "10.64.0.93",
"wiki": "commonswiki",
"channel": "DBQuery",
"type": "mediawiki",
"error": "Read timeout is reached (10.64.0.93)",
"http_method": "POST",
"@version": 1,
"host": "mw1224",
"shard": "s4",
"sql1line": "SELECT gt_id,gt_page_id,gt_lat,gt_lon,gt_primary,gt_globe,gt_type,gt_name FROM `geo_tags` WHERE gt_page_id IN ('47481531','47481533','47481535','47481536','47481539','47481541','47481549','47481552','47481553','47481557','47481559','47481560','47481563','47395115','47395117','47395120','47395122','47395123','47395124','47395125','47395127','47395133','47395134','47395137','47395138','47395139','47395140','47395141','47395142','47395145','47395146','47395147','47395149','47395154','47395156','47395157','47395158','47395160','47395162','47395163','47481566','47481570','47481572','47481575','47481577','47395116','47481578','47481581','47481583','47481586') AND (gt_page_id > 47481563 OR ( gt_page_id = 47481563 AND gt_id >= 185145944 )) ORDER BY gt_page_id,gt_id LIMIT 11 ",
"fname": "GeoData\\ApiQueryCoordinates::execute",
"errno": 2062,
"unique_id": "WxeXGApAMDsAAJcQ6fwAAACK",
"method": "Wikimedia\\Rdbms\\Database::makeQueryException",
"level": "ERROR",
"ip": "10.64.0.104",
"mwversion": "1.32.0-wmf.6",
"message": "GeoData\\ApiQueryCoordinates::execute\t10.64.0.93\t2062\tRead timeout is reached (10.64.0.93)\tSELECT gt_id,gt_page_id,gt_lat,gt_lon,gt_primary,gt_globe,gt_type,gt_name FROM `geo_tags` WHERE gt_page_id IN ('47481531','47481533','47481535','47481536','47481539','47481541','47481549','47481552','47481553','47481557','47481559','47481560','47481563','47395115','47395117','47395120','47395122','47395123','47395124','47395125','47395127','47395133','47395134','47395137','47395138','47395139','47395140','47395141','47395142','47395145','47395146','47395147','47395149','47395154','47395156','47395157','47395158','47395160','47395162','47395163','47481566','47481570','47481572','47481575','47481577','47395116','47481578','47481581','47481583','47481586') AND (gt_page_id > 47481563 OR ( gt_page_id = 47481563 AND gt_id >= 185145944 )) ORDER BY gt_page_id,gt_id LIMIT 11 ",
"normalized_message": "{fname}\t{db_server}\t{errno}\t{error}\t{sql1line}",
"url": "/w/api.php?action=query&format=json&origin=*",
"tags": [
"syslog",
"es",
"es"
],
"reqId": "WxeXGApAMDsAAJcQ6fwAAACK",
"referrer": "https://tools.wmflabs.org/locator-tool/",
"@timestamp": "2018-06-06T08:12:04.000Z",
"db_name": "commonswiki",
"db_user": "wikiuser"
},
"fields": {
"@timestamp": [
1528272724000
]
},
"sort": [
1528272724000
]
}