must be because of https://github.com/piwik/piwik/blob/master/plugins/PDFReports/PDFReports.php#L45

can you try disabling the pdf report plugin ?

Yes this is probably the cause, however this should only be triggered via the browser if you did not enable cron archiving.
Are you using Cron archiving and did you disable 'trigger archiving via browser' in the admin setings?

Also reading the code runScheduledTasks() it is designe to run once maximum in parallel, but maybe it fails to ensure this condition.

Julien, if you want to replicate, you can use the script in misc/test_cookies_GenerateHundredsWebsitesAndVisits.php to generate thousands of websites and replicate the issue.

Thanks, disabling the PDF report plugin indeed solves the issue.

I am not using cron archiving because it's too slow, unfortunately (we're processing a huge number of requests every day, and even a 8-core dedicated server with SSD can't cope with that). Since many of our Piwik users never login to Piwik, triggering archiving via the browser avoids archiving all the sites whose statistics are never viewed.

I'll probably write a Piwik plugin that stores the date of the last visit for each user, and use that information to run archiving via cron only for users that have login recently.

casting a vote for implementing suggested solution in 1836#comment:7 :

It is not the best performance wise (each call to runTasks() will result in selecting all websites and comparing all timezones), but it will work fine. To make it fast for a Piwik server with thousands of websites, we could for example record, on each website update, the earliest and latest timezone available in the _option table (but this will be a feature request when we hit problems, not yet the case :)

Cyril can you please contact me by email, maybe I can use your dataset for performance testing and improving Archiving speed.

OK.

(In [3684]) fixes #1981, adding getUniqueSiteTimezones to SitesManager API