wav3front Updates within the panel would more likely change the vhost cofigs. Its updating the enhance panel version that will cause docker OLS to update thereby rendering your webconsole settings undone.

I've not seen this as an issue on a variety of VPS - > Dedi's what's your setup as maybe there's an IO Wait issue somewhere?

and what are the server specs?

wav3front OK, at least you've tried to tune it for more throughput. What about DB slow queries? Is it a WP site? A 1 minute pause is pretty significant, bad plugin maybe?

Honestly I am not sure what else to suggest.

wav3front I am personally thinking DB, so maybe have a look here. Although I wouldn't rule out php workers entirely.

wav3front

Do you notice any 500 or 503 errors when seeing these deadlock messages?

Do you have any package restrictions for resources at all? If so what about setting up a separate package with no restrictions and seeing if one of these sites still has issues? possible nproc or io issue? I used to see cpu spikes with some restrictions on.

As for OLS have you looked at initTimeout, pcKeepAliveTimeout?

Tried xdebug or deep php logging could it be a poorly formatted php script causing infinite loops, or some really long running threads... have you tried opening up the timeout for PHP execution to something un-godly to see if you can catch something in htop?

Is it even possible to put these sites, or even one site on a seperate server, such that you can set some wild settings to see? try alternative web servers just incase.

Do you have this or see anything in it? /usr/local/lsws/logs/stderr.log

wav3front If it's so old and came from MySQL 5.x What's the table type? MyISAM? InnoDB took over as the default table of choice, surely MariaDB would of complained a bit. What's the collation it's using. Is there anyway of checking and spinning off a clone to play with these, if they're even applicable?

initTimeout is under: External App > SAPI > lsphp: Initial Request Timeout (secs)

In same area there is Connection Keep-Alive Timeout

He had his under this wsgiDefaults config setting, but that's not as relevent within webconfig as there rails/python/node, you're needing PHP only.

I was reading through this post: here

There was also mention of zlib setting, but I don't think it's that, but you might as well try... what version of your server are you on, as my current default is 1.7.19 and 1.8.2 is available. There's another post on here about updating the OLS webserver. It's possible there's been fixes since then as people was complaining about this as late as 1.7.12 in that post.

Might be worth switching that site on to a server you can switch to apache, if the issue goes away, it's OLS, if it doesn't then it's something else, either likely php or db.

Another thing might be to temporary use netdata, since you can look through the metrics and correlate with pauses and try drill down to any iowaits or cpu spikes. That said some are concerned removing it doesn't clean up properly, so again might be something to do on a different server. I had some horrible CPU spikes and didn't know what was causing them until I saw which client php process was with netdata... you already know what client is the issue, but it might give more detail across the board to review.

Does this only affect this site, or does the pauses effect other sites at the same time?

Also have you given this a try? enhance php strace it talks looking for hangs.

Beyond this all I can think of is something like newrelic or php Xray? (not used it but might help you get vision on what's happening) I've setup Xdebug in the past for looking into why LSWS was failing on long executions when I configured the server to allow them. It helped but it's a pain to setup and it was my own code I was working on.

If you've got PHP pretty much set to what it was prior to moving the site, then it really could be something with Mariadb.

I know you said you'd used slow query but what about:
Try Configure Long Query Time: Define the time threshold for a query to be considered “slow”. You can set the long_query_time system variable to a value in seconds (e.g., 5 seconds). For MariaDB 10.11 and later, use log_slow_query_time instead.
SET GLOBAL long_query_time = 5; // or SET GLOBAL log_slow_query_time = 5;

and set it to like 45second, so you can isolate them long pauses and try see if it's caused by DB, if not, then must be PHP loop/ poor execution. Likewise what if you set the php execution down to say 20seconds, can you break the site instead of it hanging?

I think your at the stage of trying to isolate the what and where rather than the how. Fingers crossed for you!