Query issues – how to diagnose?

I have a WordPress install on a dedicated server with decent memory (upwards of 8GB)

Since upgrading to 3.8, I started getting mysql disconnects/timeouts, better known as

MySQL server has gone away

I enabled error_log for a bit, i.e.

ini_set('log_errors',TRUE);
ini_set('error_reporting', E_ALL);
ini_set('error_log', dirname(__FILE__) . '/error_log.txt');

This resulted in an immense file – basically the error_log grows by about a GB every 4 minutes or so.

I AM caching queries

query_cache_type = 1
query_cache_limit = 8M
query_cache_size = 512M

I was able to temporarily fix the issue by setting
max_allowed_packet = 16M

Then I installed Debug Bar and checked queries on homepage. Debug Bar tells me there are 729 queries!

The slow ones are:

SELECT option_name, option_value FROM wp_options WHERE autoload = 'yes'
require(‘wp-blog-header.php’), require_once(‘wp-load.php’), require_once(‘wp-config.php’), require_once(‘wp-settings.php’), wp_not_installed, is_blog_installed, wp_load_alloptions #1
7.5ms

UPDATEwp_optionsSEToption_value...WHEREoption_name= 'wpseo_titles'
require(‘wp-blog-header.php’), require_once(‘wp-includes/template-loader.php’), include(‘/themes/weaver-ii-pro/page.php’), weaverii_get_header, get_header, locate_template, load_template, require_once(‘/themes/weaver-ii-pro/header.php’), wp_title, apply_filters(‘wp_title’), call_user_func_array, WPSEO_Frontend->title, apply_filters(‘wpseo_title’), call_user_func_array, WPSEO_Frontend->title_test_helper, update_option
55.0ms

UPDATEwp_optionsSEToption_value...WHEREoption_name= 'wpseo_titles'
require(‘wp-blog-header.php’), require_once(‘wp-includes/template-loader.php’), include(‘/themes/weaver-ii-pro/page.php’), weaverii_get_header, get_header, locate_template, load_template, require_once(‘/themes/weaver-ii-pro/header.php’), wp_head, do_action(‘wp_head’), call_user_func_array, Facebook_Open_Graph_Protocol::add_og_protocol, apply_filters(‘fb_meta_tags’), call_user_func_array, WPSEO_OpenGraph->facebook_filter, WPSEO_OpenGraph->og_title, WPSEO_Frontend->title, apply_filters(‘wpseo_title’), call_user_func_array, WPSEO_Frontend->title_test_helper, update_option
56.4ms

UPDATEwp_optionsSEToption_value...WHEREoption_name= 'wpseo_titles'
require(‘wp-blog-header.php’), require_once(‘wp-includes/template-loader.php’), include(‘/themes/weaver-ii-pro/page.php’), weaverii_get_footer, get_footer, locate_template, load_template, require_once(‘/themes/weaver-ii-pro/footer.php’), wp_footer, do_action(‘wp_footer’), call_user_func_array, WPSEO_Frontend->flush_cache, WPSEO_Frontend->title, apply_filters(‘wpseo_title’), call_user_func_array, WPSEO_Frontend->title_test_helper, update_option
56.0ms

SELECT option_value FROM wp_options WHERE option_name = 'dismissed_update_core' LIMIT 1
require(‘wp-blog-header.php’), require_once(‘wp-includes/template-loader.php’), include(‘/themes/weaver-ii-pro/page.php’), weaverii_get_footer, get_footer, locate_template, load_template, require_once(‘/themes/weaver-ii-pro/footer.php’), wp_footer, do_action(‘wp_footer’), call_user_func_array, wp_admin_bar_render, do_action_ref_array, call_user_func_array, wp_admin_bar_updates_menu, wp_get_update_data, get_core_updates, get_site_option, get_option
9.6ms

I do have lots (~50) plugins installed, and I use Weaver II Pro theme. Most of these plugins are essential to get what I need out of WordPress (I use WordPress as a CMS). This is a live install so I can’t really disable everything and then enable one by one to see what’s breaking things (if not core). Is there another way to figure out the problem by looking at the Debug Bar’s output?