Super Slow WP Site and High CPU Usage - How to Fix and possible to redo everything from scratch?

16 replies
Hi folks, need your guidance, I hope it's not too much of a trouble.

My site (David Simple Photography - Simple Flash Photography Tips, Beginner's Lessons, all Free! - non-IM related) has been experiencing CPU Throttling penalties for quite some time. To the point that bluehost shuts down my site once in a while as my site's server load is affecting the other sites, according to them.

One of the most obvious problems may be plug-ins, so I turned off and deleted quite a few of them and saw some improvements in terms of CPU Throttle stats the past few hours (used to be 800sec-4000sec per HOUR last night to this morning - note, I'm in Asia), then after I removed like 5-6 plugins, mostly social sharing, related post/linkwithin, ppinger, cloudflare, etc. The CPU Throttling report on BH dropped to between 300-800 sec. per hour.

The site's still quite slow according to Google Site Speed (new Analytics).

- Nissin Di622 Review page logged in 352.72 average load time (11 views)
- Flash Buying Guide is next at 151.31 average (3 page views)

The rest drops gradually from 80 to 8 sec rather quickly after those two pages.

Some site info:

- Hosted on Bluehost
- Latest WP install with a custom theme made by a friend
- Site is >2years old, about 100+ posts and articles.
- Current loaded/active plug-ins: All In One Webmaster, Amazon Localizer, cbnet Ping Optimizer, Dean's Permalinks Migration, Easy Privacy Policy, FeedBurner FeedSmith, Force gzip (newly installed this morning), Google Analyticator, Google XML Sitemap, Growmap Anti Spambot Plugin, IntenseDebate, JavaScript to Footer, Jetpack Lite, NextGEN Gallery, Onswipe, Pingler, Pretty Link Lite, SEO Ultimate, TinyMCE Advanced, TOC For Wordpress, Vibe SEO Pack, W3 Total Cache, WP-Optimize, WP tags to Technorati.
- Site average stats: 29K Visits/Mo, 24K Unique, 44K Pageviews, 2:16 Ave Visit.

My other sites (much smaller sites, some are niche sites) don't have a problem with load time, they pretty much load between 2-10sec depending on image load).
_
My Questions

- Based on those info above (I know they're not much), can you pinpoint what the problems may be?
- If not, is it possible to start from scratch (clean WP install, clean DB, use a standard theme for test) without losing posts and comments? Will the problems just repeat itself when I restore the DB?
- If that's not possible or too complex, what's your best suggestion on tracing the root cause and how do I track site performance?

I apologize if my questions aren't that techy. I know very little about PHP and databases, but I do pick things up quickly if they're not too complex.

Hope you can help me out. Thanks.
#cpu #fix #high #redo #scratch #site #slow #super #usage
  • Profile picture of the author Jonas B
    What you can do is disable most of the plugins (so only the essential ones should be enabled) and see if it helps.. because one bad plugin can make it worse for others..

    As you have the latest version, a plugin can be the only problem imo.
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  • Profile picture of the author ernestrategos
    Check yoast dot com website,while in there search the word optimizing.

    You could have a plugin with many non cached queries amongst other things, there are plugins so you can diagnose what's going on, make some coffee, you will take some time for sure, but I know you'll succeed, blessings.
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  • Profile picture of the author SteveJohnson
    I can't even view the site, it times out.

    It's virtually impossible to troubleshoot this from a distance, but here's where to start: make sure you're at the latest WP version (3.2.1 at the moment). Revert to the twentyten or twentyeleven theme that comes packaged with WP, and deactivate ALL of your plugins.

    If you don't see a dramatic improvement, you'll need to have someone who's knowledgeable in WP look into it further.
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  • Profile picture of the author davidtong
    Hi guys, thanks

    Here's an update:

    According to Bluehost, our entire server has been getting DDOS attacks, so they moved our sites temporarily to a dedicated host until it gets sorted out.

    However, my account is still getting CPU Throttled and they gave me a whole list of things to check.

    I tried turning off all the plug-ins and used PluginHogDetector to track the total time it takes to load the site.

    The main 2 plug-ins that causes the site to slow down were Nextgen gallery, Pretty Links and the older Feedsmith plug-ins. But not significantly, the entire loading time was still under 5 secs.

    I'm thinking it's no longer a plug-in issue and maybe a bad database or something (query stuff, which I have no clue on)?

    It seems like BH is seeing something wrong with my main site and throttling things... My other sites (shared with the same account) are totally fine. It's this large site that has the problem.

    I thought about moving my main 'money' site to another hosting account just so it won't affect all my other sites, but before doing so, I think I need to rule out it's not my DB/WP/Theme/Plugin that are f-in things up.

    When I run a check on my site in Woorank, it says the site loads in between 1.9-2.5sec (homepage), that sounds OK to me...

    But why is the site getting up to 2000 sec of CPU throttling at any given point? The past 30mins alone, CPU Throttling stats is showing 60-sec throttles every minute.

    Oh lastly, do you guys know anybody doing such kind of troubleshooting service and how much?
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  • Profile picture of the author davidtong
    BTW, here's what BH support gave me... I honestly haven't reached the DB section of their recommended links...

    We setup your site on a dedicated IP address temporarily so it can avoid almost all, if not all, of the problems that might affect it from the DDoS.

    PHPMyAdmin appears to be working properly. If you are still having problems with it, try resetting your MySQL password, then use your cPanel username and the newly-set MySQL password to log into it.

    Make sure you are using correct settings to access your FTP and email accounts. Both are working properly. If your settings are correct, it should work for you too. Keep in mind that you cannot use the IP address nor can you use box447.bluehost.com in your settings because of the DDoS. Your settings will have to use davidleetong.com or mail.davidleetong.com for now. This also means that, if you are using SSL in your mail settings, you may need to turn it off for the time being.

    If it is a server issue, your other sites will also be affected, but if your main site is the most active site, it is more likely that it will be the first one to notice the problems because it's trying to use more resources than the others.

    I also notice that the account has been throttled from time to time.
    Some things that can contribute to this are: page size, how much content is on a single page and how much data it has to load on that page, image size/resolution, video/audio/media size. Database size, database optimization, long queries, erroneous queries, non-cached sites, broken scripts, and much more.

    See also: https://www.bluehost.com/cgi/help/000564

    The following articles will help you work through many of these issues.
    Web Page Analyzer - free website optimization tool website speed test check website performance report from web site optimization (This site will analyze your pages and see if they are built to load quickly based only on content)
    Reducing CPU Usage and Speeding Load Time | WordPress Guides and Stuff (This site deals specifically with WordPress optimization, but covers areas that will work for a vast majority of other sites/software as well)
    Gain Valuable SEO Power with Caching by Christopher Ross (Caching optimization)
    Minimize round-trip times (This site deals with changing where JavaScript gets sourced)
    Optimizing MySQL: Queries and Indexes — DatabaseJournal.com (This site, all 4 pages, deal with database optimization)
    https://www.bluehost.com/cgi/help/000496 (This deals with a very simple repair/optimization on your databases)

    Those should be able to help you in optimizing your sites.
    Thank you,
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  • Profile picture of the author hitmobi
    I'm pretty sure it's not the whole problem but something weird is going on with your scripts.

    It says jquery is not defined for this little weird piece of code:

    "}).call(this, evt); } } } })</script>"

    Broken scripts can influence the speed.
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  • Profile picture of the author davidtong
    Hitmobi: Where do you see that and honestly, I have no clue where to start.

    I'll redo your suggestions, turn every plug-in off, switch to basic theme and let it be for a few days.

    I'll get back to you guys.
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  • Profile picture of the author davidtong
    Update, turned off everything (plugins) other than Ultimate SEO and Analytics, reverted back to twenty eleven the past 8hrs...

    No diff, the CPU Throttle stats are still 900sec/min the past 12hrs...

    It seems to be a DB issue. BH also said my htaccess was too big (11K)...

    I checked the tables for my site, there are a lot of items there that remain (mostly from plug-ins I tried then uninstalled in the past), is there a way to get rid of them?

    Is it OK that my wp_options is 2.9MB?

    Stumped on detecting which item is causing high CPU usage when all plug-ins are already off.
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  • Profile picture of the author davidtong
    Tons of errors in the log file as well...

    MAIN error_log:
    [Sun Oct 09 21:21:23 2011] [error] [client 67.195.115.163] Premature end of script headers: viewtopic.php
    [Sun Oct 09 21:21:23 2011] [error] [client 67.195.112.121] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed
    [Sun Oct 09 21:21:25 2011] [error] [client 173.70.69.126] Premature end of script headers: index.php, referer: *New Jersey Collaborating Center for Nursing - Thinking About Nursing School?
    [Sun Oct 09 21:21:26 2011] [error] [client 66.249.67.72] Premature end of script headers: index.php
    [Sun Oct 09 21:21:27 2011] [error] [client 66.249.71.137] Premature end of script headers: index.php
    [Sun Oct 09 21:21:27 2011] [error] [client 66.249.67.195] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed
    [Sun Oct 09 21:21:28 2011] [error] [client 66.249.68.144] Premature end of script headers: viewtopic.php
    [Sun Oct 09 21:21:29 2011] [error] [client 98.114.38.199] Premature end of script headers: index.php
    [Sun Oct 09 21:21:30 2011] [error] [client 141.0.8.230] Premature end of script headers: index.php
    [Sun Oct 09 21:21:32 2011] [error] [client 66.249.68.51] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed
    [Sun Oct 09 21:21:32 2011] [error] [client 220.181.94.237] Premature end of script headers: viewtopic.php
    [Sun Oct 09 21:21:32 2011] [error] [client 173.254.122.166] Script timed out before returning headers: karma_storyqueue.php
    (more of those actually)

    PHP error_log:

    [16-Jul-2011 15:28:00] WordPress database error Table 'davidlee_reviews.wp_ezinearticles' doesn't exist for query SELECT * FROM `wp_ezinearticles` made by activate_plugin, do_action, call_user_func_array, wp_ezinearticles_install, W3_Db->query
    [21-Jul-2011 06:40:33] PHP Warning: Cannot modify header information - headers already sent by (output started at /home2/davidlee/public_html/main/wp-content/plugins/rel-nofollow-for-tags-in-posts-and-pages/add-nofollow.php:2189) in /home2/davidlee/public_html/main/wp-includes/pluggable.php on line 934
    [21-Jul-2011 06:40:34] PHP Warning: Cannot modify header information - headers already sent by (output started at /home2/davidlee/public_html/main/wp-content/plugins/rel-nofollow-for-tags-in-posts-and-pages/add-nofollow.php:2189) in /home2/davidlee/public_html/main/wp-includes/pluggable.php on line 934
    [21-Jul-2011 06:43:39] PHP Warning: Cannot modify header information - headers already sent by (output started at /home2/davidlee/public_html/main/wp-content/plugins/rel-nofollow-for-tags-in-posts-and-pages/add-nofollow.php:2189) in /home2/davidlee/public_html/main/wp-includes/pluggable.php on line 934
    [21-Jul-2011 06:43:39] PHP Warning: Cannot modify header information - headers already sent by (output started at /home2/davidlee/public_html/main/wp-content/plugins/rel-nofollow-for-tags-in-posts-and-pages/add-nofollow.php:2189) in /home2/davidlee/public_html/main/wp-includes/pluggable.php on line 934
    [03-Aug-2011 10:56:17] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 288
    [04-Aug-2011 23:36:20] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 288
    [06-Aug-2011 07:36:08] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 288
    [19-Aug-2011 19:38:27] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [22-Aug-2011 17:08:29] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [28-Aug-2011 23:02:54] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [01-Sep-2011 02:48:12] WordPress database error Table 'davidlee_reviews.wp_sds_hits' doesn't exist for query SELECT * FROM wp_sds_hits WHERE status_code=404 AND redirect_url='' AND url NOT LIKE '%/favicon.ico' ORDER BY id DESC made by require_once, require_once, require_once, require_once, do_action, call_user_func_array, SEO_Ultimate->init, SU_FofsLog->upgrade, W3_Db->query
    [01-Sep-2011 21:28:09] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [04-Sep-2011 14:50:26] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [04-Sep-2011 20:45:23] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [12-Sep-2011 21:41:17] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [14-Sep-2011 03:09:41] PHP Warning: Division by zero in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 20
    [14-Sep-2011 03:10:49] PHP Warning: Division by zero in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 20
    [19-Sep-2011 05:48:23] PHP Warning: Division by zero in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 20
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 18
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 44
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 54
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 72
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 80
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 88
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 96
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 104
    [20-Sep-2011 15:01:10] PHP Warning: preg_match_all() [<a href='function.preg-match-all'>function.preg-match-all</a>]: Unknown modifier '2' in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 112
    [02-Oct-2011 04:23:13] PHP Fatal error: Call to a member function get_permalink() on a non-object in /home2/davidlee/public_html/main/wp-content/plugins/nextgen-gallery/nggfunctions.php on line 289
    [03-Oct-2011 14:11:55] PHP Warning: Division by zero in /home2/davidlee/public_html/main/wp-content/plugins/vibe-seo-pack/lib/post-audit.php on line 20

    /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/error_log:
    [26-Jul-2011 02:18:54] PHP Warning: require_once(ABSPATHWPINC/class-feed.php) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [26-Jul-2011 02:18:54] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'ABSPATHWPINC/class-feed.php' (include_path='.:/usr/lib64/php:/usr/lib/php:/usr/share/pear') in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [29-Jul-2011 04:19:32] PHP Warning: require_once(ABSPATHWPINC/class-feed.php) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [29-Jul-2011 04:19:32] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'ABSPATHWPINC/class-feed.php' (include_path='.:/usr/lib64/php:/usr/lib/php:/usr/share/pear') in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [01-Aug-2011 08:42:36] PHP Warning: require_once(ABSPATHWPINC/class-feed.php) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [01-Aug-2011 08:42:36] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'ABSPATHWPINC/class-feed.php' (include_path='.:/usr/lib64/php:/usr/lib/php:/usr/share/pear') in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [01-Aug-2011 21:10:29] PHP Fatal error: Class 'WP_Widget' not found in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/google-analytics-stats-widget.php on line 9
    [01-Aug-2011 23:52:59] PHP Fatal error: Call to undefined function add_option() in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/google-analyticator.php on line 52
    [04-Aug-2011 02:14:16] PHP Warning: require_once(ABSPATHWPINC/class-feed.php) [<a href='function.require-once'>function.require-once</a>]: failed to open stream: No such file or directory in /home2/davidlee/public_html/main/wp-content/plugins/google-analyticator/class.analytics.stats.php on line 5
    [04-Aug-2011 02:14:16] PHP Fatal error: require_once() [<a href='function.require'>function.require</a>]: Failed opening required 'ABSPATHWPINC/class-feed.php' (includ
    it's like practically all my plug-ins have error logs.

    How do I get back to a clean slate without losing my content and stuff?
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  • Profile picture of the author hitmobi
    hey!

    You have the same problem as this guy:
    Javascript errors from Google Adsense - Stack Overflow

    I don't know if this is the only problem but it sure is a part of it.
    I'm not sure what is causing this problem. Did you do something with google ads and after that the site slowed down?

    EDIT: i might be steering you in a wrong direction here. This could be caused by just a script error.

    EDIT: Ok i know what your problem here is:
    You have included jQuery on line 545.
    However there's a script way before that tries to use jquery
    This script starts on line 105:
    <script type="text/javascript">
    jQuery.noConflict();
    jQuery(document).ready(function($) {
    $(document).ready(function(){
    var smp_cookie_name_a = 'smp_1309861662264_a';//1
    var smp_cookie_name_b = 'smp_1309861662264_b';//2
    var smp_cookie_num_visits = 1;
    var smp_show_mode = 2;
    function smp_show_popup(){
    setTimeout(function() { $.fn.colorbox({
    width:"550px",
    height:"300px",
    iframe:true,
    opacity:0.25,
    speed:500,
    overlayClose:true,
    href:'/smp_popup.html'})
    },
    3500);
    }
    function smp_reset_cookies(){
    c_value_a = $.cookie(smp_cookie_name_a);
    c_value_b = $.cookie(smp_cookie_name_b);
    if (smp_show_mode == 1 && c_value_b != null){
    $.cookie(smp_cookie_name_b, null, { path: '/', expires: 0 });
    return true;
    } else if (smp_show_mode == 2 && c_value_a != null){
    $.cookie(smp_cookie_name_a, null, { path: '/', expires: 0 });
    return true;
    } else {
    return false;
    }
    }
    $(document).ready(function(){
    var date = new Date();
    if (!smp_reset_cookies()){
    c_value_a = $.cookie(smp_cookie_name_a);
    c_value_b = $.cookie(smp_cookie_name_b);
    if (smp_show_mode == 1){
    date.setTime(date.getTime() + (120 * 24 * 60 * 60 * 1000));
    c_value = c_value_a;
    smp_cookie_name = smp_cookie_name_a;
    } else if (smp_show_mode == 2){
    date.setTime(date.getTime() + (100000 * 24 * 60 * 60 * 1000));
    c_value = c_value_b;
    smp_cookie_name = smp_cookie_name_b;
    }
    if (c_value == null){
    $.cookie(smp_cookie_name, '0', { path: '/', expires: date });
    smp_show_popup();
    } else {
    //cookie exists
    if (smp_show_mode == 2){
    date.setTime(date.getTime() + (100000 * 24 * 60 * 60 * 1000));
    c_value++;
    $.cookie(smp_cookie_name, c_value, { path: '/', expires: date });
    if (c_value < smp_cookie_num_visits){
    smp_show_popup();
    }
    }
    }
    }
    });
    });
    });
    </script>
    You need to include jquery in your header.
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  • Profile picture of the author Ken Durham
    Looks like some path problems among other things. I think your error log is telling you a lot. Keep in mind that just one error can cascade into many other errors.
    The easy way would be to do a clean install and then import just the main WP tables.
    Clean up any configuration data that doesn't belong and then start adding your plugins slowly, with extreme prejudice. Just because it sounds good doesn't mean it is good. If you want to try out different plugins then set up a development install in a different directory and different DB. This is where you play with and test plugins, on your development site, not on your production site
    Signature

    yes, I am....

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  • Profile picture of the author davidtong
    Sorry I'm not a programmer, may I know what to add to my header (jquery-wise).

    I'll try to slowly sniff out other issues. It seems like many of them are caused by old, deactivated, uninstalled plug-ins. Is there a way to clean them out from my site and database?

    I've already migrated to a new server with a new WP installation (but of course, imported content from old DB).
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  • Profile picture of the author verilix
    Have you tried using something like WP Super Cache? It dropped my load times from 15 seconds to about 6-8 seconds.
    Signature
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  • Profile picture of the author davidtong
    Yup, it's running super cache for the past few years now...
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  • Profile picture of the author SupporTech
    Please try to locate this error logs cuz sometimes it is the culprit, the script is keep on running at the back while it has no use!
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