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PHP-FPM CPU Pinned at 100% for hours

Discussion in 'Nginx, PHP-FPM & MariaDB MySQL' started by moshbit, May 14, 2020.

  1. moshbit

    moshbit Member

    53
    10
    8
    Jun 15, 2014
    Ratings:
    +13
    Local Time:
    12:19 PM
    1.15.0
    MariaDB 10.1.33
    First off, apologies if this is not the correct area for posting this, feel free to move it if necessary.

    Please fill in any relevant information that applies to you:
    • CentOS Version: CentOS 7.6 64bit
    • Centmin Mod Version Installed: 123.09beta01
    • Nginx Version Installed: nginx/1.17.10 (180420-034515-centos7-kvm-5cd76ab)
    • PHP Version Installed:

      PHP 7.4.5 (cli) (built: May 12 2020 18:54:55) ( NTS )
      Copyright (c) The PHP Group
      Zend Engine v3.4.0, Copyright (c) Zend Technologies

    • MariaDB MySQL Version Installed: Server version: 10.3.22-MariaDB MariaDB Server
    • When was last time updated Centmin Mod code base ? : 24 hours ago
    • Persistent Config:
    Code:
    MARCH_TARGETNATIVE='n'
    LETSENCRYPT_DETECT='y'
    I was running about 5 WP sites each on their own VPS droplet on Digital Ocean but recently combined them into one VPS and doubled the CPU/Ram/Storage (Intel(R) Xeon(R) Gold 6140 CPU 2 cores, 8gb ram, 50gb ssd). I also upgraded to php 7.4.5 from 7.3 a few days ago, but this issue predates that upgrade (i.e. 100% cpu usage) by a few days.

    I've looked at glances and top and see that there are 3 or so processes from php-fpm: pool www that seem to be taking up most of the CPU processes, but I don't know how to analyze further than this to find out which script is causing the issue.

    The only other change I've made is max_children set to 30, the error log was still coming up saying it was hitting that limit every once in a while so i set it to it's current 40.

    What can I do to find out which script is causing all this CPU usage?
     
  2. eva2000

    eva2000 Administrator Staff Member

    44,163
    10,066
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +15,556
    Local Time:
    5:19 AM
    Nginx 1.17.x
    MariaDB 5.5/10.x
    Raising php max children probably increased your cpu load, you need to make sure you have enough cpu cores to handle your PHP-FPM usage requirements. Your php issues most likely are partially due to PHP-FPM needing tuning. So best to start read thoroughly the guide at PHP-FPM - How to troubleshoot & optimize PHP-FPM server? :)

    Also DigitalOcean VPS servers I have tested to be the slowest of the VPS providers I use DigitalOcean - Linode - Vultr - Benchmarks - Upcloud - 13-Way VPS Server Benchmark Comparison Tests - Upcloud vs DigitalOcean vs Linode vs Vultr vs Hetzner. So can't rule out your DO VPS being part of the problem too.


    Centmin Mod is provide as is, so short of scripted related bugs or issues, any further optimisation to the web stack components - nginx, php-fpm, mariadb mysql, csf firewall etc or web app specific configurations are left to the Centmin Mod user to deal with. So I do not provide any free support for such.

    Bad gateway 502 /504 timeouts are usually related to Nginx timing out waiting on PHP-FPM to respond as PHP-FPM is overloaded or overwhelmed with requests, so may need to tune PHP-FPM values. It also maybe due to PHP-FPM in turn being queued and backed up waiting on MariaDB MySQL server to respond - so also need to look at MySQL.

    You'll need to tune your PHP-FPM settings with php-fpm main pool config file at /usr/local/etc/php-fpm.conf (overview of config files) and this is left up to end user to do but here's a thread for starters to enable PHP-FPM status page output outlined at
    Enabling PHP-FPM status also allows setting up 3rd party PHP-FPM status metric monitoring from services like:

    Checking PHP-FPM etc logs



    You'll also need to check into your PHP-FPM, Nginx and MariaDB logs which you can find as outlined at How to troubleshoot Centmin Mod initial install issues

    Server logs include Nginx, PHP-FPM, MariaDB MySQL error logs as well as others. You can find your Centmin Mod install/menu logs at FAQ 7 and server logs at FAQ 19 at Centmin Mod FAQ (most up to date info in FAQ so always read that first). Spoiler tag below has info too but may not be up to date.

    Some of Centmin Mod's installed software will have their own access and error logs which maybe useful for diagnosing errors or give info, notes, or warning notices.

    Note: There's no support provided by me for diagnosing such errors which may occur for various reasons including misconfiguration of installed php/mysql scripts or applications.

    In SSH2 telnet you can use tail command to view the last X number of lines in the file.

    For example for viewing last 10 lines in the file for:

    For Nginx access and error logs:
    Code:
      tail -10 /usr/local/nginx/logs/access.log
      tail -10 /usr/local/nginx/logs/error.log
    
    For specific domainname.com access and error log:
    Code:
      tail -10 /home/nginx/domains/domainname.com/log/access.log
      tail -10 /home/nginx/domains/domainname.com/log/error.log
    
    For other system error logs located at /var/log:

    list /var/log files in ascending time order so the most recently modified files are at the bottom
    Code:
      ls -lhrt /var/log
    
    Code:
    total 2.7M
    -rw------- 1 root  root    0 Aug 29 15:33 tallylog
    -rw------- 1 root  root    0 Aug 29 15:33 spooler
    drwx------ 3 root  root 4.0K Aug 29 15:35 samba
    drwxr-xr-x 2 root  root 4.0K Aug 29 15:35 mail
    -rw-r--r-- 1 root  500     0 Oct  8 18:13 dmesg.old
    -rw------- 1 root  500     0 Oct  8 18:13 boot.log
    -rw-r--r-- 1 root  500     0 Oct  8 18:14 dmesg
    drwx------ 2 root  root 4.0K Oct  8 18:14 httpd
    drwxr-xr-x 2 root  root 4.0K Oct  8 19:08 php-fpm
    -rw-rw---- 1 mysql root 2.3K Oct  9 12:38 mysqld.log
    -rw------- 1 root  root 9.2K Oct 26 10:48 yum.log
    -rw------- 1 root  utmp  94K Nov  7 22:59 btmp
    drwxr-xr-x 2 root  root 4.0K Nov  8 00:00 sa
    -rw------- 1 root  root 269K Nov  8 21:39 messages
    -rw------- 1 root  root 110K Nov  8 23:08 secure
    -rw-rw-r-- 1 root  utmp  43K Nov  8 23:08 wtmp
    -rw-r--r-- 1 root  root 144K Nov  8 23:08 lastlog
    -rw------- 1 root  root  69K Nov  8 23:08 lfd.log
    -rw------- 1 root  root 332K Nov  8 23:08 maillog
    -rw------- 1 root  500  1.6M Nov  8 23:10 cron
    
    For PHP-FPM error log:
    Code:
      tail -10 /var/log/php-fpm/www-error.log
    
    and/or
    Code:
      /var/log/php-fpm/www-php.error.log
    
    For MySQL / MariaDB error log:
    Code:
      tail -10 /var/log/mysqld.log
    
    For CSF firewall LFD log:
    Code:
      tail -10 /var/log/lfd.log
    
    For Mail log:
    Code:
      tail -10 /var/log/maillog
    
    For Cron job logs:
    Code:
      tail -10 /var/log/cron
    

    How to edit php.ini and php-fpm configuration files ?



    Centmin Mod install created command short cuts outlined here to allow you to quickly edit your /usr/local/lib/php.ini file and your /usr/local/etc/php-fpm.conf file. Full list of command shortcuts below:
    • Edit php.ini = phpedit ( /usr/local/lib/php.ini )
    • Edit my.cnf = mycnf ( /etc/my.cnf )
    • Edit php-fpm.conf = fpmconf ( /usr/local/etc/php-fpm.conf )
    • Edit nginx.conf = nginxconf ( /usr/local/nginx/conf/nginx.conf )
    • Edit (nginx) virtual.conf = vhostconf - only edits /usr/local/nginx/conf/conf.d/virtual.conf not the additional vhost domain.com.conf files added later
    • Edit (nginx) php.conf = phpinc ( /usr/local/nginx/conf/php.conf )
    • Edit (nginx) drop.conf = dropinc ( /usr/local/nginx/conf/drop.conf )
    • Edit (nginx) staticfiles.conf = statfilesinc ( /usr/local/nginx/conf/staticfiles.conf )
    • nginx stop/start/restart = ngxstop/ngxstart/ngxrestart
    • php-fpm stop/start/restart = fpmstop/fpmstart/fpmrestart
    • mysql stop/start/restart = mysqlstop/mysqlstart/mysqlrestart
    • nginx + php-fpm stop/start/restart = npstop/npstart/nprestart
    • memcached stop/start/restart =memcachedstop/memcachedstart/memcachedrestart
    • csf stop/start/restart = csfstop/csfstart/csfrestart

    Troubleshooting Tools



    However, there's many linux tools and scripts that can help you figure out what was causing the load issues and when.

    Tools and commands you will want to read up on and learn for basic system admin tasks and troubleshooting.
    Notes:
    However, Centmin Mod users are free to help each other out and ask questions or give answers on this community forum. My hopes are that this community forum evolves so that more veteran long time Centmin Mod users help new Centmin Mod users out :)
     
    • Useful Useful x 1
  3. moshbit

    moshbit Member

    53
    10
    8
    Jun 15, 2014
    Ratings:
    +13
    Local Time:
    12:19 PM
    1.15.0
    MariaDB 10.1.33
    Yeah, I've had weird quirks with DO quite often, where as I've had zero issues with Linode; so I moved this project over to Linode after doing a fresh install of centminmod and everything has been working great since then. Thanks for the advice :)
     
    • Informative Informative x 2
  4. eva2000

    eva2000 Administrator Staff Member

    44,163
    10,066
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +15,556
    Local Time:
    5:19 AM
    Nginx 1.17.x
    MariaDB 5.5/10.x
    Great to hear. I think DigitalOcean's popularity has basically overcrowded their VPS host nodes so performance is down on average and well all the Kernel level meltdown/spectre like mitigation patches have meant alot of Intel cpus have lost their performance over time. Linode has same problem on that end but their newer VPS seem to be AMD EPYC based so less affected by those Kernel level mitigations.
     
    • Informative Informative x 1