Cleaning Up WordPress – Large wp_options.idb

Did your tiny AWS Bitnami WordPress server run out of disk space? The culprit may be unoptimized data tables in MySQL. Finding a 4.9GB wp_options.idb file on your server is not as uncommon as you may think. What makes it surprising is when you look at your wp_options entries and discover there are only 300 rows in that table with limited text in the option_value column.

Thankfully there is an easy fix as long as you can get enough disk space to manage the task. Start by looking for any log files or other files you are CERTAIN you don’t need so you can shut down web, php, and mysql services.

Finding Large Files

# sudo find / -xdev -type f -size +50M -print | sudo xargs ls -lh | sudo sort -k5,5 -h -r

This command finds all files on the drive over 50M in size.

Look for specific MySQL raw data files (wp_options.idb for example) in that list. Remember the table name for later.

Stopping System Services

Stop the services. On an AWS Bitnami WP server they have their own special control scripts in place of the standard Linux services library.

bitnami@ip-172-31-87-127:/opt/bitnami/mysql$ sudo /opt/bitnami/ctlscript.sh stop mysql


usage: /opt/bitnami/ctlscript.sh help
       /opt/bitnami/ctlscript.sh (start|stop|restart|status)
       /opt/bitnami/ctlscript.sh (start|stop|restart|status) mysql
       /opt/bitnami/ctlscript.sh (start|stop|restart|status) php-fpm
       /opt/bitnami/ctlscript.sh (start|stop|restart|status) apache

help       - this screen
start      - start the service(s)
stop       - stop  the service(s)
restart    - restart or start the service(s)
status     - show the status of the service(s)

Stop all the services, then start MySQL only.

Cleaning Up MySQL

If you are doing system admin commands you should know how to find your data access credentials in the wp-config.php file. No need to go into that here. Find the credentials and login to MySQL.

No OPTIMIZE that table (and any others that you suspect have unusually large .idb files).

mysql> OPTIMIZE NO_WRITE_TO_BINLOG TABLE wp_options;

That’s it. One simple command may easily recover 4.9GB of disk space , making a 4.9GB file on a 9GB drive get back to a more reasonable 10MB.

Why WordPress core or cron jobs are not doing this on a regular basis is a question for another day…

AWS LEMP Stacks and EFS Issues

Lesson learned — if you are using EFS on production systems you want to be using provisioned throughput mode.

But, before we get into that, let’s go over the details of this implementation…

Service Configuration

We utilize AWS EC2 instances to run multiple WordPress sites hosted in different directories. The configuration is fairly standard: 2+ servers configured as part of an load-balanced cluster. The servers run from the same image meaning they use the same underlying software stack.

Part of that image includes a mounted EFS (Elastic File Storage) directory , used to share WordPress resources between all nodes in the cluster. The original architecture was designed to host not only the typically-shared wp-content/uploads folder of WordPress via this EFS mount but also the code. The thought was that sharing the code in this way would allow a system admin to easily update WordPress core, plugins, or themes from the typical wp-admin web login. Any code updates would immediately be reflected across all nodes.

EFS Web App Code Hosting – A Bad Idea

Turns out this is a bad idea for a few reasons. First of all, EFS volumes are mounted using the NFS4 (network file storage) protocol — this defines how the operating system handles file read/write operations for a network mounted drive. While NFS4 is fairly robust, the throughput of ANY network drive, even on a high speed AWS data center backbone, is much slower than a local drive such as an EBS volume.

That means that even on a good day every PHP file, JavaScript file, or anything else needed to serve up that WordPress web page are going to be a bit slower than normal.

However, the bigger problem comes to light if you happen to choose the default, and pushed as “the mode to use” by Amazon, EFS throughput mode known as “Burst mode”.

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Internet Enabled Voting For US Elections

Internet enabled voting is a must IMO. Many that are afraid of the security risks and remote hacking have a very shallow, if any, understanding of the risks involved.

To claim physical (paper) voting is more secure is absurd. Every country that has used that system, including ours, has encountered fraud in some form.

Maybe this is the perfect catalyst for getting our Internet providers to finally enable IPV6. It would make external attacks a couple orders of magnitude more difficult. Not too mention providing direct 1:1 accountability to track every single device used to vote.

https://www.npr.org/2019/11/07/776403310/in-2020-some-americans-will-vote-on-their-phones-is-that-the-future

Internet Enabled Voting For US Elections

apple.news/A2hlUbDHwRjifTbSwv6fOZQ

Internet enabled voting is a must IMO. Many that are afraid of the security risks and remote hacking have a very shallow, if any, understanding of the risks involved.

To claim physical (paper) voting is more secure is absurd. Every country that has used that system, including ours, has encountered fraud in some form.

Maybe this is the perfect catalyst for getting our Internet providers to finally enable IPV6. It would make external attacks a couple orders of magnitude more difficult. Not too mention providing direct 1:1 accountability to track every single device used to vote.

Converting A Standalone Instance Into An EC2 Load Balanced Cluster

Creating a new web application that resides on an AWS load balanced cluster is easy with the Elastic Beanstalk assistant. That is a great solution if you want to run every web service or application on their own instances. It is not a great fit for complex environments like the one being used for Store Locator Plus®.

Store Locator Plus® has several environments running within the same master domain. Multiple servers and load balancers creates a security certificate nightmare. Not too mention it starts racking up EC2 server fees quickly if they each became their own cluster. The better option is to retain a server instance that allows us to run our SaaS offering, our buy-and-own plugin store, our documentation site, and our demo site from a single disk image. We want to setup a full EC2 Load Balanced Cluster to gain the benefits of horizontal scaling on a server hosting multiple domains and web apps.

While this is easy to do with a single EC2 instance that hosts multiple host names for the storelocatorplus.com domain, making it scalable under load is the trick. It turns out Elastic Beanstalk is not a good fit. Instead we need to build a load balanced cluster “from scratch”. We’ll need to combine a machine image from a running server with a Launch Template. We will need an Application Load Balancer that will have instances attached and detached automatically from an Auto Scaling Group that we will also create.

Our environment also has a configured EC2 instance to run the web application stacks, mostly WordPress, locally on an EBS volume that uses an Amazon Aurora MySQL RDS database in multiple zones for performance and reliability. These two features make it easy to replicate the disk image for the software portion and maintain a persistent DB store across all instances.

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