Error establishing connection to database – WordPress solution

solutions for wordpress database errors

A crashed database is a problem I’ve encountered across multiple WordPress websites. When trying to load the site you’re faced with a dreaded “Error establishing a database connection” message. Restarting the DB service usually clears things up. But, sometimes it won’t restart at all – which is why I started automating nightly data dumps to an S3 bucket.

Recently, one particular site kept going down unusually often. I assumed it was happening due to low computing resources on the EC2 t3.micro instance. I decide to spin up a a new box with more RAM (t3.small) and migrate the entire WordPress setup.

Since I couldn’t be sure of what was causing the issue, I needed a way to monitor the health of my WordPress websites. I decided to write code that would periodically ping the site, and if it is down send an email alert and attempt to restart the database.

warning message when a website can't connect to the database

The first challenge was determining the status of the database. Even if it crashed, my site would still return a 200 OK response. I figured I could use cURL to get the homepage content, and then strip out any HTML tags to check the text output. If the text did match the error message, I could take further action.

Next, I needed to programmatically restart MySql. This is the command I run to do it manually: sudo service mariadb restart 

After doing some research, I found that I could use shell_exec() to run it from my PHP code. Unfortunately, Apache wouldn’t let the (non-password using) web server user execute that without special authorization. I moved that command to its own restart-db.sh file, and allowed my code to run it by adding this to the visudo file: apache ALL=NOPASSWD: /var/www/html/restart-db.sh

I also needed to make the file executable by adjusting permissions: sudo chmod +x /var/www/html/restart-db.sh

Once those pieces were configured, my code would work:

<?php

$url = "http://www.antpace.com/blog";
$curl_connection = curl_init();

curl_setopt($curl_connection, CURLOPT_URL, $url);

curl_setopt($curl_connection, CURLOPT_RETURNTRANSFER, true);
$curl_response = curl_exec($curl_connection);
$plain_text = strip_tags($curl_response);

if(strpos($plain_text, "Error establishing a database connection") !== false){
	echo "The DB is down.";
        
        //restart the database
        shell_exec('sudo /var/www/html/restart-db.sh');
        
        //send notification email
        import 'send-email.php';
        send_email();
}else{
	echo "The DB is healthy.";
}

?>

You can read more about how to send a notification email in another post that I wrote on this blog.

Create the cron job

A cron job is a scheduled task in Linux that runs at set times. For my PHP code to effectively monitor the health of the database, it needs to run often. I decided to execute it every five minutes. Below are three shell commands to create a cron job.

The first creates the cron file for the root user:

sudo touch /var/spool/cron/root

The next appends my cron command to that file:

echo "*/5 * * * * sudo wget -q 127.0.0.1/check-db-health.php" | sudo tee -a /var/spool/cron/root

And, the last sets the cron software to listen for that file:

sudo crontab /var/spool/cron/root

Alternatively, you can create, edit, and set the cron file directly by running sudo crontab -e . The contents of the cron file can be confirmed by running sudo crontab -l .

 

Automatic MySQL dump to S3

Automatic MySQL dump to S3

I have had some lousy luck with databases. In 2018, I created a fitness app for martial artists, and quickly gained over a hundred users in the first week. Shortly after, the server stopped resolving and I didn’t know why. I tried restarting it, but that didn’t help. Then, I stopped the EC2 instance from my AWS console. Little did I know, that would wipe the all of the data from that box. Ouch.

Recently, a client let me know that their site wasn’t working. A dreaded “error connecting to the database” message was all that resolved. I’d seen this one before – no sweat. Restarting the database usually does the trick: “sudo service mariadb restart”. The command line barked back at me: “Job for mariadb.service failed because the control process exited with error code.”

Uh-oh.

The database was corrupted. It needed to be deleted and reinstalled. Fortunately, I just happen to have a SQL dump for this site saved on my desktop. This was no way to live – in fear of the whims of servers.

Part of the issue is that I’m running MySQL on the same EC2 instance as the web server.  A more sophisticated architecture would move the database to RDS. This would provide automated backups, patches, and maintenance. It also costs more.

To keep cost low, I decided to automate MySQL dumps and upload to an S3 bucket. S3 storage is cheap ($0.20/GB), and data transfer from EC2 is free.

AWS Setup

The first step was to get things configured in my Amazon Web Services (AWS) console. I created a new S3 bucket. I also created a new IAM user, and added it to a group that included the permission policy “AmazonS3FullAccess”.

AWS policy to allow full S3 access
This policy provides full access to all buckets.

I went to the security credentials for that user, and copied down the access key ID and secret. I would use that info to access my S3 bucket programatically. All of the remaining steps take place from the command line, via SSH, against my server. From a Mac terminal, you could use a command like this to connect to an EC2 instance:

ssh -i /Users/antpace/Documents/keys/myKey.pem ec2-user@ec2-XX-XX-XX.us-west-2.compute.amazonaws.com

Once connected, I installed the software to allow programatic access to AWS:

curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
unzip awscliv2.zip
sudo ./aws/install

Here is the reference for installing the AWS CLI on Linux.

Shell script

Shell scripts are programs that can be run directly by Linux. They’re great for automating tasks. To create the file on my server I ran: “nano backup.sh”. This assumes you already have the nano text editor installed. If not: “sudo yum install nano” (or, “sudo apt install nano”, depending on your Linux flavor).

Below is the full code I used. I’ll explain what each part of it does.

Credit: This code was largely inspired by a post from Marcelo Gornstein.

#!/bin/bash
AWS_ACCESS_KEY_ID=XXX \
AWS_SECRET_ACCESS_KEY=XXX \
S3_BUCKET=myBucketsName \
MYSQL_HOST=localhost \
MYSQL_PORT=3306 \
MYSQL_USER=XXX \
MYSQL_PASS=XXX \
MYSQL_DB=XXX \

cd /tmp
file=${MYSQL_DB}-$(date +%a).sql
mysqldump \
  --host ${MYSQL_HOST} \
  --port ${MYSQL_PORT} \
  -u ${MYSQL_USER} \
  --password="${MYSQL_PASS}" \
  ${MYSQL_DB} > ${file}
if [ "${?}" -eq 0 ]; then
  gzip ${file}
  AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} aws s3 cp ${file}.gz s3://${S3_BUCKET}
  rm ${file}.gz
else
  echo "sql dump error"
  exit 1
fi

The first line tells the system what interpreter  to use: “#!/bin/bash”. Bash is a variation of the shell scripting language. The next eight lines are variables that contain details about my AWS S3 bucket, and the MySQL database connection.

After switching to a temporary directory, the filename is built. The name of the file is set to the database’s name plus the day of the week. If that file already exists (from the week previous), it’ll be overwritten.  Next, the sql file is created using mysqldump and the database connection variables from above. Once that operation is complete, then we zip the file, upload it to S3, and delete the zip from our temp folder.

If the mysqldump operation fails, we spit out an error message and exit the program. (Exit code 1 is a general catchall for errors. Anything other than 0 is considered an error. Valid error codes range between 1 and 255.)

Before this shell script can be used, we need to change its file permissions so that it is executable: “chmod +x backup.sh”

After all of this, I ran the file manually, and made sure it worked: “./backup.sh”

Sure enough, I received a success message. I also checked the S3 bucket and made sure the file was there.

S3 file dump

Scheduled Cronjob

The last part is to schedule this script to run every night. To do this, we’ll edit the Linux crontab file: “sudo crontab -e”. This file controls cronjobs – which are scheduled tasks that the system will run at set times.

The file opened in my terminal window using the vim text editor – which is notoriously harder to use than the nano editor we used before.

I had to hit ‘i’ to enter insertion mode. Then I right clicked, and pasted in my cronjob code. Then I pressed the escape key to exit insertion mode. Finally, I typed “wq!” to save my changes and quit.

Remember how crontab works:

minute | hour | day-of-month | month | day-of-week

I set the script to run, every day, at 2:30am:

30 2 * * * sudo /home/ec2-user/backup.sh

And that’s it. I made sure to check the next day to make sure my cronjob worked (it did). Hopefully now, I won’t lose production data ever again!

Request Time Too Skewed (update)

A while after setting this up, I randomly checked my S3 buckets to make sure everything was still working. Although it had been for most of my sites, one had not been backed up in almost 2 months! I shelled into that machine, and tried running the script manually. Sure enough, I received an error: “An error occurred (RequestTimeTooSkewed) when calling the PutObject operation: The difference between the request time and the current time is too large.

I checked the operating system’s current date and time, and it was off by 5 days. I’m not sure how that happened. I fixed it by installing and running “Network Time Protocol”:

sudo yum install ntp
sudo ntpdate ntp.ubuntu.com

After that, I was able to run my backup script successfully, without any S3 errors.

 


Nano text-editor tip I learned along the way:

You can delete chunks of text content using Nano. Use CTRL + Shift + 6 to enter selection mode, move the cursor to expand the block, and press CTRL + K to delete it.

 

Launching a website on AWS

Using AWS for a website

In 2008 I deployed my first website to production. It used a simple LAMP stack , a GoDaddy domain name, and HostGator hosting.

Since 2016, I’ve used AWS as my primary cloud provider. And this year, I’m finally cancelling my HostGator package. Looking through that old server, I found artifacts of past projects – small businesses and start-ups that I helped develop and grow. A virtual memory lane.

Left on that old box was a site that I needed to move to a fresh EC2 instance. This is an opportunity to document how I launch a site to Amazon Web Services.

Amazon Elastic Compute Cloud

To start, I launch a new EC2 instance from the AWS console. Amazon’s Elastic Compute Cloud provides “secure and resizable compute capacity in the cloud.” When prompted to choose an Amazon Machine Image (AMI), I select “Amazon Linux 2 AMI”. I leave all other settings as default. When I finally click “Launch”, it’ll ask me to either generate a new key file, or use an existing one. I’ll need that file later to SSH or sFTP into this instance. A basic Linux server is spun up, with little else installed.

Linux AMI
Amazon Linux 2 AMI is free tier eligible.

Next, I make sure that instance’s Security Group allows inbound traffic on SSH, HTTP, and HTTPS. We allow all traffic via HTTP and HTTPS (IPv4 and IPv6, which is why there are 2 entries for each). That way end-users can reach the website from a browser. Inbound SSH access should not be left wide open. Only specific IP addresses should be allowed to command-line in to the server. AWS has an option labeled “My IP” that will populate it for your machine.

Inbound security rules
Don’t allow all IPs to access SSH in a live production environment.

Configure the server

Now that the hosting server is up-and-running, I can command-line in via SSH from my Mac’s terminal using the key file from before. This is what the command looks like:

 ssh -i /Users/apace/my-keys/keypair-secret.pem ec2-user@ec2-XXX-XXX-XX.us-east-2.compute.amazonaws.com

Make sure everything is up-to-date by running “sudo yum update“.  I begin installing the required software to host a website:

sudo amazon-linux-extras install -y lamp-mariadb10.2-php7.2 php7.2

That command gives me Apache, PHP, and MariaDB – a basic LAMP stack. This next one installs the database server:

sudo yum install -y httpd mariadb-server

MariaDB is a fork of the typical MySQL, but with better performance.

Start Apache: “sudo systemctl start httpd“. And, make sure it always starts when the server boots up “sudo systemctl enable httpd

The server setup is complete. I can access an Apache test page from a web browser by navigating to the EC2 instance’s public IP address.

Apache test page
A test page shows when no website files are present.

I’ll take my website files (that are stored on my local machine and synched to a Git repo) and copy them to the server via sFTP.

Copy website files to server
I use FileZilla to access my EC2 public directory

I need to make sure the Linux user I sFTP with owns the directory “/var/www/html”, or else I’ll get a permission denied error: sudo chown -R ec2-user /var/www/html

* AWS Documentation Reference

Domain name and Route 53

Instead of having to use the EC2 server’s public address to see my website from a browser, I’ll point a domain name at it. AWS Route 53 helps with this. It’s a “DNS web service” that routes users to websites by mapping domain names to IP addresses.

In Route 53 I create a new “hosted zone”, and enter the domain name that I’ll be using for this site.  This will automatically generate two record sets: a Name Server (NS) record and a Start-of-Authority (SOA) record. I’ll create one more, an IPv4 address (A) record. The value of that record should be the public IP address that I want my domain to point at. You’ll probably also want to add another, identical to the last one, but specifying “www” in the record name.

Finally, I’ll head over to my domain name registrar, and find my domain name’s settings. I update the nameserver values there to match those in my Route 53 NS record set. It’ll likely take some time for this change to be reflected in the domain’s settings. Once that is complete, the domain name will be pointing at my new EC2 instance.

And that’s it – I’ve deployed my website to AWS. The next step is to secure my site by configuring SSL and HTTPS.

If you’re migrating a dynamic WordPress site, you’ll require a some additional steps to complete the migration.