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My Server is Slow! The Ultimate Guide to Debugging High CPU and RAM Usage on Linux

DNS Management, Email Server Management, Hosting Management, Plesk Control Panel, Server Management, Server Security, Web Security

It happens to every server administrator.

One minute, your website is flying. The next minute, it’s crawling. Your SSH terminal is lagging, database queries are timing out, and your customers are getting angry.

Your first instinct might be to blame the hosting provider. But 90% of the time, the hardware is fine. The problem is a “Bottleneck” inside your operating system. A rogue script, a memory leak, or a traffic spike is eating up your resources.

But how do you find the culprit?

In this guide, we will turn you into a Linux Detective. We will teach you how to use professional diagnostic tools to identify exactly what is slowing down your VPS or Dedicated Server and how to fix it.

Step 1: The First Look (Load Average)

Before we dive deep, we need to check the “pulse” of your server.

Log in to your server via SSH (Ref: Essential SSH Commands Guide) and type:

uptime

Output: load average: 0.50, 1.20, 5.00

What does this mean? These numbers represent the system load over the last 1, 5, and 15 minutes.

  • The Rule of Thumb: If the number is lower than your CPU core count, you are fine.
  • The Danger Zone: If you have a 2 Core VPS and your load is 4.00, your server is overloaded by 200%. Traffic is waiting in line to be processed.

Step 2: Debugging CPU & RAM (Meet htop)

The standard top command is confusing. We recommend htop. It gives you a colorful, interactive dashboard.

Install it:

# Ubuntu/Debian
sudo apt install htop -y

# CentOS/Almalinux
sudo yum install htop -y

Run it:

htop

Scenario A: High CPU Usage (The Red Bars)

Look at the top bars. If CPU is hitting 100% (Red):

  1. Look at the process list below.
  2. Find the process with the highest CPU%.
  3. Common Culprits:
    • php-fpm or httpd: You likely have heavy traffic or a bad WordPress plugin.
    • mysqld: Your database queries are inefficient.
    • kswapd0: Your RAM is full, and the CPU is working hard to move data to the disk (Thrashing).

Scenario B: High RAM Usage (The Memory Leak)

Linux loves to use RAM. But there is a difference between “Good” usage and “Bad” usage.

  • Green Bar: Used memory. If this is full, you are in trouble.
  • Yellow/Blue Bar: Cache/Buffers. This is good. Linux uses empty RAM to cache files to make them faster. Don’t worry about this.

The Fix: If a process is eating all your RAM, press F9 inside htop to kill it.

Step 3: The Silent Killer (Disk I/O)

Sometimes CPU and RAM look fine, but the server is still slow. This is usually Disk I/O (Input/Output).

If your website is trying to read/write thousands of files at once, the disk gets “jammed.”

The Tool: iotop

sudo apt install iotop -y
sudo iotop

Look for the “DISK WRITE” column.

  • If mysqld is writing heavily, you might need to optimize your database.
  • If backup-script is running, schedule it for 3 AM when traffic is low.

Note: All VPSPioneer VPS plans run on NVMe SSDs, which drastically reduce I/O bottlenecks compared to traditional SATA SSDs.

Step 4: Solutions and Optimization

You found the problem. Now, how do you fix it?

1. Optimize Your Software

  • Database: Use a tool like mysqltuner to check your configuration.
  • PHP: Upgrade to PHP 8.1 or 8.2 (It handles CPU much better than PHP 7.4).
  • Caching: Install Redis or Memcached to stop hitting the database for every request.

2. Block Bad Traffic

If the high CPU is caused by a bot attack, block the IP using your firewall.

3. The Vertical Scale (Upgrade)

If your code is optimized, you aren’t under attack, but your resource usage is still hitting 100% constantly, there is only one conclusion: You have outgrown your plan.

Success is a good problem to have! If your business is growing, your infrastructure must grow with it.

  • Action: Upgrade your plan instantly via the VPSPioneer Client Area to add more CPU Cores and RAM.

Frequently Asked Questions (FAQ)

Q: Why does Linux say my RAM is 99% full even when idle? A: Linux follows the philosophy: “Unused RAM is wasted RAM.” It fills empty RAM with disk caching to speed up file access. Use the command free -h and look at the “Available” column. If “Available” is high, you are fine.

Q: What is kswapd0 and why is it using 100% CPU? A: This is the process that manages Virtual Memory (Swap). If it is running high, it means you have run out of physical RAM and the server is struggling to swap data to the hard drive. You need to upgrade your RAM immediately.

Q: Can VPSPioneer optimize my server for me? A: Our standard VPS plans are unmanaged (Self-Managed). However, if you face persistent issues, our Server Optimization team can offer paid consultation for advanced optimization.