“Premature optimization is the root of all evil but lack of optimisation is the root of outages.”

Table of Contents

• Introduction

• Architecture Overview

• Why Optimisation Is Required

• Nginx Optimisations & Parameter Calculations

• PHP-FPM Optimisations & Parameter Calculations

• MySQL Optimisations & Parameter Calculations

• System-Level Optimisations (Linux)

• Practical Example: Small vs Medium vs Large Server

• Interesting Facts & Statistics

• FAQs

• Key Takeaways

• Conclusion

1. Introduction

Modern web applications rely heavily on the Nginx + PHP + MySQL (LEMP) stack. While default configurations work for testing, they are not suitable for production traffic.

Optimisation ensures:

• Faster page load time

• Better concurrency handling

• Lower memory and CPU usage

• Higher stability under load

This document explains what to optimise, why to optimise, and how to calculate parameters practically.

2. Architecture Overview

A typical request flow:

• Client sends HTTP request

• Nginx handles connection & static content

• PHP-FPM processes dynamic PHP requests

• MySQL serves data from database

• Response sent back to client

Each layer must be tuned together, not individually.

3. Why Optimisation Is Required

Default settings:

• Are conservative

• Waste available RAM

• Limit concurrency

• Cause slow response under load

Common Problems Without Optimisation

• 502 / 504 Gateway errors

• High CPU load

• PHP-FPM “server reached max_children”

• MySQL “Too many connections”

4. Nginx Optimisations & Parameter Calculations

Key Nginx Parameters worker_processes auto; worker_connections 4096;

What is worker_processes Number of worker processes Best practice: match CPU cores

nproc Example: 4 CPU cores → worker_processes 4; What is worker_connections Maximum connections per worker

Total Max Connections worker_processes × worker_connections

Example

4 × 4096 = 16,384 concurrent connections

Recommended Extra Optimisations

use epoll; multi_accept on;

use epoll; multi_accept on;

sendfile on; tcp_nopush on; tcp_nodelay on;

keepalive_timeout 65; keepalive_requests 1000;`

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5. PHP-FPM Optimisations & Parameter Calculations

Key PHP-FPM Settings

pm = dynamic pm.max_children = 20 pm.start_servers = 5 pm.min_spare_servers = 5 pm.max_spare_servers = 10

pm = dynamic pm.max_children = 20 pm.start_servers = 5 pm.min_spare_servers = 5 pm.max_spare_servers = 10

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How to Calculate pm.max_children

• Find average PHP process memory: ps -ylC php-fpm --sort:rss

• Formula: Available RAM for PHP / Avg PHP process size

Example

• Available RAM: 2 GB

• Avg PHP process: 100 MB

2048 / 100 ≈ 20 pm.max_children = 20

Other Important PHP Optimisations

request_terminate_timeout = 60 max_execution_time = 60 memory_limit = 256M

request_terminate_timeout = 60 max_execution_time = 60 memory_limit = 256M

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Enable OPcache

opcache.enable=1 opcache.memory_consumption=256 opcache.max_accelerated_files=20000

opcache.enable=1 opcache.memory_consumption=256 opcache.max_accelerated_files=20000

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6. MySQL Optimisations & Parameter Calculations

Key MySQL Parameters

innodb_buffer_pool_size = 2G innodb_buffer_pool_instances = 2 max_connections = 200

innodb_buffer_pool_size = 2G innodb_buffer_pool_instances = 2 max_connections = 200

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How to Calculate innodb_buffer_pool_size

• Allocate 60–70% of total RAM (dedicated DB server)

Example

• Server RAM: 4 GB

4 × 70% ≈ 2.8 GB Use 2G or 3G

Connection Calculation

Additional Recommended Settings

query_cache_type = 0 slow_query_log = 1 slow_query_log_file = /var/log/mysql/slow.log long_query_time = 2

query_cache_type = 0 slow_query_log = 1 slow_query_log_file = /var/log/mysql/slow.log long_query_time = 2

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7. System-Level Optimisations (Linux)

File Descriptors

ulimit -n 100000

Kernel Tuning

net.core.somaxconn = 65535 net.ipv4.tcp_max_syn_backlog = 65535 vm.swappiness = 10

8. Practical Server Size Examples

Small Server (2 CPU / 2 GB RAM)

• Nginx workers: 2

• worker_connections: 2048

• PHP max_children: 10

• MySQL buffer pool: 1G

Medium Server (4 CPU / 8 GB RAM)

• Nginx workers: 4

• worker_connections: 4096

• PHP max_children: 30–40

• MySQL buffer pool: 4–5G

Large Server (8 CPU / 16 GB RAM)

• Nginx workers: 8

• worker_connections: 8192

• PHP max_children: 60–80

• MySQL buffer pool: 10–12G

Practical Demonstration (Images Explained)

Step 1. NGINX OPTIMISATION

Parameter Calculations Step 1.1 Backup current nginx.conf

sudo cp /etc/nginx/nginx.conf /etc/nginx/nginx.conf.bak

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Step 1.2 Check current config

cat /etc/nginx/nginx.conf

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Screenshot: Current state before changes

Step 1.3 Edit nginx.conf

sudo nano /etc/nginx/nginx.conf

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Replace/update with this optimized config:

user www-data;  worker_processes 2; # = nproc (2 cores)  worker_rlimit_nofile 65535;  pid /run/nginx.pid;  include /etc/nginx/modules-enabled/*.conf;*

user www-data;  worker_processes 2; # = nproc (2 cores)  worker_rlimit_nofile 65535;  pid /run/nginx.pid;  include /etc/nginx/modules-enabled/*.conf;*

events { worker_connections 1024; # 2 x 1024 = 2048 total connections use epoll; # Linux best event model multi_accept on; # Accept multiple connections at once }

http {

Basic Settings

sendfile on; tcp_nopush on; tcp_nodelay on; keepalive_timeout 30; # Reduced from default 75s keepalive_requests 100; types_hash_max_size 2048; server_tokens off; # Hide nginx version

client_max_body_size 20m; client_body_buffer_size 128k; client_header_buffer_size 1k; large_client_header_buffers 4 8k; client_body_timeout 12; client_header_timeout 12; send_timeout 10;

include /etc/nginx/mime.types; default_type application/octet-stream;

Logging Settings

access_log /var/log/nginx/access.log; error_log /var/log/nginx/error.log warn; # Only warn+ to reduce I/O

Gzip Settings

gzip on; gzip_vary on; gzip_proxied any; gzip_comp_level 3; # Level 3 = good ratio, low CPU gzip_min_length 1024; # Don't compress tiny files gzip_buffers 16 8k; gzip_http_version 1.1; gzip_types text/plain text/css text/javascript application/javascript application/json application/xml image/svg+xml font/woff2;

Open File Cache

open_file_cache max=1000 inactive=20s; open_file_cache_valid 30s; open_file_cache_min_uses 2; open_file_cache_errors on;

FastCGI Cache (optional - enable per site)

fastcgi_cache_path /var/cache/nginx levels=1:2 keys_zone=PHPCACHE:10m max_size=100m inactive=60m use_temp_path=off;

include /etc/nginx/conf.d/.conf; include /etc/nginx/sites-enabled/; }`

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Step 1.4 Create FastCGI cache directory

sudo mkdir -p /var/cache/nginx  sudo chown www-data:www-data /var/cache/nginx

sudo mkdir -p /var/cache/nginx  sudo chown www-data:www-data /var/cache/nginx

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Step 1.5 Test and reload Nginx

sudo nginx -t  sudo systemctl reload nginx

sudo nginx -t  sudo systemctl reload nginx

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Screenshot: nginx -t showing syntax is ok and test is successful

Step 1.6 Verify Nginx is running with new settings

sudo nginx -T | grep -E "worker_processes|worker_connections|gzip|keepalive_timeout" systemctl status nginx

sudo nginx -T | grep -E "worker_processes|worker_connections|gzip|keepalive_timeout" systemctl status nginx

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Screenshot: Running status + key parameters

Step 2. PHP-FPM OPTIMISATION

Parameter Calculations Available RAM for PHP-FPM: ~150MB (conservative, leaving room for MySQL + Nginx) Average PHP-FPM process size: ~30-40MB Formula: pm.max_children = 150 / 35 ≈ 4

PHP-FPM Parameters Calculation pm Formula: Dynamic (best for variable traffic) Value: dynamic

pm.max_children Formula: 150MB ÷ 35MB/process Value: 4

pm.start_servers Formula: pm.max_children / 2 Value: 2

pm.min_spare_servers Formula: pm.start_servers / 2 Value: 1

pm.max_spare_servers Formula: pm.start_servers Value: 2

pm.max_requests Formula: Prevent memory leaks Value: 500

Step 2.1 Check PHP-FPM version path

php -v  ls /etc/php/

php -v  ls /etc/php/

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Step 2.2 Backup pool config

sudo cp/etc/php/8.4/fpm/pool.d/www.conf/etc /php/8.4/fpm/pool.d/www.conf.bak sudo cp /etc/php/8.4/fpm/php.ini /etc/php/8.4/fpm/php.ini.bak

sudo cp/etc/php/8.4/fpm/pool.d/www.conf/etc /php/8.4/fpm/pool.d/www.conf.bak sudo cp /etc/php/8.4/fpm/php.ini /etc/php/8.4/fpm/php.ini.bak

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Step 2.3 Check current PHP process memory usage

• Run this to see actual PHP-FPM process sizes

ps aux | grep php-fpm | grep -v grep | awk '{sum += $6} END {print "Total RSS:", sum/1024, "MB"; print "Count:", NR; print "Avg per process:", sum/NR/1024, "MB"}'

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Screenshot: Current process sizes.

Step 2.4 Edit PHP-FPM pool config

sudo nano /etc/php/8.4/fpm/pool.d/www.conf

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Find and update these values (search with Ctrl+W in nano):

[www] user = www-data group = www-data

[www] user = www-data group = www-data

listen = /run/php/php8.4-fpm.sock listen.owner = www-data listen.group = www-data

pm = dynamic pm.max_children = 4 pm.start_servers = 2 pm.min_spare_servers = 1 pm.max_spare_servers = 2 pm.max_requests = 500 ;Restart workers after 500 requests (prevents memory leaks) pm.process_idle_timeout = 10s

pm.status_path = /status ; Enable FPM status page ping.path = /ping

slowlog = /var/log/php8.4-fpm-slow.log request_slowlog_timeout = 5s ; Log requests taking > 5 seconds security.limit_extensions = .php`

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Step 2.5 Tune PHP OPcache sudo nano /etc/php/8.4/mods-available/opcache.ini

zend_extension=opcache

; Enable OPcache opcache.enable=1 opcache.enable_cli=0

; Memory: 64MB for low-RAM server opcache.memory_consumption=64 opcache.interned_strings_buffer=8 opcache.max_accelerated_files=10000

; Production settings (set validate_timestamps=0 in prod) opcache.validate_timestamps=1 opcache.revalidate_freq=60

opcache.save_comments=1 opcache.max_wasted_percentage=10 opcache.use_cwd=1

; JIT (PHP 8.x feature) opcache.jit_buffer_size=32M opcache.jit=1255`

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Step 2.6 Tune PHP.ini key values sudo nano /etc/php/8.4/fpm/php.ini

Find and update:  ; Memory limit per PHP process  memory_limit = 128M

Find and update:  ; Memory limit per PHP process  memory_limit = 128M

; Upload/POST limits upload_max_filesize = 20M post_max_size = 25M max_execution_time = 60 max_input_time = 60

; Error handling (production) display_errors = Off log_errors = On error_log = /var/log/php_errors.log

; Session handling session.gc_maxlifetime = 1440 session.cookie_httponly = 1 session.cookie_secure = 1

; Disable dangerous functions disable_functions = exec,passthru,shell_exec,system,proc_open,popen`

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Step 2.7 Restart PHP-FPM and verify

sudo php-fpm8.4 -t  sudo systemctl restart php8.4-fpm  sudo systemctl status php8.4-fpm

sudo php-fpm8.4 -t  sudo systemctl restart php8.4-fpm  sudo systemctl status php8.4-fpm

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Screenshot: PHP-FPM status showing active (running)

Step 2.8 Verify OPcache is active

php -r "var_dump(opcache_get_status());" | head -30

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• or check via CLI

php -i | grep -E "opcache|OPcache"

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Screenshot: OPcache enabled status

Step 2.9 Check PHP-FPM processes after restart

ps aux | grep php-fpm | grep -v grep

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• Should show master + 2 worker processes (pm.start_servers=2)

Screenshot: FPM process list

Step 3. MYSQL OPTIMISATION

Parameter Calculations

RAM budget for MySQL: ~200MB (out of 914MB total)

innodb_buffer_pool_size Formula: ~20% of RAM (shared server) Value: 192M

innodb_buffer_pool_instances Formula: buffer_pool ÷ 128M Value: 1

max_connections Formula: Low RAM = conservative Value: 50

innodb_log_file_size Formula: 25% of buffer pool Value: 48M

tmp_table_size Formula: Memory temporary tables Value: 16M

max_heap_table_size Formula: Same as tmp_table_size Value: 16M

thread_cache_size Formula: Reuse threads Value: 8

table_open_cache Formula: Open tables cache Value: 400

Step 3.1 Check current MySQL config and status

sudo cp /etc/mysql/mysql.conf.d/mysqld.cnf /etc/mysql/mysql.conf.d/mysqld.cnf.bak

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• Check current variables

mysql -u root -p -e "SHOW VARIABLES LIKE 'innodb_buffer_pool%';"  mysql -u root -p -e "SHOW VARIABLES LIKE 'max_connections';"  mysql -u root -p -e "SHOW STATUS LIKE 'Threads_connected';"

mysql -u root -p -e "SHOW VARIABLES LIKE 'innodb_buffer_pool%';"  mysql -u root -p -e "SHOW VARIABLES LIKE 'max_connections';"  mysql -u root -p -e "SHOW STATUS LIKE 'Threads_connected';"

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Screenshot: Current MySQL variables

Step 3.2 Check actual MySQL memory usage

mysql -u root -p -e "  SELECT  ROUND(@@innodb_buffer_pool_size/1024/1024, 0) AS 'Buffer Pool MB',  ROUND(@@key_buffer_size/1024/1024, 0) AS 'Key Buffer MB',  @@max_connections AS 'Max Connections',  @@thread_stack/1024 AS 'Thread Stack KB';  "

mysql -u root -p -e "  SELECT  ROUND(@@innodb_buffer_pool_size/1024/1024, 0) AS 'Buffer Pool MB',  ROUND(@@key_buffer_size/1024/1024, 0) AS 'Key Buffer MB',  @@max_connections AS 'Max Connections',  @@thread_stack/1024 AS 'Thread Stack KB';  "

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Screenshot: Current MySQL memory config

Step 3.3 Edit MySQL config

sudo nano /etc/mysql/mysql.conf.d/mysqld.cnf

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Add/update under [mysqld]:

[mysqld]  pid-file = /var/run/mysqld/mysqld.pid  socket = /var/run/mysqld/mysqld.sock  datadir = /var/lib/mysql  log-error = /var/log/mysql/error.log

[mysqld]  pid-file = /var/run/mysqld/mysqld.pid  socket = /var/run/mysqld/mysqld.sock  datadir = /var/lib/mysql  log-error = /var/log/mysql/error.log

===== MEMORY SETTINGS =====

Server has 914MB RAM - allocate ~200MB for MySQL

innodb_buffer_pool_size = 192M # Main InnoDB cache (most important!) innodb_buffer_pool_instances = 1 # 1 instance (< 1GB pool) innodb_log_file_size = 48M # ~25% of buffer pool innodb_log_buffer_size = 8M innodb_flush_log_at_trx_commit = 2 # Slight risk, big perf gain (use 1 for strict ACID)

===== CONNECTION SETTINGS =====

max_connections = 50 # Low RAM = keep connections limited thread_cache_size = 8 # Reuse threads, avoid creation overhead wait_timeout = 120 # Kill idle connections after 2 min interactive_timeout = 120

===== QUERY CACHE (removed in MySQL 8.0, skip) =====

MySQL 8.0 removed query_cache - use ProxySQL or app-level cache

===== TABLE CACHE =====

table_open_cache = 400 table_definition_cache = 400

===== TEMP TABLES =====

tmp_table_size = 16M max_heap_table_size = 16M

===== InnoDB I/O =====

innodb_file_per_table = 1 innodb_flush_method = O_DIRECT # Avoid double buffering with OS cache innodb_read_io_threads = 2 # = CPU cores innodb_write_io_threads = 2 # = CPU cores

===== SLOW QUERY LOG =====

slow_query_log = 1 slow_query_log_file = /var/log/mysql/slow.log long_query_time = 2 # Log queries > 2 seconds log_queries_not_using_indexes = 1

===== BINARY LOG (disable if not using replication) =====

skip-log-bin # Uncomment if no replication needed`

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Step 3.4 Validate and restart MySQL

sudo mysqld --validate-config  sudo systemctl restart mysql  sudo systemctl status mysql

sudo mysqld --validate-config  sudo systemctl restart mysql  sudo systemctl status mysql

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Screenshot: MySQL status active

Step 3.5 Verify new MySQL variables

mysql -u root -p -e "  SELECT 'innodb_buffer_pool_size' AS Variable,  ROUND(@@innodb_buffer_pool_size/1024/1024,0) AS 'Value (MB)'  UNION SELECT 'max_connections', @@max_connections  UNION SELECT 'innodb_log_file_size MB', ROUND(@@innodb_log_file_size/1024/1024,0)  UNION SELECT 'tmp_table_size MB', ROUND(@@tmp_table_size/1024/1024,0)  UNION SELECT 'thread_cache_size', @@thread_cache_size;  "

mysql -u root -p -e "  SELECT 'innodb_buffer_pool_size' AS Variable,  ROUND(@@innodb_buffer_pool_size/1024/1024,0) AS 'Value (MB)'  UNION SELECT 'max_connections', @@max_connections  UNION SELECT 'innodb_log_file_size MB', ROUND(@@innodb_log_file_size/1024/1024,0)  UNION SELECT 'tmp_table_size MB', ROUND(@@tmp_table_size/1024/1024,0)  UNION SELECT 'thread_cache_size', @@thread_cache_size;  "

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Screenshot: New values confirmed

Step 3.6 Check MySQL memory usage post-restart

free -h  ps aux | sort -k6 -rn | head -10

free -h  ps aux | sort -k6 -rn | head -10

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Screenshot: Overall memory after all services tuned

“Measure first, tune second, and monitor always.”

Step 4. FINAL VERIFICATION

Step 4.1 Check all services running

systemctl status nginx php8.4-fpm mysql --no-pager

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Step 4.2 Full memory picture

free -h  ps aux --sort=-%mem | head -15

free -h  ps aux --sort=-%mem | head -15

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Step 4.3 Check nginx + PHP working together

Test nginx config is still valid  sudo nginx -t

Test nginx config is still valid  sudo nginx -t

Test PHP-FPM socket exists ls -la /run/php/php8.4-fpm.sock

Check FPM status (if you added status page to your site config) curl http://localhost/status`

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Step 4.4 Check MySQL slow log is active

mysql -u root -p -e "SHOW VARIABLES LIKE 'slow_query%';"

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Step 4.5 Final health summary

echo "=== NGINX ===" && nginx -v && systemctl is-active nginx  echo "=== PHP-FPM ===" && php -v | head -1 && systemctl is-active php8.4-fpm  echo "=== MYSQL ===" && mysql --version && systemctl is-active mysql  echo "=== MEMORY ===" && free -h

echo "=== NGINX ===" && nginx -v && systemctl is-active nginx  echo "=== PHP-FPM ===" && php -v | head -1 && systemctl is-active php8.4-fpm  echo "=== MYSQL ===" && mysql --version && systemctl is-active mysql  echo "=== MEMORY ===" && free -h

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Screenshot: Final health check

Your server is fully optimised. All phases verified:

• Phase 0 Swap 2GB active

• Phase 1 Nginx tuned

• Phase 2 PHP-FPM + OPcache + JIT enabled

• Phase 3 MySQL InnoDB / connections / slow query log active

9. Interesting Facts & Statistics

• 1 second delay can reduce conversions by 7%

• OPcache can improve PHP performance by 2–3×

• MySQL buffer pool cache hit ratio above 99% is ideal

• Nginx handles 10× more concurrent connections than traditional servers

11. FAQs

Q1. Should I optimise Nginx, PHP, or MySQL first? Start with PHP-FPM and MySQL, then tune Nginx.

Q2. Can wrong tuning crash the server? Yes. Over-allocating RAM causes OOM kills.

Q3. Are these values fixed forever? No. Recalculate after traffic growth.

Q4. Do I need load testing? Yes. Use tools like ab, wrk, or k6.

12. Key Takeaways

• Optimisation is calculation-based, not guesswork

• PHP-FPM memory calculation is critical

• MySQL buffer pool has the biggest performance impact

• Nginx handles concurrency, not application logic

• Monitoring is mandatory after tuning

13. Conclusion

Optimising Nginx + PHP + MySQL is not about copying configs from the internet—it is about understanding server resources, calculating limits, and balancing load across layers. A well-optimised stack:

• Handles higher traffic

• Reduces downtime

• Improves user experience

• Saves infrastructure cost

About the Author:Narendra is a DevOps Engineer at AddWebSolution, specializing in automating infrastructure to improve efficiency and reliability.