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Troubleshooting Munin Update Failures and Complete Guide to the Let’s Encrypt Plugin in WHM

This article explains how to troubleshoot Munin update failures in WHM and provides a complete guide to using the Let’s Encrypt plugin for AutoSSL. It includes steps for diagnosing Munin issues, verifying file ownership, running Munin manually, understanding wildcard SSL behavior, plugin limitations, and recreating Let’s Encrypt registration.

MuninLet’s EncryptAutoSSL

~3 min read • Updated Feb 21, 2026

1. Fixing Munin Update Failures


The Munin plugin in WHM displays system metrics such as CPU, Exim, Apache, MySQL usage, and more using the rrdtool logging system. If Munin fails to update, follow the steps below to resolve the issue.


1.1 Check if Munin Runs During Nightly Maintenance


Ensure that nightly cron maintenance is running and that a Munin crontab entry exists.


The following command should return output similar to this:


crontab -u munin -l

*/5 * * * * /usr/local/cpanel/3rdparty/perl/526/bin/munin-cron

1.2 Verify File Ownership


Ensure that the directories below are owned by munin:munin:


  • /var/lib/munin
  • /var/log/munin

Important: If ownership is incorrect, Munin will update log files but will not update graphs.


To correct ownership, run:


chown -R munin:munin /var/log/munin
chown -R munin:munin /var/lib/munin

1.3 Run Munin Manually


To run Munin manually, execute:


sudo -u munin munin-cron

1.4 Check the Results


New entries should appear in:


/var/log/munin/munin-update


Refresh the Munin interface to update daily graphs.


Note: Weekly graphs update after the time configured in the Munin crontab entry.



2. The Let’s Encrypt Plugin for AutoSSL


This plugin allows AutoSSL to issue certificates from the Let’s Encrypt provider, the default AutoSSL provider in cPanel & WHM. Let’s Encrypt supports wildcard SSL certificates and enforces rate and domain limits.


2.1 Important Notes


  • Let’s Encrypt is the default provider for all future SSL and Wildcard SSL certificates.
  • The Common Name (CN) of an SSL certificate is cosmetic and does not affect security.
  • An SSL certificate covers all domains listed in the SAN (Subject Alternative Name) field.

3. Wildcard Domains


Let’s Encrypt allows AutoSSL to use wildcard domains to reduce the number of domains included in each certificate.


For example, if you have:


  • example.com
  • www.example.com
  • mail.example.com

AutoSSL will request a certificate for:


  • example.com
  • *.example.com

This wildcard certificate covers all first-level subdomains.


Benefits:


  • Smaller certificate size
  • Faster SSL/TLS handshake
  • Reduced risk of hitting Let’s Encrypt domain limits

4. Limitations


  • Wildcard SSL cannot be issued using HTTP DCV challenges.
  • You cannot obtain wildcard certificates if using third-party DNS hosting.

5. Recreate Your Let’s Encrypt Registration


If your Let’s Encrypt registration becomes corrupted or expires, you may need to recreate it.


Steps:


  • Go to WHM » Home » SSL/TLS » Manage AutoSSL
  • Select Let’s Encrypt as your AutoSSL provider
  • Enable Recreate my current registration after accepting the terms

This replaces your existing registration with a new one. It is optional and not required for normal use.


Conclusion


By following these steps, you can resolve Munin update failures and take full advantage of the Let’s Encrypt plugin for issuing SSL certificates, including wildcard SSL. Both tools play an essential role in monitoring and securing cPanel & WHM servers.


Written & researched by Dr. Shahin Siami

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