How to use Let’s Encrypt on Hypernode

in Nginx configurationTools


Let’s Encrypt is a CA Authority that provides free SSL certificates through domain validation and automated retrieval. It is started as a joint effort by big companies in the IT world to provide free and transparent SSL certification and validation through automation.

The key principles behind Let’s Encrypt are, (taken from their website):

  • Free: Anyone who owns a domain name can use Let’s Encrypt to obtain a trusted certificate at zero cost.
  • Automatic: Software running on a web server can interact with Let’s Encrypt to painlessly obtain a certificate, securely configure it for use, and automatically take care of renewal.
  • Secure: Let’s Encrypt will serve as a platform for advancing TLS security best practices, both on the CA side and by helping site operators properly secure their servers.
  • Transparent: All certificates issued or revoked will be publicly recorded and available for anyone to inspect.
  • Open: The automatic issuance and renewal protocol will be published as an open standard that others can adopt.
  • Cooperative: Much like the underlying Internet protocols themselves, Let’s Encrypt is a joint effort to benefit the community, beyond the control of any one organization.

See their website for more information about how to use Let’s Encrypt


To make use of Let’s Encrypt on Hypernodes, we installed the dehydrated Let’s Encrypt client.
This command-line utility orders and renews a certificate through the LE API and stores the retrieved certificates on disk so we can use them in the Nginx configuration.

Configure dehydrated

To configure dehydrated to manage SSL certificates for a domain, add the domain to the list of domains:

echo '' > /data/web/.dehydrated/domains.txt

Then run dehydrated to request a certificate:

dehydrated -c --create-dirs

This will create a directory tree in /data/web/certs with the configured certificates

Make sure you add an entry for each domain record you need ssl for. This means that you should add both the AND on it’s own line to the domains.txt file.

Add existing Let’s Encrypt certificates to be renewed by dehydrated

If you want to use a different Let’s Encrypt client you can do so as well, just place your cert.pem, chain.pem and fullchain.pem files in the /data/web/certs directory in a subdirectory with as name the domain name the certificate is for.

The directory tree will look like this if you have and

find /data/web/certs

When a certificate is renewed, the old certificate will be renamed to cert-unique id for recovery usage.

Manually renew your certificates

To force renewal on your certificates, even when the certificate is longer valid than 30 days, use the --force flags:

dehydrated -c --force

Be careful not to exceed the ratelimits at Let’s Encrypt!

Multiple domains for one shop

Dehydrated does support multi domain certificates but our config generator does not. This implicates that if you want to serve both your www. and apex domain over SSL, you should add both records on it’s own line to .dehydrated/domains.txt to ensure a valid nginx configuration is created for both domains.


cat ~/.dehydrated/domains.txt

Configure the Hypernode and Magento to support Let’s Encrypt

After creating certificates you need to update the Nginx configuration. This is done using the script hypernode-ssl-config-generator.
When you run this script, an SSL enabled Nginx configuration for your shop is generated in /data/web/nginx/ssl

After creating an Nginx configuration, you should adjust your Magento base URL’s to support SSL:

  • For Magento 1:
    magerun sys:store:config:base-url:set # set your baseurl to secure (https)
    magerun cache:clean
  • For Magento 2, check your base-urls with magerun2 sys:store:config:base-url:list. Then change the base-url with:
    cd ~/magento2
    magerun2 config:store:set web/secure/base_url
    magerun2 cache:clean

    Read more: ([]

Or, additionally you can make use of the scripts we created to change your baseurl provided for Magento 1 or for Magento 2

Setup a cron to automatically renew certificates

To periodically check and renew certificates, create a cronjob running dehydrated:

0 1 * * * flock -n /data/web/.dehydrated.lock chronic dehydrated --cron --create-dirs

This will check nightly at 1:00 if there are configured certificates that should be renewed.

Stop using dehydrated / Cleanup

If you want to switch to an SSL certificate managed by Byte (for example you switch to an SSL EV certificate), you can easily remove the configuration and certificated for Let’s Encrypt:

  • Remove the ssl/ directory in /data/web/nginx
  • Remove the certs/ directory in /data/web (you might want to make a backup first)
  • Remove all domains from the /data/web/.dehydrated/domains.txt
  • Remove the cronjob from your crontab
  • Renew the Nginx configuration by running hypernode-ssl-config-generator

If you decide to not use any SSL certificate anymore and switch back to http (not recommended), don’t forget to change your Magento base-url settings back to http : Magento 1 and Magento 2


  • By default, dehydrated renews Let’s Encrypt certificates 30 days before expiring.

  • Make sure your cron is running, else dehydrated will not automagically renew certificates before expiration.

  • You can request a maximum of 20 domains per week per IP and a maximum of 5 certificates per domain per week. See: Let’s Encrypt about ratelimits

  • “Error creating new cert :: Too many certificates already issued for: […]”
    This is not an issue with dehydrated but an API limit with boulder (the Let’s Encrypt CA request server).
    At the time of writing this you can only create 5 certificates per domain in a sliding window of 7 days.

  • “Certificate request has 123 names, maximum is 100.”
    This also is an API limit from boulder, you are requesting to sign a multi domain certificate with way too many domains.

  • “Dehyrdated: Challenge is invalid!”
    This could have multiple causes but the main reason is that Let’s Encrypt could not contact the server challenge. Could be due to a basic auth or a rewrite of the URI. Check the logs for the exact HTTP status code and act accordingly. Whitelist in the necessary nginx config file so that Let’s Encrypt can passthrough the basic authentication.

  • “My certificates are not in the Nginx config”
    This can be caused by a change in your Nginx config not picked up by the nginx-config-reloader. To manually force a reload, touch some files in /data/web/nginx`:

    touch /data/web/nginx/http.magerunmaps

    Or run hypernode-ssl-config-generator

    This error appears in Firefox and is caused by a inconsistency in our configuration. We changed this configuration by disabling OCSP stapling. If you keep getting this error, please recreate your Let’s Encrypt certificate:

    rm -rf /data/web/certs
    dehydrated -c