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Certificates, also known as SSL certificates or TLS certificates, provide systems and users with a sound method for securely communicating with them or verifying those systems and users' identity. They contain identification information (who or what the certificate belongs to) and a public key, and are signed by a third party called the Certificate Authority.

This article focuses on many details surrounding certificates on Gentoo Linux. Where needed, a slight introduction will be given to the actions or sections presented. The technical details about certificates are better served on different platforms, such as Wikipedia.

Certificate authority

Certificate authorities (should) verify the identity of a user (or owner of a system) and, when verified, sign the certificate with their own private key. This signature is then used by others to assert that a presented certificate is valid and trustworthy. The idea here is that others trust the signature of a certificate authority, and through that trust also accept the presented certificate.

History has shown however that not all certificate authorities are equally trustworthy (take DigiNotar as a prime example). Also improvements in crypto-analysis show that some important parts (such as the hashing algorithm) can contain weaknesses. In 2008 for instance, it was proven that MD5 collisions can be used to create a rogue CA certificate. As such, keeping track of the trusted certificates and their current strength is advisable.

Whenever an application (including browsers) connects to systems over an SSL/TLS connection, part of the handshake is to verify if the presented certificate is signed by a trusted certificate authority. Hence, systems need to track which CA certificates are trustworthy. The collection of trusted CA certificates is often called a truststore.

Managing the truststores on a Linux system is a complex task as applications can use different approaches for handling their certificate-based operations. In the subsequent few sections the most common CA certificate handling approaches are documented.

OpenSSL-compatible ca-certificates

OpenSSL-compatible libraries use the /etc/ssl/certs directory as the (default) truststore. All trusted certificates are listed in this directory (generally through symbolic links to their actual location), together with a single ca-certificates.crt file which has all the trusted CA certificates listed.

By default, this directory is automatically managed through the app-misc/ca-certificates package, which uses the CA certificates from Mozilla's CA certificate store and repackages them for use with OpenSSL-based applications.

On most systems, this package will already be installed:

root #emerge --ask app-misc/ca-certificates

Upon installation, this package

  1. generates the /etc/ca-certificates.conf configuration file by listing all certificates inside /usr/share/ca-certificates inside the configuration file
  2. calls the update-ca-certificates script which reads in this configuration file and updates the /etc/ssl/certs directory accordingly

The update-ca-certificates script also checks if any admin-provided certificates are in /usr/local/share/ca-certificates and adds links to those certificates to the /etc/ssl/certs directory as well.

Most users will be satisfied with the default certificate handling: it uses the CA certificate store from an upstream project that is actively pursuing the secure state of the certificates, and is automatically updated through Portage. However, administrators who want to have a more fine-grained control over which certificates are accepted for the truststore cannot update the /etc/ca-certificates.conf file manually.

New installations of the app-misc/ca-certificates will rewrite this configuration file, and the file is explicitly marked as not governed by Portage's configuration file protection:

user $emerge --info | grep ca-certificate
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf ..."


Another popular library is Mozilla's Network Security Services or NSS. Unlike the OpenSSL-based certificate support, NSS uses database files as the certificate store.

NSS starts off with a hard-coded list of trusted CA certificates inside the libnssckbi.so file, installed through the dev-libs/nss package. This list can be viewed from any of the applications using NSS capable of showing (and manipulating) the trust store, such as Chrome-compatible or Firefox-compatible browsers. However, another approach is to use the certutil application as provided by the dev-libs/nss package:

user $ln -s /usr/lib64/libnssckbi.so $HOME/.pki/nssdb
user $certutil -L -d sql:$HOME/.pki/nssdb/ -h 'Builtin Object Token'
Certificate Nickname                                         Trust Attributes

Builtin Object Token:GlobalSign Root CA                      C,C,C
Builtin Object Token:GlobalSign Root CA - R2                 C,C,C
Builtin Object Token:Verisign Class 1 Public Primary Certification Authority - G3 ,C,  

The trust attributes mentioned in the output show what trust level that attribute has and for which purpose. The certutil man page has some information about what each attribute means. The most important ones are:

  • c—Valid certificate authority
  • C—Trusted certificate authority (implies c)
  • p—Valid peer certificate (i.e. no need to validate if it is signed by a proper CA)
  • P—Trusted peer certificate (often used for self-signed certificates that need to be trusted)

The purpose of the trust attributes is for:

  • SSL—Secure communication over SSL/TLS channels
  • S/MIME—Encryption of messages and e-mail
  • JAR/XPI—Code signing

Alongside the hard-coded certificates, NSS supports a system-wide NSS databases located at /etc/pki/nssdb, and user-specific NSS databases located at ~/.pki/nssdb. The system-wide NSS database can contain the additional CA certificates that should be accepted by all users as well as system applications (and daemons) running on the system, while the user-specific database is - as the name implies - for specific user accounts.

Some applications that use the NSS library use a different certificate store than the recommended user one. Mozilla's own Firefox is a prime example of this.

To query the currently assigned CA certificates:

user $certutil -d sql:$HOME/.pki/nssdb -L

To list a certain certificate information in more detail, add the name:

user $certutil -d sql:$HOME/.pki/nssdb -L -n "EssentialSSL CA"
        Version: 3 (0x2)
        Serial Number:
        Signature Algorithm: PKCS #1 SHA-1 With RSA Encryption
        Issuer: "CN=COMODO Certification Authority,O=COMODO CA Limited,L=Salf
            ord,ST=Greater Manchester,C=GB"
            Not Before: Fri Dec 01 00:00:00 2006
            Not After : Tue Dec 31 23:59:59 2019
        Subject: "CN=EssentialSSL CA,O=COMODO CA Limited,L=Salford,ST=Greater

Application-specific stores

Some applications have their own certificate store.

Adding trusted certificates

The most common operation against truststores is to add additional trusted certificates to it. Companies often have their own PKI (Public Key Infrastructure) setup which supports the internal certificate needs, and which might require the master certificate of this PKI to be trusted, or have it as an intermediate certificate deployed across the truststores in the organization. But even end users might want to add in additional trusted certificates who might not have made the "final" list yet as managed by Mozilla.

Obtaining the certificate

First the certificate itself needs to be obtained. When an organization has its own PKI then this CA certificate can be easily provided by the responsible team, with the necessary additional precautions in place to validate that the certificate is the right one. Other CAs generally distribute their CA certificates on their websites.

End users can also obtain the certificate through the browser by reviewing the SSL/TLS connection information. For instance, with Firefox, this can be obtained through the page information, Security section, View Certificate.

Whatever the source of the certificate, it is recommended to validate the certificate itself by checking (for instance) the checksum of the certificate. Gentoo's infrastructure uses certificates from DigiCert, who has its CA certificates published online together with the thumbprint information of the certificate.

For instance, the DigiCert High Assurance EV Root CA file has the following information published alongside the certificate itself:

  • serial number—a unique identifier for the certificate
  • thumbprint—an (in this case SHA1-based) checksum on the certificate

The downloaded file, which usually has a .crt or .pem suffix, can be validated through the openssl command.

To view certificate information (including the serial number):

user $openssl x509 -in DigiCertHighAssuranceEVRootCA.crt -text
        Version: 3 (0x2)
        Serial Number:
    Signature Algorithm: sha1WithRSAEncryption
        Issuer: C=US, O=DigiCert Inc, OU=www.digicert.com, CN=DigiCert High Assurance EV Root CA
            Not Before: Nov 10 00:00:00 2006 GMT
            Not After : Nov 10 00:00:00 2031 GMT
        Subject: C=US, O=DigiCert Inc, OU=www.digicert.com, CN=DigiCert High Assurance EV Root CA
        Subject Public Key Info:
            Public Key Algorithm: rsaEncryption

To view the thumbprint:

user $openssl x509 -in DigiCertHighAssuranceEVRootCA.crt -noout -sha1 -fingerprint
SHA1 Fingerprint=5F:B7:EE:06:33:E2:59:DB:AD:0C:4C:9A:E6:D3:8F:1A:61:C7:DC:25

Including in the ca-certificates store

Once the certificate has been validated, store it in the /usr/local/share/ca-certificates location:

Ensure that the certificate uses the .crt suffix as this is the only suffix checked by the update-ca-certificates script.
root #cp DigiCertHighAssuranceEVRootCA.crt /usr/local/share/ca-certificates

Run the update-ca-certificates command to update the /etc/ssl/certs location with the new certificate.

root #update-ca-certificates
Updating certificates in /etc/ssl/certs/...
1 added, 0 removed; done
Running hooks in /etc/ca-certificates/update.d...

Including in the NSS database

When applications use the NSS library and honor the /etc/pki/nssdb location, then the following steps can be taken to include this certificate in this system-wide NSS database.

First, create the directory structure for the system-wide NSS database files:

root #mkdir -p /etc/pki/nssdb

Next, create a new database file set. A password will be asked to restrict editing of the database files to people who know the password. If all users on the system (and with access to the backups) are trustworthy, then this password can be kept empty.

root #certutil -d sql:/etc/pki/nssdb -N
Enter a password which will be used to encrypt your keys.
The password should be at least 8 characters long,
and should contain at least one non-alphabetic character.
Enter new password:
Re-enter new password:

Ensure that the database files are readable by everyone:

root #chmod go+r /etc/pki/nssdb/*
The above instructions only apply if no system-wide NSS database file set exists yet. If one exists already, then it is vital to know the password on this database set (assuming it is password-protected of course).

With the NSS database files now available, add the certificate to the store as follows:

root #certutil -d sql:/etc/pki/nssdb -A -i certificateFile.crt -n "certificateName" -t "C,,"

The trust bits used in the above example mark the certificate as trustworthy for signing certificates used for SSL/TLS communication. The name used in the command is free to choose, but make sure to have it easily distinguished from other certificates in the store.

Similar instructions can be used to include the certificate only in the NSS database of a particular user:

user $certutil -d sql:$HOME/.pki/nssdb -A -i certificateFile.crt -n "certificateName" -t "C,,"

Including in browser stores

A number of browsers, including Chromium and Firefox, do not use the system-wide CA certificate store. Most browsers have an intuitive interface to handle the certificates they manage. To add a custom certificate to Chromium (and to Chromium-based browsers), refer to this section of the 'Chromium' page; to add a custom certificate to Firefox, refer to this section of the 'Firefox' page.

Raphaël Barrois describes, on his blog, how to get Firefox and Chromium to share the same ~/.pki/nssdb/ location.

Removing certificates

Certificates that were manually added using the instructions above can be removed from the stores easily as well.

Removing from ca-certificates store

To remove the certificate from the /etc/ssl/certs location, remove it from the /usr/local/share/ca-certificates location and run the update-ca-certificates command again.

root #rm /usr/local/share/ca-certificates/certificateFile.crt
root #update-ca-certificates
Updating certificates in /etc/ssl/certs/...
0 added, 1 removed; done
Running hooks in /etc/ca-certificates/update.d...

Removing from NSS database files

To remove the certificate from any NSS database, use the certutil command as follows. The example uses the system-wide NSS database location, but can be easily adjusted for the user-specific ~/.pki/nssdb locations.

root #certutil -d sql:/etc/pki/nssdb -D -n "certificateName"

Modifying CA trusts

Although most administrators will be happy with the default CA handling, there will be situations where one wants to modify the default CA handling approaches. This could be due to - company policy requiring a fixed and company-approved list of CAs to be trusted, and nothing more - reports about trust issues with a root CA - the need or will to start off with an empty trust store and build up - requiring different trust stores per application

Whatever the reason, the next few sections will describe how to manipulate the previously discussed trust stores.

Modifying the OpenSSL-compatible ca-certificates

To handle custom CA lists, a secondary CA certificates configuration file needs to be managed, and after every installation of the app-misc/ca-certificates package the ca-certificates.conf file needs to be overwritten and update-ca-certificates needs to be executed again. This can be accomplished through Portage' /etc/portage/env sourcing.

Assuming that the secondary CA certificates configuration file is called /etc/custom-ca-certificates.conf. To have this file copied over to the ca-certificates.conf file after every app-misc/ca-certificates package installation, the following script can be used:

FILE /etc/portage/env/app-misc/ca-certificatesOverwriting the ca-certificates.conf file
# Execute this logic after the installation
post_pkg_postinst() {
  local CUSTOMFILE="/etc/custom-ca-certificates.conf"
  local CACONFIG="/etc/ca-certificates.conf"
  if [[ -f "${CUSTOMFILE}" ]] ; then
    echo "Redeploying custom ca-certificates.conf file."
    install -o root -g root -m 644 "${CUSTOMFILE}" "${CACONFIG}" && \

All that the administrator has to do now is to keep the custom-ca-certificates.conf file up to date with the certificates of the CAs he wants to trust on this system. For instance, to only trust Verisign:

FILE /etc/custom-ca-certificates.confListing only Verisign's certificates

As was mentioned before, these entries are relative to the /usr/share/ca-certificates directory. Custom certificates can be added in /usr/local/share/ca-certificates and do not need to be listed in the ca-certificates.conf file for update-ca-certificates to take them into account.

NSS-based modifications

The NSS library has three levels that might require any manipulations:

  1. the hard-coded list of trusted CAs
  2. the system-wide NSS databases
  3. the user- or application-specific NSS databases

Manipulating the hard-coded list

Although common sense would imply that applications which use the NSS library would also consult the system-wide database, this is more exception than rule. Neither Chromium nor Firefox (or any of the derived browsers) support the system-wide database. Hence, the below instructions are generally ineffective on a system-wide basis, but can be altered to suit per-application specific databases.

The recommended method for manipulating the hard-coded list is to change the trust attributes for the selected certificates in the system-wide NSS database. While the certificates are still listed in the libnssckbi.so file, they are then no longer marked as trusted.

Link in the hard-coded list, and then modify the trust bits for the certificate that needs modifying:

root #ln -s /usr/lib64/libnssckbi.so /etc/pki/nssdb
root #certutil -d sql:/etc/pki/nssdb -M -n "Builtin Object Token:certificate name" -t ",,"

Modifying the NSS databases

Any manipulation to an NSS database file can be done through the certutil command. More fancy user interfaces are available as well, but the certutil commands are easy to use and to automate.

To remove a CA certificate from the store:

user $certutil -d sql:$HOME/.pki/nssdb -D -n "certificatename"

To add a root CA certificate to the store:

user $certutil -d sql:$HOME/.pki/nssdb -A -t "C,," -n "certificatename" -i "certificate_filename"

To add an intermediate CA certificate to the store:

user $certutil -d sql:$HOME/.pki/nssdb -A -t ",," -n "certificatename" -i "certificate_filename"

To add a self-signed certificate to the store:

user $certutil -d sql:$HOME/.pki/nssdb -A -t "P,," -n "certificatename" -i "certificate_filename"

To modify the trust attributes of a certificate:

user $certutil -d sql:$HOME/.pki/nssdb -M -n "certificatename" -t "attr1,attr2,attr3"

Debugging certificate issues

This section is mostly for Gentoo developers to help with debugging common issues reported by users rather than a generic "certificate problems". That topic is much too large to reasonably tackle here, so if these tips don't help, please fallback to searching the internet like normal.

Certificate failures can be difficult to debug, not the least of which is due to the tools having hard-to-use interfaces. Here's some tips for debugging failures.


Certificates come in many different file formats, often use inconsistent or incorrect file extensions, and tools might expect inputs in specific formats. Try not to assume too much based purely on the file extension. Start with a tool like less or file to try to figure out what format it's in.

DER format is a binary format meant only for tools to read. It is usually possible to convert it to a PEM format that contains the same information, but as plain text. Some tools only accept PEM, so try converting it:

user $openssl x509 -inform der -in "DER file" -out "PEM file"

Once it's in the PEM format, view it:

user $openssl x509 -hash -text -noout -in "PEM file"

Fetching certificates from network services

To see what certificates a site is presenting over the network, use OpenSSL to start a connection and dump various useful details:

user $openssl s_client -showcerts -port 443 -CApath /etc/ssl/certs -host "HOSTNAME" </dev/null | less

To save the certificates for further analysis, simply redirect the output, then use a typical pager.

When Less is given a .pem filename, it will automatically use OpenSSL to decode & display it, and OpenSSL will only decode the first certificate it finds (while ignoring all other lines). Using < bypasses that feature to view the full file contents.
user $openssl s_client -showcerts -port 443 -CApath /etc/ssl/certs -host "HOSTNAME" </dev/null >bundle.pem
user $less bundle.pem
user $less <bundle.pem

Checking the certificate chain

The tools show subject (s) and issuer (i) lines with human readable entries so it's easy to track & correlate things. While that's not exactly how certificates are looked up (since anyone can spoof those fields), the examples here will assume the certificates are reasonable (i.e. not malicious) for the sake of brevity.

OpenSSL's s_client command will display the certificate chain. Look at example.com:

user $openssl s_client -showcerts -port 443 -CApath /etc/ssl/certs -host example.com </dev/null
Certificate chain
 0 s:C = US, ST = California, L = Los Angeles, O = Internet Corporation for Assigned Names and Numbers, CN = www.example.org
   i:C = US, O = DigiCert Inc, CN = DigiCert TLS RSA SHA256 2020 CA1
 1 s:C = US, O = DigiCert Inc, CN = DigiCert TLS RSA SHA256 2020 CA1
   i:C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA
 2 s:C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA
   i:C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA

The first certificate [subject] s:C = US, ST = California, L = Los Angeles, O = Internet Corporation for Assigned Names and Numbers, CN = www.example.org is the example.com server. It's signed by the intermediate certificate [issuer] C = US, O = DigiCert Inc, CN = DigiCert TLS RSA SHA256 2020 CA1 which is signed by the root certificate C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA. The root certificate then signs itself, and while self-signed certificates are normally not accepted, since it's in the truststore, it's trusted to do that.

OpenSSL's verify command can verify certificates manually, but it too only operates on the first certificate found in the file. Extract the individual certificates out and double check they extracted correctly:

user $sed -n '/^ 0/,/-----END CERTIFICATE-----/p' bundle.pem > server.pem
user $openssl x509 -hash -text -noout -in server.pem | grep -E -e '(Issuer|Subject):'
Issuer: C = US, O = DigiCert Inc, CN = DigiCert TLS RSA SHA256 2020 CA1
Subject: C = US, ST = California, L = Los Angeles, O = Internet Corporation for Assigned Names and Numbers, CN = www.example.org
user $sed -n '/^ 1/,/-----END CERTIFICATE-----/p' bundle.pem > intermediate.pem
user $openssl x509 -hash -text -noout -in intermediate.pem | grep -E -e '(Issuer|Subject):'
Issuer: C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA
Subject: C = US, O = DigiCert Inc, CN = DigiCert TLS RSA SHA256 2020 CA1
user $sed -n '/^ 2/,/-----END CERTIFICATE-----/p' bundle.pem > root.pem
user $openssl x509 -hash -text -noout -in root.pem | grep -E -e '(Issuer|Subject):'
Issuer: C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA
Subject: C = US, O = DigiCert Inc, OU = www.digicert.com, CN = DigiCert Global Root CA

Finally the certificates can be verified. Walk back from the root certificate which should be accepted because it's in the truststore:

user $openssl verify -CApath /etc/ssl/certs/ root.pem
root.pem: OK

Then the intermediate certificate should be accepted because its issuer is in the truststore:

user $openssl verify -CApath /etc/ssl/certs/ intermediate.pem
intermediate.pem: OK

Then the server certificate should fail! This is because the verify command only checks the truststore, and while the root certificate is in there, the intermediate certificate is not.

user $openssl verify -CApath /etc/ssl/certs/ server.pem
C = US, ST = California, L = Los Angeles, O = Internet Corporation for Assigned Names and Numbers, CN = www.example.org
error 20 at 0 depth lookup: unable to get local issuer certificate
error server.pem: verification failed

To verify the server certificate, provide the intermediate certificate at the same time. OpenSSL will take care of walking the chain of trust. Be sure to use -untrusted so the certificate isn't inadvertently added to the truststore.

user $openssl verify -CApath /etc/ssl/certs/ -untrusted intermediate.pem server.pem
server.pem: OK


How are new CA's added to Gentoo?

Gentoo does not accept any custom certificate authorities. The project does not have the time, resources, or expertise to properly vet certificate authorities which is why we utilize NSS for its truststore.

To add a new root CA to the default Gentoo install, please go through Mozilla's CA Certificate Program. Once it's accepted by Mozilla, updating Gentoo is pretty easy.

My certificate used to be recognized, but no longer is!

If a certificate used to work but no longer does, the root certificate might have been removed from the truststore because it had problems (e.g. was insecure). See Mozilla's list of removed CA's for more information.

This could also explain why a website used to work but is now marked as insecure.

Why is a certificate not recognized and/or marked as insecure?

All certificates must be trusted by an entry in the truststore, either directly by a root certificate in the truststore (which is possible, but a bit uncommon), or indirectly by intermediate certificates that themselves chain back to a trusted root certificate. The Wikipedia Chain of trust article goes into a lot more detail, as does Let’s Encrypt Chain of Trust article.

Usually when a certificate is unable to be verified, it's because an intermediate certificate is missing. For example, a service presented the last certificate in the chain (its own) and expected either to have the intermediate certificate already, or be able to fetch it from somewhere. Both of these assumptions are usually incorrect and the service should actually be providing a certificate bundle instead: not only their own certificate, but the intermediate certificates back to the relevant root certificate that is in the truststore. This way the client is able to follow the trust chain back to its own truststore.

If a certificate chain ends in a root certificate that is not in Gentoo's default truststore, see the previous FAQs.

Can intermediate certificates be added to the truststore?

See the previous FAQ about adding a new CA to Gentoo to start with. Building off of that answer, intermediate certificates are typically not included in the truststore. Maintaining the existing list of root certificates requires a lot of effort & toil and there's only <150 of those. There are orders of magnitude more intermediate certificates out there (thousands, if not more) that individual certificate authorities create & destroy as makes sense for their needs & structure. Requiring review by Mozilla, and then updates rolling out to distros & users, adds a large amount of toil for no gain.

This is the status quo for all operating systems, browsers, distros, and system builders. Gentoo alone including an arbitrary intermediate certificate won't actually help any users on all those other systems, and servers would still have to provide them to keep everyone working.

See also

The following articles on Gentoo's wiki are related to certificates as well.

External resources