passenger-config and passenger-status result in an error on CentOS7.

• CentOS Linux release 7.2.1511 (Core)
• Apache/2.4.6 (CentOS)
• Phusion Passenger 5.0.23 (Installed by `passenger-install-apache2-module`)

$ passenger-config restart-app
*** ERROR: Phusion Passenger doesn't seem to be running. If you are sure that it
is running, then the causes of this problem could be one of:

 1. You customized the instance registry directory using Apache's
    PassengerInstanceRegistryDir option, Nginx's
    passenger_instance_registry_dir option, or Phusion Passenger Standalone's
    --instance-registry-dir command line argument. If so, please set the
    environment variable PASSENGER_INSTANCE_REGISTRY_DIR to that directory
    and run this command again.
 2. The instance directory has been removed by an operating system background
    service. Please set a different instance registry directory using Apache's
    PassengerInstanceRegistryDir option, Nginx's passenger_instance_registry_dir
    option, or Phusion Passenger Standalone's --instance-registry-dir command
    line argument.

Reason

Passenger could not find instance registry directory (PassengerInstanceRegistryDir on Apache, passenger_instance_registry_dir on Nginx).

If instance registry directory is not explicitly specified, default value /tmp is used.
So instance registry dir is made in /tmp. But because Systemd PrivateTmp option is enabled on httpd (default), instance registry dir is created in httpd's private /tmp directory (/tmp/systemd-private-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-httpd.service-XXXXXX/tmp). This directory can't be found by other processes such as passenger-config or passenger-status.

This problem owes to Systemd's PrivateTmp, so it may also occurs on RHEL7 or Amazon Linux 2.

Workaround 1: Explicitly specify PassengerInstanceRegistryDir

This workaround remains Systemd's PrivateTmp enabled.
Explicitly specify Passenger's instance registry directory so that instance registry dir is not made in httpd's private /tmp directory.

[/etc/tmpfiles.d/passenger.conf:1] Line references path below legacy directory /var/run/, updating /var/run/passenger-instreg → /run/passenger-instreg; please update the tmpfiles.d/ drop-in file accordingly.

（on Apache）
/etc/httpd/conf/httpd.conf

PassengerInstanceRegistryDir /run/passenger-instreg

Because files and directories in /run is deleted on reboot, you must add config file in tmpfiles.d.
See man 5 tmpfiles.d for details.

/etc/tmpfiles.d/passenger.conf

D /run/passenger-instreg 0755 root root

You must add PASSENGER_INSTANCE_REGISTRY_DIR for the users who executes passenger-status and passenger-config.

~/.bash_profile

export PASSENGER_INSTANCE_REGISTRY_DIR=/run/passenger-instreg

If you use capistrano-passenger, you must set PASSENGER_INSTANCE_REGISTRY_DIR in the stage's deploy recipe because capistrano-passenger executes `passenger-config restart-app`.

set :default_env, {
  ...(omit)..,
  "PASSENGER_INSTANCE_REGISTRY_DIR" => "/run/passenger-instreg"
}

Finally restart system.

Workaround 2: Disable PrivateTmp on httpd.service

This workaround disables Systemd's PrivateTmp on httpd.service.

$ sudo systemctl edit httpd.service

[Service]
PrivateTmp=false

Then execute below.

$ sudo systemctl restart httpd.service

Copy /usr/lib/systemd/system/httpd.service to /etc/systemd/system and edit it.

/etc/systemd/system/httpd.service

...（omit）
PrivateTmp=false
...（omit）

Then execute below.

$ sudo systemctl daemon-reload
$ sudo systemctl restart httpd.service

Source: CentOS 7 で Phusion Passenger の passenger-status を実行するとエラーとなる - Qiita
お前らもさっさとハマって泣くべきCentOS7の落とし穴4つ - Qiita
Handle systemd PrivateTmp #1475
Systemd入門(5) - PrivateTmpの実装を見る - めもめも