MySqld Service wont start on Redhat7 after a yum update

I'm having a problem with Redhat7 after a yum update. Various services wont start and are giving permissions errors.

Similar problem to Can't start any service after installing iRedMail on CentOS but different OS, so maybe different problem.

Googling the error message brought me to the link above, so I tried some of the same fixes, see output of each below. Please help!

service mysqld restart

Redirecting to /bin/systemctl restart mysqld.service Error getting authority: Error initializing authority: Exhausted all available authentication mechanisms (tried: EXTERNAL, DBUS_COOKIE_SHA1, ANONYMOUS) (available: EXTERNAL, DBUS_COOKIE_SHA1, ANONYMOUS) (g-io-error-quark, 0) Job for mysqld.service failed because the control process exited with error code. See "systemctl status mysqld.service" and "journalctl -xe" for details.

the yum update that I performed yesterday included these packages:

grep "Mar 13.*" /var/log/yum.log  | awk '{ print $5 }' | grep policy

• selinux-policy-3.13.1-166.el7_4.9.noarch
• selinux-policy-targeted-3.13.1-166.el7_4.9.noarch

Tried reinstalling, but no change, also tried reinstalling the following, as well as the selinux policies above. (no joy)

• rpm -qi dbus
• rpm -qi polkit

systemctl status dbus

â dbus.service - D-Bus System Message Bus Loaded: loaded (/usr/lib/systemd/system/dbus.service; static; vendor preset: disabled) Active: active (running) since Wed 2018-03-14 15:12:45 UTC; 47min ago Main PID: 677 (dbus-daemon) CGroup: /system.slice/dbus.service ââ677 /bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --systemd-...

Mar 14 15:12:45 systemd[1]: Started D-Bus System Message Bus.
Mar 14 15:12:45 systemd[1]: Starting D-Bus System Message Bus...
Mar 14 15:29:10 dbus-daemon[677]: dbus[677]: [system] Unable to reload config...ed
Mar 14 15:29:10 dbus-daemon[677]: Unable to reload configuration: Failed to o...ed
Mar 14 15:29:10 dbus-daemon[677]: dbus[677]: [system] Unable to reload config...ed

journalctl -u dbus

Mar 14 15:12:45 systemd[1]: Started D-Bus System Message Bus.
Mar 14 15:12:45 systemd[1]: Starting D-Bus System Message Bus...
Mar 14 15:29:10 dbus-daemon[677]: dbus[677]: [system] Unable to reload configuration: Failed to open "/etc/dbus-1/system.conf": Permission denied
Mar 14 15:29:10 dbus-daemon[677]: Unable to reload configuration: Failed to open "/etc/dbus-1/system.conf": Permission denied

ls -l /etc/dbus-1/system.conf

-rw-r--r-- 1 root root 2991 Sep 12 2016 /etc/dbus-1/system.conf

systemctl start polkit

Error getting authority: Error initializing authority: Exhausted all available authentication mechanisms (tried: EXTERNAL, DBUS_COOKIE_SHA1, ANONYMOUS) (available: EXTERNAL, DBUS_COOKIE_SHA1, ANONYMOUS) (g-io-error-quark, 0) Job for polkit.service failed because a timeout was exceeded. See "systemctl status polkit.service" and "journalctl -xe" for details.

namei -l /etc/dbus-1/system.conf  

f: /etc/dbus-1/system.conf
drwxr-xr-x root root /
drw------- root root etc
drwxr-xr-x root root dbus-1
-rwxr-xr-x root root system.conf

Additionally, here's the full list of things that got upgraded... I'm thinking I should restore from backup...

• 1dhclient-4.2.5-58.el7_4.3.x86_64
• 1dhcp-common-4.2.5-58.el7_4.3.x86_64
• 1dhcp-libs-4.2.5-58.el7_4.3.x86_64
• 3bind-libs-9.9.4-51.el7_4.2.x86_64
• 3bind-libs-lite-9.9.4-51.el7_4.2.x86_64
• 3bind-license-9.9.4-51.el7_4.2.noarch
• 3bind-utils-9.9.4-51.el7_4.2.x86_64
• accountsservice-0.6.45-3.el7_4.1.x86_64
• accountsservice-libs-0.6.45-3.el7_4.1.x86_64
• apr-1.4.8-3.el7_4.1.x86_64
• at-3.1.13-22.el7_4.2.x86_64
• binutils-2.25.1-32.base.el7_4.2.x86_64
• colordiff-1.0.13-2.el7.noarch
• copy-jdk-configs-2.2-5.el7_4.noarch
• cryptsetup-1.7.4-3.el7_4.1.x86_64
• cryptsetup-libs-1.7.4-3.el7_4.1.x86_64
• cryptsetup-python-1.7.4-3.el7_4.1.x86_64
• curl-7.29.0-42.el7_4.1.x86_64
• device-mapper-multipath-0.4.9-111.el7_4.2.x86_64
• device-mapper-multipath-libs-0.4.9-111.el7_4.2.x86_64
• device-mapper-persistent-data-0.7.0-0.1.rc6.el7_4.1.x86_64
• dleyna-server-0.5.0-2.el7_4.x86_64
• dracut-033-502.el7_4.1.x86_64
• dracut-config-rescue-033-502.el7_4.1.x86_64
• dracut-network-033-502.el7_4.1.x86_64
• epel-release-7-11.noarch
• firefox-52.6.0-1.el7_4.x86_64
• gdb-7.6.1-100.el7_4.1.x86_64
• gdm-3.22.3-13.el7_4.x86_64
• glibc-2.17-196.el7_4.2.i686
• glibc-2.17-196.el7_4.2.x86_64
• glibc-common-2.17-196.el7_4.2.x86_64
• gtk3-3.22.10-5.el7_4.x86_64
• gtk3-immodule-xim-3.22.10-5.el7_4.x86_64
• gtk-update-icon-cache-3.22.10-5.el7_4.x86_64
• initscripts-9.49.39-1.el7_4.1.x86_64
• iptables-1.4.21-18.3.el7_4.x86_64
• iptables-services-1.4.21-18.3.el7_4.x86_64
• iwl1000-firmware-39.31.5.1-58.el7_4.noarch
• iwl100-firmware-39.31.5.1-58.el7_4.noarch
• iwl105-firmware-18.168.6.1-58.el7_4.noarch
• iwl135-firmware-18.168.6.1-58.el7_4.noarch
• iwl2000-firmware-18.168.6.1-58.el7_4.noarch
• iwl2030-firmware-18.168.6.1-58.el7_4.noarch
• iwl3160-firmware-22.0.7.0-58.el7_4.noarch
• iwl3945-firmware-15.32.2.9-58.el7_4.noarch
• iwl4965-firmware-228.61.2.24-58.el7_4.noarch
• iwl5000-firmware-8.83.5.1_1-58.el7_4.noarch
• iwl5150-firmware-8.24.2.2-58.el7_4.noarch
• iwl6000-firmware-9.221.4.1-58.el7_4.noarch
• iwl6000g2a-firmware-17.168.5.3-58.el7_4.noarch
• iwl6000g2b-firmware-17.168.5.2-58.el7_4.noarch
• iwl6050-firmware-41.28.5.1-58.el7_4.noarch
• iwl7260-firmware-22.0.7.0-58.el7_4.noarch
• java-1.7.0-openjdk-1.7.0.171-2.6.13.0.el7_4.x86_64
• java-1.7.0-openjdk-headless-1.7.0.171-2.6.13.0.el7_4.x86_64
• java-1.8.0-openjdk-1.8.0.161-0.b14.el7_4.x86_64
• java-1.8.0-openjdk-headless-1.8.0.161-0.b14.el7_4.x86_64
• kernel-3.10.0-693.21.1.el7.x86_64
• kernel-tools-3.10.0-693.21.1.el7.x86_64
• kernel-tools-libs-3.10.0-693.21.1.el7.x86_64
• kmod-20-15.el7_4.7.x86_64
• kmod-libs-20-15.el7_4.7.x86_64
• kpartx-0.4.9-111.el7_4.2.x86_64
• kpatch-0.4.0-2.el7_4.noarch
• libblkid-2.23.2-43.el7_4.2.x86_64
• libcurl-7.29.0-42.el7_4.1.x86_64
• libdb-5.3.21-21.el7_4.i686
• libdb-5.3.21-21.el7_4.x86_64
• libdb-utils-5.3.21-21.el7_4.x86_64
• libgcc-4.8.5-16.el7_4.2.i686
• libgcc-4.8.5-16.el7_4.2.x86_64
• libgomp-4.8.5-16.el7_4.2.x86_64
• libgudev1-219-42.el7_4.10.x86_64
• liblouis-2.5.2-12.el7_4.x86_64
• liblouis-python-2.5.2-12.el7_4.noarch
• libmount-2.23.2-43.el7_4.2.x86_64
• libpciaccess-0.13.4-3.1.el7_4.x86_64
• libreswan-3.20-5.el7_4.x86_64
• libsmbclient-4.6.2-12.el7_4.x86_64
• libsss_idmap-1.15.2-50.el7_4.11.x86_64
• libsss_nss_idmap-1.15.2-50.el7_4.11.x86_64
• libstdc++-4.8.5-16.el7_4.2.i686
• libstdc++-4.8.5-16.el7_4.2.x86_64
• libstoragemgmt-1.4.0-5.el7_4.x86_64
• libstoragemgmt-python-1.4.0-5.el7_4.noarch
• libstoragemgmt-python-clibs-1.4.0-5.el7_4.x86_64
• libteam-1.25-6.el7_4.3.x86_64
• libtevent-0.9.31-2.el7_4.x86_64
• libuuid-2.23.2-43.el7_4.2.x86_64
• libvirt-client-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-config-network-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-interface-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-network-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-nodedev-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-nwfilter-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-qemu-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-secret-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-core-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-disk-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-gluster-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-iscsi-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-logical-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-mpath-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-rbd-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-driver-storage-scsi-3.2.0-14.el7_4.9.x86_64
• libvirt-daemon-kvm-3.2.0-14.el7_4.9.x86_64
• libvirt-libs-3.2.0-14.el7_4.9.x86_64
• libwbclient-4.6.2-12.el7_4.x86_64
• linux-firmware-20170606-58.gitc990aae.el7_4.noarch
• microcode_ctl-2.1-22.5.el7_4.x86_64
• mutter-3.22.3-12.el7_4.x86_64
• mysql-community-client-5.7.21-1.el7.x86_64
• mysql-community-common-5.7.21-1.el7.x86_64
• mysql-community-libs-5.7.21-1.el7.x86_64
• mysql-community-libs-compat-5.7.21-1.el7.x86_64
• mysql-community-server-5.7.21-1.el7.x86_64
• nautilus-3.22.3-4.el7_4.x86_64
• nautilus-extensions-3.22.3-4.el7_4.x86_64
• net-snmp-libs-5.7.2-28.el7_4.1.x86_64
• nfs-utils-1.3.0-0.48.el7_4.2.x86_64
• python-dmidecode-3.12.2-1.1.el7.x86_64
• python-gobject-3.22.0-1.el7_4.1.x86_64
• python-gobject-base-3.22.0-1.el7_4.1.x86_64
• python-perf-3.10.0-693.21.1.el7.x86_64
• qemu-img-1.5.3-141.el7_4.6.x86_64
• qemu-kvm-1.5.3-141.el7_4.6.x86_64
• qemu-kvm-common-1.5.3-141.el7_4.6.x86_64
• rhnsd-5.0.13-7.3.el7_4.x86_64
• samba-client-libs-4.6.2-12.el7_4.x86_64
• samba-common-4.6.2-12.el7_4.noarch
• samba-common-libs-4.6.2-12.el7_4.x86_64
• samba-common-tools-4.6.2-12.el7_4.x86_64
• samba-libs-4.6.2-12.el7_4.x86_64
• selinux-policy-3.13.1-166.el7_4.9.noarch
• selinux-policy-targeted-3.13.1-166.el7_4.9.noarch
• sos-3.4-13.el7_4.noarch
• spice-glib-0.33-6.el7_4.1.x86_64
• spice-gtk3-0.33-6.el7_4.1.x86_64
• sssd-client-1.15.2-50.el7_4.11.x86_64
• swiagent-1.8.0.551-835342.x86_64
• systemd-219-42.el7_4.10.x86_64
• systemd-libs-219-42.el7_4.10.i686
• systemd-libs-219-42.el7_4.10.x86_64
• systemd-python-219-42.el7_4.10.x86_64
• systemd-sysv-219-42.el7_4.10.x86_64
• systemtap-runtime-3.1-5.el7_4.x86_64
• teamd-1.25-6.el7_4.3.x86_64
• tigervnc-license-1.8.0-2.el7_4.noarch
• tigervnc-server-minimal-1.8.0-2.el7_4.x86_64
• tuned-2.8.0-5.el7_4.2.noarch
• tzdata-2018c-1.el7.noarch
• tzdata-java-2018c-1.el7.noarch
• util-linux-2.23.2-43.el7_4.2.x86_64
• webkitgtk4-2.14.7-3.el7.x86_64
• webkitgtk4-jsc-2.14.7-3.el7.x86_64
• webkitgtk4-plugin-process-gtk2-2.14.7-3.el7.x86_64
• xorg-x11-server-common-1.19.3-11.el7_4.2.x86_64
• xorg-x11-server-Xorg-1.19.3-11.el7_4.2.x86_64

drw------- root root etc

That doesn't look correct, /etc should be drwxr-xr-x so

# chmod 755 /etc

will fix that and may fix the wider issue.