Here is the workaround:
1. disable start of ssh-agent from openssh by commenting out the use-ssh-agent
line from file "/etc/X11/Xsession.options".
2. start ssh-agent from gnome-keyring daemon and set SSH_AUTH_SOCKET variable
by adding the following to ${HOME}/.profile:
# From man gnome-keyring-daemon:
# Connect to an already running daemon and initialize it.
# This is often used to complete initialization of a daemon that was
# started by PAM using the --login argument.
# Output is SSH_AUTH_SOCKET=path_to_the_socket
if [ -z "$SSH_AUTH_SOCK" ]; then
export `/usr/bin/gnome-keyring-daemon --start`
fi
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https://bugs.launchpad.net/bugs/1586835
Title:
ssh-agent fighting gnome-keyring on Ubuntu Gnome 16.04
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