Q:

ssh authentication failure with public/private keys

I'm setting up a Continuous Deployment pipeline on gitlab.
Unfortunately, when trying to ssh from the pipeline to the target server, the authentication fails.
I am asking the question here because I am fairly sure the problem is unix related and not gitlab.
Here is the setup:

Using ssh-keygen I created a key pair.
I added the public key in ~/.ssh/authorized_keys on the server.
The private key is export in an env var 'SSH_PRIVATE_KEY' on the client server.
permissions on the server: ~/.ssh 700, ~/.ssh/authorized_keys 600
sshd configs on the server are all defaults.

On commit, gitlab spins up a docker executor (docker image node:11.2).
Then, those commands are executed inside the container:
'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
eval $(ssh-agent -s)

    ##
    ## Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
    ## We're using tr to fix line endings which makes ed25519 keys work
    ## without extra base64 encoding.
    ## https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
    ##
echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add - > /dev/null

mkdir -p ~/.ssh
chmod 700 ~/.ssh

echo "$SSH_PRIVATE_KEY" > ~/.ssh/known_hosts
chmod 644 ~/.ssh/known_hosts
ssh -vvv user@server

I followed the instructions here: https://docs.gitlab.com/ce/ci/ssh_keys/
Here is the output of my execution: 
Running with gitlab-runner 11.5.0 (3afdaba6)
  on Runner2 7eb17b67
Using Docker executor with image node:11.2 ...
Pulling docker image node:11.2 ...
Using docker image sha256:e9737a5f718d8364a4bde8d82751bf0d2bace3d1b6492f6c16f1526b6e73cfa4 for node:11.2 ...
Running on runner-7eb17b67-project-40-concurrent-0 via server...
Fetching changes...
Removing node_modules/
HEAD is now at aa4a605 removing bugged command line
Checking out aa4a6054 as integrate_cd...
Skipping Git submodules setup
Checking cache for default...
No URL provided, cache will be not downloaded from shared cache server. Instead a local version of cache will be extracted. 
Successfully extracted cache
$ which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )
/usr/bin/ssh-agent
$ eval $(ssh-agent -s)
Agent pid 14
$ echo "$SSH_PRIV_KEY" | ssh-add - > /dev/null
Identity added: (stdin) ((stdin))
$ mkdir -p ~/.ssh
$ chmod 700 ~/.ssh
$ echo "$SSH_KNOWNHOST_KEY" > ~/.ssh/known_hosts
$ chmod 644 ~/.ssh/known_hosts
$ ssh -p 5555 -vvv user@server
OpenSSH_7.4p1 Debian-10+deb9u4, OpenSSL 1.0.2l  25 May 2017
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
Pseudo-terminal will not be allocated because stdin is not a terminal.
debug2: resolving "server" port 22
debug2: ssh_connect_direct: needpriv 0
debug1: Connecting to servee[x.x.x.x] port 22
debug1: Connection established.
debug1: permanently_set_uid: 0/0
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_rsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_rsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_dsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_dsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_ecdsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_ecdsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_ed25519 type -1
debug1: key_load_public: No such file or directory
debug1: identity file /root/.ssh/id_ed25519-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_7.4p1 Debian-10+deb9u4
debug1: Remote protocol version 2.0, remote software version OpenSSH_7.2
debug1: match: OpenSSH_7.2 pat OpenSSH* compat 0x04000000
debug2: fd 3 setting O_NONBLOCK
debug1: Authenticating to server:22 as 'user'
debug3: put_host_port: [server]:22
debug3: hostkeys_foreach: reading file "/root/.ssh/known_hosts"
debug3: record_hostkey: found key type RSA in file /root/.ssh/known_hosts:2
debug3: record_hostkey: found key type ECDSA in file /root/.ssh/known_hosts:4
debug3: record_hostkey: found key type ED25519 in file /root/.ssh/known_hosts:6
debug3: load_hostkeys: loaded 3 keys from [server]:22
debug3: order_hostkeyalgs: prefer hostkeyalgs: ecdsa-sha2-nistp256-cert-v01@openssh.com,ecdsa-sha2-nistp384-cert-v01@openssh.com,ecdsa-sha2-nistp521-cert-v01@openssh.com,ssh-ed25519-cert-v01@openssh.com,ssh-rsa-cert-v01@openssh.com,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,ssh-ed25519,rsa-sha2-512,rsa-sha2-256,ssh-rsa
debug3: send packet: type 20
debug1: SSH2_MSG_KEXINIT sent
debug3: receive packet: type 20
debug1: SSH2_MSG_KEXINIT received
debug2: local client KEXINIT proposal
debug2: KEX algorithms: curve25519-sha256,curve25519-sha256@libssh.org,ecdh-sha2-nistp256,ecdh-sha2-nistp384,ecdh-sha2-nistp521,diffie-hellman-group-exchange-sha256,diffie-hellman-group16-sha512,diffie-hellman-group18-sha512,diffie-hellman-group-exchange-sha1,diffie-hellman-group14-sha256,diffie-hellman-group14-sha1,ext-info-c
debug2: host key algorithms: ecdsa-sha2-nistp256-cert-v01@openssh.com,ecdsa-sha2-nistp384-cert-v01@openssh.com,ecdsa-sha2-nistp521-cert-v01@openssh.com,ssh-ed25519-cert-v01@openssh.com,ssh-rsa-cert-v01@openssh.com,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,ssh-ed25519,rsa-sha2-512,rsa-sha2-256,ssh-rsa
debug2: ciphers ctos: chacha20-poly1305@openssh.com,aes128-ctr,aes192-ctr,aes256-ctr,aes128-gcm@openssh.com,aes256-gcm@openssh.com,aes128-cbc,aes192-cbc,aes256-cbc
debug2: ciphers stoc: chacha20-poly1305@openssh.com,aes128-ctr,aes192-ctr,aes256-ctr,aes128-gcm@openssh.com,aes256-gcm@openssh.com,aes128-cbc,aes192-cbc,aes256-cbc
debug2: MACs ctos: umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-sha1
debug2: MACs stoc: umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-sha1
debug2: compression ctos: none,zlib@openssh.com,zlib
debug2: compression stoc: none,zlib@openssh.com,zlib
debug2: languages ctos: 
debug2: languages stoc: 
debug2: first_kex_follows 0 
debug2: reserved 0 
debug2: peer server KEXINIT proposal
debug2: KEX algorithms: curve25519-sha256@libssh.org,ecdh-sha2-nistp256,ecdh-sha2-nistp384,ecdh-sha2-nistp521,diffie-hellman-group-exchange-sha256,diffie-hellman-group14-sha1
debug2: host key algorithms: ssh-rsa,rsa-sha2-512,rsa-sha2-256,ssh-dss,ecdsa-sha2-nistp256,ssh-ed25519
debug2: ciphers ctos: chacha20-poly1305@openssh.com,aes128-ctr,aes192-ctr,aes256-ctr,aes128-gcm@openssh.com,aes256-gcm@openssh.com
debug2: ciphers stoc: chacha20-poly1305@openssh.com,aes128-ctr,aes192-ctr,aes256-ctr,aes128-gcm@openssh.com,aes256-gcm@openssh.com
debug2: MACs ctos: umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-sha1
debug2: MACs stoc: umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-sha1
debug2: compression ctos: none,zlib@openssh.com
debug2: compression stoc: none,zlib@openssh.com
debug2: languages ctos: 
debug2: languages stoc: 
debug2: first_kex_follows 0 
debug2: reserved 0 
debug1: kex: algorithm: curve25519-sha256@libssh.org
debug1: kex: host key algorithm: ecdsa-sha2-nistp256
debug1: kex: server->client cipher: chacha20-poly1305@openssh.com MAC: <implicit> compression: none
debug1: kex: client->server cipher: chacha20-poly1305@openssh.com MAC: <implicit> compression: none
debug3: send packet: type 30
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug3: receive packet: type 31
debug1: Server host key: ecdsa-sha2-nistp256 SHA256:1MfReEPXf/ResuMnmG/nEgimB5TxF1AcA2j4LBHBbTU
debug3: put_host_port: [x.x.x.x]:22
debug3: put_host_port: [server]:22
debug3: hostkeys_foreach: reading file "/root/.ssh/known_hosts"
debug3: record_hostkey: found key type RSA in file /root/.ssh/known_hosts:2
debug3: record_hostkey: found key type ECDSA in file /root/.ssh/known_hosts:4
debug3: record_hostkey: found key type ED25519 in file /root/.ssh/known_hosts:6
debug3: load_hostkeys: loaded 3 keys from [server]:22
debug3: hostkeys_foreach: reading file "/root/.ssh/known_hosts"
debug1: Host '[server]:22' is known and matches the ECDSA host key.
debug1: Found key in /root/.ssh/known_hosts:4
Warning: Permanently added the ECDSA host key for IP address '[x.x.x.x]:22' to the list of known hosts.
debug3: send packet: type 21
debug2: set_newkeys: mode 1
debug1: rekey after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug3: receive packet: type 21
debug1: SSH2_MSG_NEWKEYS received
debug2: set_newkeys: mode 0
debug1: rekey after 134217728 blocks
debug2: key: (stdin) (0x55ff2d56d630), agent
debug2: key: /root/.ssh/id_rsa ((nil))
debug2: key: /root/.ssh/id_dsa ((nil))
debug2: key: /root/.ssh/id_ecdsa ((nil))
debug2: key: /root/.ssh/id_ed25519 ((nil))
debug3: send packet: type 5
debug3: receive packet: type 7
debug1: SSH2_MSG_EXT_INFO received
debug1: kex_input_ext_info: server-sig-algs=<rsa-sha2-256,rsa-sha2-512>
debug3: receive packet: type 6
debug2: service_accept: ssh-userauth
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug3: send packet: type 50
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug3: start over, passed a different list publickey,keyboard-interactive
debug3: preferred gssapi-keyex,gssapi-with-mic,publickey,keyboard-interactive,password
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: (stdin)
debug3: send_pubkey_test
debug3: send packet: type 50
debug2: we sent a publickey packet, wait for reply
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug1: Trying private key: /root/.ssh/id_rsa
debug3: no such identity: /root/.ssh/id_rsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_dsa
debug3: no such identity: /root/.ssh/id_dsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_ecdsa
debug3: no such identity: /root/.ssh/id_ecdsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_ed25519
debug3: no such identity: /root/.ssh/id_ed25519: No such file or directory
debug2: we did not send a packet, disable method
debug3: authmethod_lookup keyboard-interactive
debug3: remaining preferred: password
debug3: authmethod_is_enabled keyboard-interactive
debug1: Next authentication method: keyboard-interactive
debug2: userauth_kbdint
debug3: send packet: type 50
debug2: we sent a keyboard-interactive packet, wait for reply
debug3: receive packet: type 60
debug2: input_userauth_info_req
debug2: input_userauth_info_req: num_prompts 1
debug1: read_passphrase: can't open /dev/tty: No such device or address
debug3: send packet: type 61
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug2: userauth_kbdint
debug3: send packet: type 50
debug2: we sent a keyboard-interactive packet, wait for reply
debug3: receive packet: type 60
debug2: input_userauth_info_req
debug2: input_userauth_info_req: num_prompts 1
debug1: read_passphrase: can't open /dev/tty: No such device or address
debug3: send packet: type 61
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug2: userauth_kbdint
debug3: send packet: type 50
debug2: we sent a keyboard-interactive packet, wait for reply
debug3: receive packet: type 60
debug2: input_userauth_info_req
debug2: input_userauth_info_req: num_prompts 1
debug1: read_passphrase: can't open /dev/tty: No such device or address
debug3: send packet: type 61
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug2: we did not send a packet, disable method
debug1: No more authentication methods to try.
Permission denied (publickey,keyboard-interactive).
ERROR: Job failed: exit code 1

I think the ssh interesting part is this:
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: (stdin)
debug3: send_pubkey_test
debug3: send packet: type 50
debug2: we sent a publickey packet, wait for reply
debug3: receive packet: type 51
debug1: Authentications that can continue: publickey,keyboard-interactive
debug1: Trying private key: /root/.ssh/id_rsa
debug3: no such identity: /root/.ssh/id_rsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_dsa
debug3: no such identity: /root/.ssh/id_dsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_ecdsa
debug3: no such identity: /root/.ssh/id_ecdsa: No such file or directory
debug1: Trying private key: /root/.ssh/id_ed25519
debug3: no such identity: /root/.ssh/id_ed25519: No such file or directory
debug2: we did not send a packet, disable method
debug3: authmethod_lookup keyboard-interactive
debug3: remaining preferred: password

It tries to authenticate 

debug2: we sent a publickey packet, wait for reply

But failed with SSH_MSG_USERAUTH_FAILURE right after

debug3: receive packet: type 51

Then it tries a couple public keys that do not exists on the runner.
What is happening? What can cause SSH_MSG_USERAUTH_FAILURE?
Thank you.

A:

Found the answer. 
I got my hand on the logs from the server I was trying to connect too:

sshd[40354]: Authentication refused: bad ownership or modes for
  directory /web

Turns out the user had more rights that supposed on his home repository. Fixed it to drwxr-xr-x resolved the issue.
So it seems that ssh validates the modes for 

.ssh/
.ssh/authorized_keys 
the user HOME repository

