LinuxHost¶

The LinuxHost adapter facilitates launching jobs immediately without using a batch scheduler or resource manager. Use cases for this non-traditional job adapter include:

Interactive work on login nodes, such as remote desktop or IDE
Providing an option to start an interactive session immediately, without any queue time imposed
Using OnDemand on systems that do not have a supported scheduler installed

The adapter pieces together several tools to achieve behavior similar to what a scheduler offers:

ssh: connects from the web node to a configured host such as a login node.
tmux: Specially named tmux sessions offer the ability to rediscover running jobs
timeout: is used to set a ‘walltime’ after which the job is killed
pstree: is used to detect the job’s parent sinit process so that it can be killed
singularity: containerization provides a PID namespace without requiring elevated privileges that ensures that all child processes are cleaned up when the job either times out or is killed

Note

There are many recipes for managing processes on arbitrary Linux hosts, and we will be exploring others in future development of this adapter.

The adapter and target host can be configured to either:

Enable launching any software installed on the target host
Enable launching a specific application container

The cluster configuration can be shared between both strategies and each interactive app plugin individually configured to use the appropriate strategy.

Launch any software on target host¶

Install on the target host a Singularity base OS image matching the OS of the target host. In the cluster configuration example below we use /opt/ood/linuxhost_adapter/centos_7.6.sif as the target host is running CentOS7.
See Cluster Configuration below to add the cluster configuration file for the target host

This base image is used to provide an unprivileged PID namespace when launching the app. To make the rest of the software installed on the host available to launch within the image, most/all of the host file system is bind-mounted into the running container. For this reason many existing interactive apps will just work when launched by the LinuxHost adapter.

Launch specific application containers¶

Install the specific application containers on the target host.
See Cluster Configuration below to add the cluster configuration file for the target host. Specify a default application container for singularity_image: and singularity_bindpath: even if you will override it.
In each interactive app plugin, specify the image to launch and host directories to mount by setting the native attribute singularity_container and singularity_bindpath. In interactive app plugins these attributes may be set in the file submit.yml. For example:

---
batch_connect:
  template: vnc
script:
  native:
     singularity_bindpath: /fs,/home
     singularity_container: /usr/local/modules/netbeans/netbeans_2019.sif

Cluster Configuration¶

A YAML cluster configuration file for a Linux host looks like:

# /etc/ood/config/clusters.d/owens_login.yml
---
v2:
  metadata:
    title: "Owens"
    url: "https://www.osc.edu/supercomputing/computing/owens"
    hidden: true
  login:
    host: "owens.osc.edu"
  job:
    adapter: "linux_host"
    submit_host: "owens.osc.edu"  # This is the head for a login round robin
    ssh_hosts: # These are the actual login nodes
      - owens-login01.hpc.osc.edu
      - owens-login02.hpc.osc.edu
      - owens-login03.hpc.osc.edu
    site_timeout: 7200
    debug: true
    singularity_bin: /usr/bin/singularity
    singularity_bindpath: /etc,/media,/mnt,/opt,/run,/srv,/usr,/var,/users
    singularity_image: /opt/ood/linuxhost_adapter/centos_7.6.sif
    # Enabling strict host checking may cause the adapter to fail if the user's known_hosts does not have all the roundrobin hosts
    strict_host_checking: false
    tmux_bin: /usr/bin/tmux

with the following configuration options:

adapter: This is set to linux_host.
submit_host: The target execution host for jobs. May be the head for a login round robin. May also be “localhost”.
ssh_hosts: All nodes the submit_host can DNS resolve to.
site_timeout: The number of seconds that a user’s job is allowed to run. Distinct from the length of time that a user selects.
debug: When set to true job scripts are written to $HOME/tmp.UUID_tmux and $HOME/tmp.UUID_sing for debugging purposes. When false those files are written to /tmp and deleted as soon as they have been read.
singularity_bin: The absolute path to the singularity executable on the execution host(s).
singularity_bindpath: The comma delimited list of paths to bind mount into the host; cannot simply be / because Singularity expects certain dot files in its containers’ root; defaults to: /etc,/media,/mnt,/opt,/run,/srv,/usr,/var,/users.
singularity_image: The absolute path to the Singularity image used when simply PID namespacing jobs; expected to be a base distribution image with no customizations.
strict_host_checking: When false the SSH options include StrictHostKeyChecking=no and UserKnownHostsFile=/dev/null this prevents jobs from failing to launch.
tmux_bin: The absolute path to the tmux executable on the execution host(s).

Warning

This adapter was designed with the primary goal of launching installed software on the target host, not launching specific application containers. As a result, even if your use of this adapter is reserved to launching specific application containers, you currently must specify a value in the cluster config for singularity_bindpath and singularity_image, even if these will be specified in each interactive app plugin.

Note

In order to communicate with the execution hosts the adapter uses SSH in BatchMode. The adapter does not take a position on whether authentication is performed by user owned passwordless keys, or host-based authentication; however OSC has chosen to provide host based authentication to its users.

Enforce resource limits on the target host¶

By default the adapter does not limit the user’s CPU or memory utilization, only their “walltime”. The following are two examples of ways to implement resource limits for the LinuxHost Adapter using cgroups.

Approach #1: Systemd user slices¶

With systemd it is possible to manage the resource limits of user logins through each user’s slice. The limits applied to a user slice are shared by all processes belonging to that user, this is not a per-job or per-node resource limit but a per-user limit. When setting the limits keep in mind the sum of all user limits is the max potential resource consumption on a single host.

First update the PAM stack to include the following line:

session     required      pam_exec.so type=open_session /etc/security/limits.sh

This goes into a file used by the sshd PAM configs which on CentOS/RHEL default to /etc/pam.d/password-auth-ac and needs to be included in the proper position, after pam_systemd.so. Also set pam_systemd.so to required:

session     optional      pam_keyinit.so revoke
session     required      pam_limits.so
session     required      pam_systemd.so
session     required      pam_exec.so type=open_session /etc/security/limits.sh
session     [success=1 default=ignore] pam_succeed_if.so service in crond quiet use_uid
session     required      pam_unix.so
session     optional      pam_sss.so

The following example of /etc/security/limits.sh is used by OSC on interactive login nodes. Adjust MemoryLimit and CPUQuota to meet the needs of your site. See man systemd.resource-control

#!/bin/bash
set -e

PAM_UID=$(id -u "${PAM_USER}")

if [ "${PAM_SERVICE}" = "sshd" -a "${PAM_UID}" -ge 1000 ]; then
        /usr/bin/systemctl set-property "user-${PAM_UID}.slice" \
                MemoryAccounting=true MemoryLimit=64G \
                CPUAccounting=true \
                CPUQuota=700%
fi

Approach #2: libcgroup cgroups¶

The libcgroup cgroups rules and configurations are a per-group resource limit where the group is defined in the examples at /etc/cgconfig.d/limits.conf. The following examples limit resources of all tmux processes launched for the LinuxHost Adapter so they all share 700 CPU shares and 64GB of RAM. This requires setting tmux_bin to a wrapper script that in this example will be /usr/local/bin/ondemand_tmux.

Example of /usr/local/bin/ondemand_tmux:

#!/bin/bash
exec tmux "$@"

Setup the cgroup limits at /etc/cgconfig.d/limits.conf:

group linuxhostadapter {
        memory {
                memory.limit_in_bytes="64G";
                memory.memsw.limit_in_bytes="64G";
        }
        cpu {
                cpu.shares="700";
        }
}

Setup the cgroup rules at /etc/cgrules.conf:

*:/usr/local/bin/ondemand_tmux memory linuxhostadapter/
*:/usr/local/bin/ondemand_tmux cpu linuxhostadapter/

Start the necessary services:

sudo systemctl start cgconfig
sudo systemctl start cgred
sudo systemctl enable cgconfig
sudo systemctl enable cgred

Troubleshooting¶

Undetermined state¶

Your job can be in an ‘undetermined state’ because you haven’t listed all the ssh_hosts. ssh_hosts should be anything the submit_host can DNS resolve to. You submit your job the submit_host, but OnDemand is going to poll the ssh_hosts for your job and in this case, your running a job on a node that OnDemand is not polling.

# /etc/ood/config/clusters.d/no_good_config.yml
---
v2:
  job:
    submit_host: "owens.osc.edu"  # This is the head for a login round robin
    ssh_hosts: # These are the actual login nodes
      - owens-login01.hpc.osc.edu
      - owens-login02.hpc.osc.edu
      - # I need 03 and 04 here!

In this example I’ve only configured hosts 01 and 02 (above), but I got scheduled on 03 (you can tell by the ‘job name’) so the adapter now cannot find my job.

../../_images/linux_host_undetermined.png

error while loading shared libraries¶

The default mounts for singularity are '/etc,/media,/mnt,/opt,/srv,/usr,/var,/users'. It’s likely either you’ve overwritten this with too few mounts (like /lib, /opt or /usr) or your container lacks the library in question.

If the library exists on the host, consider mounting it into the container. Otherwise install it in the container definition and rebuild the container.

The job just exists with no errors.¶

This is where turning debug on with debug: true is really going to come in handy.

Enable this, and you’ll see the two shell scripts that ran during this job. Open the file ending in _tmux and you’ll see something like below.

export SINGULARITY_BINDPATH=/usr,/lib,/lib64,/opt
# ... removed for brevity
ERROR_PATH=/dev/null
({
timeout 28800s /usr/bin/singularity exec  --pid /users/PZS0714/johrstrom/src/images/shelf/centos.sif /bin/bash --login /users/PZS0714/johrstrom/tmp.73S0QFxC5e_sing
} | tee "$OUTPUT_PATH") 3>&1 1>&2 2>&3 | tee "$ERROR_PATH"

Export the SINGULARITY_BINDPATH so you’re sure to have the same mounts, and run this /usr/bin/singularity exec ... tmp.73S0QFxC5e_sing command manually on one of the ssh hosts. This will emulate what the linuxhost adapter is doing and you should be able to modify and rerun until you fix the issue.

D-Bus errors¶

Maybe you’ve seen something like below. Mounting /var into the container will likely fix the issue.

Launching desktop 'xfce'...
process 195: D-Bus library appears to be incorrectly set up; failed to read machine uuid: UUID file '/etc/machine-id' should contain a hex string of length 32, not length 0, with no other text
See the manual page for dbus-uuidgen to correct this issue.
  D-Bus not built with -rdynamic so unable to print a backtrace

Again, mounting var fixed this error too.

Starting system message bus: Could not get password database information for UID of current process: User "???" unknown or no memory to allocate password entry

Note

Subsequent versions of the adapter are expected to use unshare for PID namespacing as the default method instead of Singularity. Singularity will continue to be supported.