Jiriaf-fw

JRM Deployment Using FireWorks

This guide provides an overview of the JRM deployment process. Two main components are involved in the deployment: the FireWorks launchpad and the JRM deployment script. The FireWorks launchpad is a MongoDB database that stores the JRM workflows, while the JRM deployment script is a bash script that sets up and runs a Docker container to launch Slurm jobs for deploying JRMs.

FireWorks Launchpad Setup

We adopt FireWorks to manage the JRM deployment. The FireWorks is a workflow management system that facilitates the execution of complex workflows. Please check the FireWorks and NERSC intro to FireWorks for more details.

Launchpad Configuration File for FireWorks

• The file /FireWorks/util/my_launchpad.yaml is a MongoDB configuration file for the launchpad used by FireWorks
• Make sure that the MongoDB port (default is 27017) is accessible to the container. If it's not, verify if the port is open to all interfaces.

Setup on the Database Server

• Establish the database and user as specified in the my_launchpad.yaml file. You can use the FireWorks/util/create_db.sh script to create the database and user.

Setup on the Compute Node

• Prepare the Python environment according to the requirements.txt file.
• Use the FireWorks/util/create_project.py script to set up configuration files. This script will generate two files: my_qadapter.yaml and my_fworker.yaml. You can refer to the example files FireWorks/util/my_launchpad.yaml and FireWorks/util/my_qadapter.yaml for guidance.
• Make sure that the MongoDB is accessible from the compute node. If it's not, consider using SSH tunneling to establish a connection to MongoDB.

JRM Deployment

Now that the FireWorks launchpad is set up, you can proceed with the JRM deployment. The deployment process involves the following steps:

Prerequisites

One must have a NERSC account and have set up the private key (e.g. ~/.ssh/nersc) for log into Perlmutter.

This is due to the fact that the we need the following SSH connections to Perlmutter from the local machine. (They are handled automatically.)

1. Connect to FireWorks MongoDB database.

cmd = f"ssh -i ~/.ssh/nersc -J {self.remote_proxy} -NfR 27017:localhost:27017 {self.remote}"

2. Connect to the K8s API server.

cmd = f"ssh -i ~/.ssh/nersc -J {self.remote_proxy} -NfR {apiserver_port}:localhost:{apiserver_port} {self.remote}"

3. Connect to the JRM for metrics of the JRM.

cmd = f"ssh -i ~/.ssh/nersc -J {self.remote_proxy} -NfL *:{kubelet_port}:localhost:{kubelet_port} {self.remote}"

Step 1: Create SSH Connections

Run the jrm-create-ssh-connections binary. It is an HTTP server that listens on port 8888. This creates SSH connections (db port, apiserver port, and jrm port) as shown in the prerequisites for the JRM deployment. For more details, check the create-ssh-connections/jrm-fw-create-ssh-connections.go file.

Here's what it does:

1. Looks for available ports from 10000 to 19999 on localhost. 2. Runs the commands from FireWorks/gen_wf.py to create SSH connections.

Note: It considers listening ports as NOT available. So, ensure to delete ports that are not in use anymore when deleting JRMs.

To-Do: Add a feature to delete the ports. One can identify the ports by checking the database and searching for the Completed fireworks.

Step 2: Configure Environment Variables

The main.sh script is responsible for initializing the environment variables required to launch JRMs. It sets the following variables:

• nnodes: This represents the number of nodes.
• nodetype: This defines the type of node.
• walltime: This is the walltime allocated for the slurm job and JRM.
• nodename: This is the name assigned to the node.
• site: This is the site name.
• account: This is the account number used for allocation at NERSC.
• qos: This is the queue of service. Refer to compute sites for more details.
• ssh_remote: This is the remote machine to establish SSH connections. (see prerequisites)
• ssh_remote_proxy: This is the remote proxy machine to establish SSH connections. (see prerequisites)
• ssh_key: This is the SSH key used to establish SSH connections. (see prerequisites)
• custom_metrics_ports : This is the port used for custom metrics. It can be multiple ports separated by space. For example, "8080 8081".

The script also creates a directory at $HOME/jrm-launch/logs to store logs. The path to this directory is saved in the logs environment variable.

If one needs to alter these environment variables, one can do so by modifying the FireWorks/gen_wf.py and FireWorks/create_config.sh files.

Step 3: Execute the Script

Pull the docker image jlabtsai/jrm-fw:latest from Docker Hub. This image is used to run the JRM deployment. Execute the main.sh script. This script sets up and initiates a Docker container, which is used to launch Slurm jobs for deploying JRMs. The script accepts the following arguments:

1. add_wf: This argument adds a JRM workflow to the FireWorks database. 2. get_wf: This argument retrieves the table of workflows from the FireWorks database. 3. delete_wf: This argument removes a specific workflow from the FireWorks database.

Walltime Discrepancy Between JRM and Slurm Job

The JIRIAF_WALLTIME variable in FireWorks/gen_wf.py is intentionally set to be 60 seconds less than the walltime of the Slurm job. This is to ensure that the JRM has enough time to initialize and start running.

Once JIRIAF_WALLTIME expires, the JRM will be terminated. The commands for tracking the walltime and terminating the JRM are explicitly defined in the FireWorks/gen_wf.py file, as shown below:

sleep $JIRIAF_WALLTIME
echo "Walltime $JIRIAF_WALLTIME has ended. Terminating the processes."
pkill -f "./start.sh"

Network Map

The figure below serves as an example to illustrate all the ports and SSH tunnelings utilized in the JRM deployment process.

Release Ports and Remove nodes in K8s Cluster on local machine

To release the used ports and remove the nodes in K8s cluster on local, we follow these steps:

1. Refer to the FireWorks launchpad database. Identify the FireWorks (fws) that are in the COMPLETED or RUNNING states. Note that some fws might appear as RUNNING but are actually lost runs if they have been disconnected from the launchpad for a certain period (default is 4 hours).
2. Collect the port numbers from the spec.ssh_metrics.port and spec.ssh_custom_metrics.port.mapped_port fields.
3. Send a POST request to the jrm-delete-ssh-connections endpoint. This will delete the ports and remove the nodes in the K8s cluster.

Ports used in the JRM deployment:

• 27017: MongoDB port
• 8888: SSH connection port
• API_SERVER_PORT: K8s API server port
• 10250: JRM port for metrics server (Select from the available ports in the range of 10000-19999)
• x: Custom metrics ports (Select from the available ports in the range of 20000-49999) (optional)

SSH tunnelings:

On the local machine JIRIAF2301, we establish three essential SSH connections to login04 on Perlmutter when deploying JRMs:

1. ssh -NfR 27017:localhost:27017 login04 for MongoDB
2. ssh -NfR API_SERVER_PORT:localhost:API_SERVER_PORT login04 for K8s API server
3. ssh -NfL *10250:localhost:10250 login04 for JRM metrics
4. ssh -NfL *x:localhost:x login04 for custom metrics (optional)

On the compute node, we establish an SSH connections to the login04 on Perlmutter:

1. ssh -NfL API_SERVER_PORT:localhost:API_SERVER_PORT login04 for K8s API server
2. ssh -NfR *10250:localhost:10250 login04 for JRM metrics
3. ssh -NfR x:localhost:8080 login04 for custom metrics. 8080 is the port where the custom metrics are exposed. (optional)

Figure

Network Map

Github

Check out GitHub

To-do

• [x ] Add a feature to delete the ports. One can identify the ports by checking the database and searching for the Completed fireworks.
• [ ] Automatically generate a prometheus configuration file with mapped ports of custom metrics. This will help in monitoring the custom metrics of JRMs.