Tracking UNKNOWN states in Rocoto and suggested updates - TerrenceMcGuinness-NOAA/global-workflow GitHub Wiki

Rocoto is a workflow management system designed to manage and monitor batch jobs on various high-performance computing (HPC) systems. Here are some key points about its functionality:

Batch System Integration:
- Rocoto integrates with multiple batch systems like TORQUE, MOAB, SLURM, and COBALT. Each batch system has a corresponding class (e.g., TORQUEBatchSystem, MOABTORQUEBatchSystem, SLURMBatchSystem, COBALTBatchSystem) that handles job submission, status checking, and deletion.
Job Management:
- The system can submit jobs, check their statuses, and delete them as needed. For example, the submit, status, and delete methods in the batch system classes handle these operations.
Error Handling and Logging:
- Rocoto includes robust error handling and logging mechanisms. Errors are logged and printed to standard error, and specific exceptions like WorkflowMgr::SchedulerDown are raised when batch system commands fail.
Configuration and Initialization:
- The system is configurable, with timeouts and other settings being read from a configuration object during initialization. For example, the initialize methods in the batch system classes read configuration settings to set up timeouts and other parameters.
XML Parsing:
- Rocoto parses XML output from batch system commands to build job status records. For instance, the refresh_jobqueue method in TORQUEBatchSystem parses XML output from the qstat command.
Proxy Mechanism:
- The BQSProxy class acts as a proxy to batch system servers, handling communication and retries in case of connection errors.
Command-Line Tools:
- The bin/ and sbin/ directories contain various command-line tools for interacting with the Rocoto system, such as rocotoboot, rocotocheck, rocotorun, and rocotostat.

Overall, Rocoto is designed to facilitate the management of complex workflows on HPC systems by providing a unified interface for interacting with different batch systems, handling job submission and monitoring, and ensuring robust error handling and logging.

TerrenceMcGuinness-NOAA: What are the states Rocoto displays for the jobs being tracked in the Bash System?

GitHub Copilot: The states Rocoto displays for the jobs being tracked in the Torque Batch System are:

QUEUED - This state is assigned when the job state matches any of the following: Q, H, W, S, T.
RUNNING - This state is assigned when the job state matches either R or E.
UNKNOWN - This state is assigned when the job state does not match any of the above.

These states are determined in the following part of the code:

case jobstat.content
  when /^Q$/,/^H$/,/^W$/,/^S$/,/^T$/
    record[:state]="QUEUED"
  when /^R$/,/^E$/
    record[:state]="RUNNING"
  else
    record[:state]="UNKNOWN"
end

TerrenceMcGuinness-NOAA: What does UNKOWN mean specificly?

GitHub Copilot: In the context of the provided code, the UNKNOWN state is assigned to a job when its job_state does not match any of the predefined states (Q, H, W, S, T, R, E). This means that the job is in a state that is not recognized or handled by the current logic in the script.

Here's the relevant part of the code for clarity:

case jobstat.content
  when /^Q$/,/^H$/,/^W$/,/^S$/,/^T$/
    record[:state]="QUEUED"
  when /^R$/,/^E$/
    record[:state]="RUNNING"
  else
    record[:state]="UNKNOWN"
end

If jobstat.content (the state of the job) does not match any of the specified states (Q, H, W, S, T, R, E), the job's state is set to UNKNOWN. This typically indicates that the job is in an unexpected or unhandled state, which might require further investigation or handling in the script.

TerrenceMcGuinness-NOAA: When a job has been flagged as UNKNOWN can that state be rectified when rocotorun is executed again?

GitHub Copilot: Yes, the state of a job flagged as UNKNOWN can potentially be rectified when rocotorun is executed again. The rocotorun command is typically used to manage and monitor workflows, and it will re-evaluate the status of jobs by querying the job scheduler (in this case, using qstat). If the job scheduler provides updated information on the job's state, rocotorun will update the job's status accordingly.

Here's a step-by-step explanation of how this works:

Initial Job Status Check: When rocotorun is executed, it runs the qstat command to get the current status of all queued jobs.
Parsing Job Status: The output of qstat is parsed, and job records are created. If the job state is not recognized, it is flagged as UNKNOWN.
Re-execution of rocotorun: When rocotorun is executed again, it will repeat the process of querying the job scheduler and parsing the job statuses.
State Update: If the job scheduler now provides a recognized state for the previously UNKNOWN job, rocotorun will update the job's status from UNKNOWN to the new state.

This means that the UNKNOWN state is not permanent and can be updated based on the latest information from the job scheduler.

TerrenceMcGuinness-NOAA: How can I troubleshoot and handle jobs flagged as UNKNOWN in rocotorun?

GitHub Copilot: To troubleshoot and handle jobs flagged as UNKNOWN in rocotorun, you can follow these steps:

Log Detailed Information: Enhance logging to capture more details about jobs flagged as UNKNOWN. This can help in understanding why the job state is not recognized.
Review Job Scheduler Output: Manually run the qstat -x command to inspect the raw output. This can help identify any unexpected job states or issues with the job scheduler.
Update Job State Mapping: Ensure that all possible job states from the job scheduler are correctly mapped in your code. If there are new or undocumented states, add them to the case statement.
Retry Mechanism: Implement a retry mechanism to re-check the job status after a certain interval. Sometimes, transient issues can cause temporary UNKNOWN states.
Alerting and Notification: Set up alerts or notifications for jobs that remain in the UNKNOWN state for an extended period. This can prompt manual intervention.

Here is an updated version of your code with enhanced logging and a retry mechanism:

require 'etc'
require 'libxml'

# Get the username of this process
username = Etc.getpwuid(Process.uid).name

# Method to run qstat and parse job statuses
def fetch_job_statuses
  queued_jobs = ""
  errors = ""
  exit_status = 0
  queued_jobs, errors, exit_status = WorkflowMgr.run4("qstat -x", @qstat_x_timeout)

  # Raise SchedulerDown if the qstat failed
  raise WorkflowMgr::SchedulerDown, errors unless exit_status == 0

  # Return if the qstat output is empty
  return if queued_jobs.empty?

  # Parse the XML output of qstat, building job status records for each job
  queued_jobs_doc = LibXML::XML::Parser.string(queued_jobs, options: LibXML::XML::Parser::Options::HUGE).parse

  queued_jobs_doc
rescue LibXML::XML::Error, Timeout::Error, WorkflowMgr::SchedulerDown => e
  WorkflowMgr.log("Error fetching job statuses: #{e.message}")
  WorkflowMgr.stderr("Error fetching job statuses: #{e.message}", 3)
  raise WorkflowMgr::SchedulerDown
end

# Retry mechanism for fetching job statuses
def retry_fetch_job_statuses(retries = 3, delay = 5)
  attempts = 0
  begin
    attempts += 1
    return fetch_job_statuses




  rescue WorkflowMgr::SchedulerDown => e
    if attempts < retries
      WorkflowMgr.log("Retrying fetch job statuses (attempt #{attempts})...")
      sleep(delay)
      retry
    else
      WorkflowMgr.log("Failed to fetch job statuses after #{attempts} attempts.")
      raise e
    end
  end
end

# Fetch job statuses with retry
queued_jobs_doc = retry_fetch_job_statuses

# For each job, find the various attributes and create a job record
queued_jobs = queued_jobs_doc.root.find('//Job')
queued_jobs.each do |job|
  # Initialize an empty job record
  record = {}

  # Look at all the attributes for this job and build the record
  job.each_element do |jobstat|
    case jobstat.name
    when /Job_Id/
      record[:jobid] = jobstat.content.split(".").first
    when /job_state/
      case jobstat.content
      when /^Q$/, /^H$/, /^W$/, /^S$/, /^T$/
        record[:state] = "QUEUED"
      when /^R$/, /^E$/
        record[:state] = "RUNNING"
      else
        record[:state] = "UNKNOWN"
        WorkflowMgr.log("Job #{record[:jobid]} has an unknown state: #{jobstat.content}")
      end
      record[:native_state] = jobstat.content
    when /Job_Name/
      record[:jobname] = jobstat.content
    when /Job_Owner/
      record[:user] = jobstat.content
    when /Resource_List/
      # Handle resource list attributes if needed
    end
  end

  # Process the job record (e.g., store it, update status, etc.)
end

Key Enhancements:

Enhanced Logging: Added detailed logging for jobs with UNKNOWN state.
Retry Mechanism: Implemented a retry mechanism to handle transient issues.
Manual Inspection: Encouraged manual inspection of qstat -x output for unexpected states.

These steps should help you better handle and troubleshoot jobs flagged as UNKNOWN in rocotorun.

Disclaimer: The above work was done solely by Prompting ChatGTP-4o using GitHub Co-Pilot.