#!/usr/bin/env python import logging from pprint import pprint from subprocess import call, PIPE, Popen from typing import List, Dict from typing import Optional import typer from pymongo import MongoClient from pymongo.collection import Collection from pymongo.cursor import Cursor from pymongo.database import Database from requests import get, Response from tabulate import tabulate app = typer.Typer() class SimJobQuery: fields = {} def __init__(self): # type: () -> None self.fields = { "submitLowMS": None, "submitHighMS": None, "startLowMS": None, "startHighMS": None, "endLowMS": None, "endHighMS": None, "startRow": 1, "maxRows": 100, "serverId": None, "computeHost": None, "userid": None, "simId": None, "jobId": None, "taskId": None, "hasData": None, "waiting": None, "queued": None, "dispatched": None, "running": None, "completed": None, "failed": None, "stopped": None, } def params(self): return {k: v for k, v in self.fields.items() if v is not None} class HealthQuery: fields = {} def __init__(self): # type: () -> None self.fields = { "check": "all", } def params(self): return {k: v for k, v in self.fields.items() if v is not None} # class slurm_job: # fields = { # "jobid": None, # "name": None, # "state": None, # "submit_time": None, # "start_time": None, # "exec_host": None, # "reason": None # } # # class vcell_job: # fields = { # "owner_userid": None, # "slurm_name": None, # "simulationKey": None, # "jobIndex": None, # "taskID": None, # "schedulerStatus": None, # "hasData": None, # "vcellServerID": None, # "queueDate": None, # "simexe_startDate": None, # "simexe_latestUpdateDate": None, # "computeHost": None, # "detailedStateMessage": None # } def set_debug(debug: bool) -> None: logger = logging.getLogger("paramiko") console_handler = logging.StreamHandler() formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') console_handler.setFormatter(formatter) logger.addHandler(console_handler) if debug: logger.setLevel(logging.DEBUG) console_handler.setLevel(logging.DEBUG) else: logger.setLevel(logging.WARN) console_handler.setLevel(logging.WARN) def slurmquery(debug: bool, slurmhost: str, partitions: str): """ :param bool debug: whether to show debug information :param str slurmhost: slurm node for running queries :param str partitions: comma separated list of slurm partitions :returns list of dict: """ # if args.debug: # print "sudo docker run --rm "+args.vcellbatch+" "+options+" SendErrorMsg" if debug: print(f"ssh {slurmhost} squeue -p {partitions}" f" -O jobid:25,name:25,state:13,submittime,starttime,batchhost,reason") proc = Popen(['ssh', slurmhost, 'squeue', '-p', partitions, '-O', 'jobid:25,name:25,state:13,submittime,starttime,batchhost,reason'], stdout=PIPE) stdout, stderr = proc.communicate() return parse_slurm(stdout.decode('utf-8')) def parse_slurm(squeue_output: str) -> List[Dict]: """ JOBID NAME STATE SUBMIT_TIME START_TIME EXEC_HOST REASON 418774 V_REL_130234420_7_0 RUNNING 2018-05-09T23:34:36 2018-05-10T09:41:36 shangrila01 None """ table = [[str(i) for i in line.split()] for line in squeue_output.splitlines()] """ [['JOBID', 'NAME', 'STATE', 'SUBMIT_TIME', 'START_TIME', 'EXEC_HOST', 'REASON'], ['418774', 'V_REL_130234420_7_0', 'RUNNING', '2018-05-09T23:34:36', '2018-05-10T09:41:36', 'shangrila01', 'None']] """ list_of_dict: List[Dict] = [dict(zip(table[0], row)) for row in table[1:]] """ [{'NAME': 'V_REL_130234420_7_0', 'START_TIME': '2018-05-10T09:41:36', 'REASON': 'None', 'JOBID': '418774', 'STATE': 'RUNNING', 'SUBMIT_TIME': '2018-05-09T23:34:36', 'EXEC_HOST': 'shangrila01'} ] """ return list_of_dict def merge_slurm_vcell(showjobs_ouptput, slurmjobs_output): merged_list = [] for vcell_job in showjobs_ouptput: merged_job = vcell_job.copy() site = str(vcell_job['vcellServerID']) sim_key = str(vcell_job['simulationKey']) job_index = str(vcell_job['jobIndex']) task_id = str(vcell_job['taskID']) slurm_job_name = 'V_' + site + '_' + sim_key + '_' + job_index + '_' + task_id merged_job['vcSimID'] = slurm_job_name merged_job['found'] = 'vcell' matching_slurmjobs = list(filter(lambda slurmjob: slurmjob['NAME'] == slurm_job_name, slurmjobs_output)) if matching_slurmjobs is not None and len(matching_slurmjobs) > 0 and matching_slurmjobs[0] is not None: merged_job.update(matching_slurmjobs[0]) merged_job['found'] += ',slurm' merged_list.append(merged_job) for slurm_job in slurmjobs_output: matching_vcell_job = list(filter(lambda job: job.get('vcSimID') == slurm_job['NAME'], merged_list)) if matching_vcell_job is None or len(matching_vcell_job) == 0: merged_job = slurm_job.copy() merged_job['found'] = 'slurm' merged_list.append(merged_job) return merged_list def sim_query(query: SimJobQuery, host_port: str) -> List[Dict]: """ :param SimJobQuery query: query parameters for /admin/jobs :param str host_port: vcell api host:port separated by colon :returns list of dict: """ r = get('https://' + host_port + '/admin/jobs', params=query.params()) logger = logging.getLogger("paramiko") logger.debug(r.url) json = r.json() """ [{ u'computeHost' = {unicode} u'shangrila14' u'detailedState' = {unicode} u'WORKEREVENT_PROGRESS' u'detailedStateMessage' = {unicode} u'0.270433' u'hasData' = {bool} True u'jobIndex' = {int} 0 u'onwer_userkey' = {unicode} u'120840072' u'owner_userid' = {unicode} u'975464864' u'queueDate' = {unicode} u'May 10, 2018 6:40:20 AM' u'queueId' = {unicode} u'QUEUE_ID_NULL' u'queuePriority' = {int} 5 u'schedulerStatus' = {unicode} u'RUNNING' u'simexe_latestUpdateDate' = {unicode} u'May 10, 2018 2:07:32 PM' u'simexe_startDate' = {unicode} u'May 10, 2018 6:41:27 AM' u'simulationKey' = {unicode} u'130250352' u'submitDate' = {unicode} u'May 10, 2018 6:40:20 AM' u'taskID' = {int} 0 u'vcellServerID' = {unicode} u'REL'} ] """ return json @app.command(name="showjobs", help="show simulation jobs (using vcell database and slurm)") def showjobs_command(userid: Optional[str] = typer.Option(None, "--userid", "-u", help="job owner"), sim_id: Optional[int] = typer.Option(None, "--simId", "-s", help="simulation id"), job_id: Optional[int] = typer.Option(None, "--jobId", "-j", help="sim job id (index for scans/trials)"), task_id: Optional[int] = typer.Option(None, "--taskId", "-t", help="sim task id (for job restarts)"), status: str = typer.Option("wqdr", help="job status (default wqdr) " "a-all, w-waiting, q-queued, d-dispatched, " "r-running, c-completed, s-stopped"), max_rows: int = typer.Option(500, "--maxRows", "-m"), host: str = typer.Option("vcellapi.cam.uchc.edu", "--host", help='host of server'), api_port: int = typer.Option(443, "--apiport", help='port of api service'), slurm_host: str = typer.Option("vcell-service.cam.uchc.edu", "--slurmhost"), partition: str = typer.Option("vcell2,vcell", help="slurm partition"), debug: bool = typer.Option(False, is_flag=True) ) -> None: set_debug(debug) query = SimJobQuery() query.fields['userid'] = userid query.fields['simId'] = sim_id query.fields['jobId'] = job_id query.fields['taskId'] = task_id query.fields['waiting'] = True if ('w' in status or 'a' in status) else False query.fields['queued'] = True if ('q' in status or 'a' in status) else False query.fields['dispatched'] = True if ('d' in status or 'a' in status) else False query.fields['running'] = True if ('r' in status or 'a' in status) else False query.fields['completed'] = True if ('c' in status or 'a' in status) else False query.fields['failed'] = True if ('f' in status or 'a' in status) else False query.fields['stopped'] = True if ('s' in status or 'a' in status) else False query.fields['maxRows'] = max_rows api_host_port = host + ":" + str(api_port) json_response = sim_query(query, api_host_port) slurm_jobs = slurmquery(debug, slurm_host, partition) merged_jobs = merge_slurm_vcell(json_response, slurm_jobs) col_names = ["JOBID", "STATE", "NAME", "EXEC_HOST", "found", "owner_userid", "vcSimID", "schedulerStatus", "hasData", "queueDate", "simexe_startDate", "simexe_latestUpdateDate", "computeHost", "detailedStateMessage"] table = [[row.get(col_name, '') for col_name in col_names] for row in merged_jobs] print(tabulate(table, headers=col_names)) @app.command(name="slurmjobs", help="query slurm running jobs") def slurmjobs_command(slurm_host: str = typer.Option("vcell-service.cam.uchc.edu", "--slurmhost", help="slurm host"), slurm_partition: str = typer.Option("vcell2,vcell", "--partition", "-p", help="slurm partition"), debug: bool = typer.Option(False, is_flag=True)) -> None: set_debug(debug) # 'NAME': 'V_REL_130234420_7_0', # 'START_TIME': '2018-05-10T09:41:36', # 'REASON': 'None', # 'JOBID': '418774', # 'STATE': 'RUNNING', # 'SUBMIT_TIME': '2018-05-09T23:34:36', # 'EXEC_HOST': slurm_jobs: List[Dict] = slurmquery(debug, slurm_host, slurm_partition) col_names = ["JOBID", "STATE", "NAME", "EXEC_HOST", "START_TIME", "SUBMIT_TIME", "REASON"] table = [[row.get(col_name, '') for col_name in col_names] for row in slurm_jobs] print(tabulate(table, headers=col_names)) @app.command(name="logjobs", help="show simulation job logs (needs rewrite to query ElasticSearch)") def logjobs_command(sim_id: Optional[int] = typer.Option(None, "--simId", "-s", help="simulation id"), job_id: Optional[int] = typer.Option(None, "--jobId", "-j", help="sim job id (index for scans/trials)"), task_id: Optional[int] = typer.Option(None, "--taskId", "-t", help="sim task id (for job restarts)"), host: str = typer.Option("vcellapi.cam.uchc.edu", "--host", help='host of server'), mongo_port: int = typer.Option(27017, "--mongoport", help='port of mongodb service'), max_rows: int = typer.Option(1000, "--maxRows", "-m", help="max records returned from Mongo"), debug: bool = typer.Option(False, is_flag=True)): print("Mongo logs are gone: re-implement as ElasticSearch query (move this to vcell-su for ES credentials") # # set_debug(debug) # client = MongoClient("mongodb://" + host + ":" + str(mongo_port)) # db: Database = client['test'] # collection: Collection = db['logging'] # query = {} # if sim_id is not None: # query["simId"] = str(sim_id) # if job_id is not None: # query["jobIndex"] = str(job_id) # if task_id is not None: # query["taskId"] = str(task_id) # pprint(query) # result_set: Cursor = collection.find(query).limit(max_rows) # table = [] # col_names = ["computeHost", "destination", "simId", "jobIndex", "taskId", "serviceName", "simMessageMsg"] # rowcount = 0 # for record in result_set: # table.append([record.get(col_name, '') for col_name in col_names]) # rowcount += 1 # if rowcount < 10 and debug: # pprint(record) # # print(tabulate(table, headers=col_names)) @app.command(name="killjobs", help="kill simulation job (from a vcell-batch container)") def killjobs_command(userid: Optional[str] = typer.Option(None, "--userid", "-u", help="job owner"), sim_id: Optional[int] = typer.Option(None, "--simId", "-s", help="simulation id"), job_id: Optional[int] = typer.Option(None, "--jobId", "-j", help="sim job id (index for scans/trials)"), task_id: Optional[int] = typer.Option(None, "--taskId", "-t", help="sim task id (for job restarts)"), host: str = typer.Option("vcellapi.cam.uchc.edu", "--host", help='host of server'), msg_port: int = typer.Option(8161, "--msgport", help='port of message server'), vcell_batch: Optional[str] = typer.Option(None, "--vcellbatch"), # or "schaff/vcell-batch:latest" debug: bool = typer.Option(False, is_flag=True) ) -> None: set_debug(debug) if vcell_batch is None: p1 = Popen(['sudo', 'docker', 'image', 'ls'], stdout=PIPE) p2 = Popen(['grep', 'vcell-batch'], stdin=p1.stdout, stdout=PIPE) p3 = Popen(['head', '-1'], stdin=p2.stdout, stdout=PIPE) stdout, stderr = p3.communicate() parts = stdout.decode('utf-8').strip().split() if len(parts) < 2: raise Exception("didn't find local vcell-batch docker image, specify using --vcellbatch") vcell_batch = parts[0] + ':' + parts[1] print('found vcell-batch image: ' + vcell_batch) options = " --msg-userid admin" options += " --msg-password admin" options += " --msg-host " + host options += " --msg-port " + str(msg_port) options += " --msg-job-userid " + userid options += " --msg-job-simkey " + str(sim_id) options += " --msg-job-jobindex " + str(job_id) options += " --msg-job-taskid " + str(task_id) options += " --msg-job-errmsg " + "killed" if debug: print("sudo docker run --rm " + vcell_batch + " " + options + " SendErrorMsg") return_code = call("sudo docker run --rm " + vcell_batch + " " + options + " SendErrorMsg", shell=True) if return_code == 0: print("kill message sent") else: print("unable to send kill message") def health_query(query: HealthQuery, host_port: str): r: Response = get('https://' + host_port + '/health', params=query.params()) logger = logging.getLogger("paramiko") logger.debug(r.url) json = r.json() return json @app.command(name="health", help="site status - as formerly queried by Nagios") def health_command(host: str = typer.Option("vcellapi.cam.uchc.edu", "--host", help="host of server"), api_port: int = typer.Option(443, "--apiport", help="port of api server"), monitor: str = typer.Option("sle", "--monitor", help="monitor type (default 'sle') s-simulation, l-login, e-events") ) -> None: apihostport = host + ":" + str(api_port) query = HealthQuery() if 'e' in monitor: # {"timestamp_MS":1525270930943,"transactionId":5, # "eventType":"LOGIN_SUCCESS","message":"login success (5)"} query.fields['check'] = 'all' json_response = health_query(query, apihostport) col_names = ["timestamp_MS", "transactionId", "eventType", "message"] table = [[row.get(col_name, '') for col_name in col_names] for row in json_response] print(tabulate(table, headers=col_names)) if 's' in monitor: # {"nagiosStatusName":"OK","nagiosStatusCode":0,"elapsedTime_MS":7400} query.fields['check'] = 'sim' json_response = health_query(query, apihostport) message = str(json_response.get('message', "''")) print('Simulation(status=' + str(json_response.get('nagiosStatusName')) + ', elapsedTime=' + str(int(json_response.get('elapsedTime_MS')) / 1000.0) + ' seconds' + ', message=' + message + ')') if 'l' in monitor: # {"nagiosStatusName":"OK","nagiosStatusCode":0,"elapsedTime_MS":7400} query.fields['check'] = 'login' json_response = health_query(query, apihostport) message = str(json_response.get('message', "''")) print('Login(status=' + str(json_response.get('nagiosStatusName')) + ', elapsedTime=' + str(int(json_response.get('elapsedTime_MS')) / 1000.0) + ' seconds' + ', message=' + message + ')') def main(): app() if __name__ == "__main__": main()