Remotely check of SGE cluster jobs through SSH using paramiko

check_jobs.py

#!/usr/bin/env python3

import paramiko
import os
import warnings
warnings.filterwarnings('ignore')

keyfile = os.path.expanduser('~')+'/.ssh/id_rsa.pub'
cred = {"username": "mattia",
       "hostname": "scc.uni-konstanz.de",
       "key_filename": keyfile,
      }

ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh.connect(**cred)

stdin, stdout, stderr = ssh.exec_command("qstat -s sr")

jobs = [j.strip().split()[0] for j in stdout.readlines()[3:-3]]

for job in jobs:
    stdin, stdout, stderr = ssh.exec_command(f"qstat -j {job} | egrep 'cwd|job_name'")
    lines = stdout.readlines()
    cwd = lines[0].strip().split()[1]
    name = lines[1].strip().split()[1]
    
    stdin, stdout, stderr = ssh.exec_command(f"tail {cwd}/{name}.o{job}")
    out = stdout.readlines()
    print(f"OUT LOG for job {job}:")
    print("=====================")
    print(*out)

    stdin, stdout, stderr = ssh.exec_command(f"tail -n 5 {cwd}/{name}.e{job}")
    err = stdout.readlines()
    print(f"ERR LOG for job {job}:")
    print("=====================")
    print(*err)