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Remotely check of SGE cluster jobs through SSH using paramiko
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#!/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) | |
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