Created
March 15, 2016 08:59
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submit job via pipe to SGE's qsub using python subprocess
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| #!/usr/bin/env python | |
| import sys | |
| import subprocess | |
| case = int(sys.argv[1]) | |
| queue = "all.q" | |
| jobName = "test%i" % case | |
| cmd = "echo %i; date; sleep 2; date" % case | |
| echoArgs = ["echo", "-e", "'%s'" % cmd] | |
| print(" ".join(echoArgs)) | |
| qsubArgs = ["qsub", "-cwd", "-j", "y", "-V", "-q", queue, "-N", jobName] | |
| print(" ".join(qsubArgs)) | |
| if case == 1: | |
| wholeCmd = " ".join(echoArgs) + " | " + " ".join(qsubArgs) | |
| out = subprocess.Popen(wholeCmd, shell=True, stdout=subprocess.PIPE) | |
| out = out.communicate()[0] | |
| if case == 2: | |
| wholeCmd = " ".join(echoArgs) + " | " + " ".join(qsubArgs) | |
| out = subprocess.Popen(wholeCmd, shell=False, stdout=subprocess.PIPE) | |
| out = out.communicate()[0] | |
| if case == 3: | |
| # http://stackoverflow.com/a/13332300/597069 | |
| echoProc = subprocess.Popen(echoArgs, stdout=subprocess.PIPE) | |
| out = subprocess.check_output(qsubArgs, stdin=echoProc.stdout) | |
| echoProc.wait() | |
| if case == 4: | |
| # http://stackoverflow.com/a/17129244/597069 | |
| echoProc = subprocess.Popen(echoArgs, stdout=subprocess.PIPE) | |
| qsubProc = subprocess.Popen(qsubArgs, stdin=echoProc.stdout, stdout=subprocess.PIPE) | |
| echoProc.stdout.close() | |
| out = qsubProc.communicate()[0] | |
| echoProc.wait() | |
| jobId = out.split()[2] | |
| print jobId |
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