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I'm not sure if python subprocess stuck the system. I run the GenomeAnalysisTK-3.4-46 as a subprocess through the python os.system(). But the java GenomeAnalysisTK.jar command status turned to "D" which can't be killed. when i run top -u username i get this, but if i click 'c', it stuck the terminal.

Beside, if i run the command ps aux,the command is blocked and the terminal is stuck. Even though the system runs well, it's really annoying monitoring your commands when the terminal stuck all the time.

I tried to figure out how it stuck system command,i prompted strace ps aux,i got this, the process can't be killed, and more and more command blocked when met the process. What i can do is reboot server manually by pressing power off, because restart command didn't work.

My python version is 2.7.6, and ubuntu release is Ubuntu 14.04 LTS.

I want to know how it happened and how to fix it up not by pressing power off.

Cœur
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C.J. Liu
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    *«java GenomeAnalysisTK.jar command status turned to "D" which can't be killed.»* -- ["kill -9 (SIGKILL) always works"](http://unix.stackexchange.com/q/5642/1321). – jfs Nov 28 '15 at 16:48
  • see also, [Best way to kill all child processes](http://stackoverflow.com/q/392022/4279) and [How to terminate a python subprocess launched with shell=True](http://stackoverflow.com/q/4789837/4279) – jfs Nov 28 '15 at 16:53
  • `ps` is stuck? It would be interesting to see if the folks on _serverfault.com_ had some insight. – tdelaney Nov 28 '15 at 17:02
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    I'd say your server is overloaded.. What configuration does it have? There is "load average: 347.87". OMG. 347? Also there is a java process that takes.. what.. 2136% CPU.. How many CPU cores do you have there? 8 users and 1444 running processes.. As for me, it does not have resources for every process... – baldr Nov 28 '15 at 17:30
  • 'D' status process can't be killed, i tried many times; not `ps` stuck, it is `ps aux or ps ef` stuck terminal. The server has 96 cores with 1000gig memory, it was not server but the terminal stuck, the other process ran well. – C.J. Liu Dec 01 '15 at 07:19

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