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Useful shell commands » History » Version 22

Amber Herold, 08/08/2012 10:45 AM

1 1 Amber Herold 
h1. Useful shell commands
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Link to "top 10 cheat sheets":http://www.cyberciti.biz/tips/linux-unix-commands-cheat-sheets.html.





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h3. make a folder writable





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<pre> chmod -R g+rw eman_recon14</pre>





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h3. change the owner of a folder and its contents





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<pre>





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chown -R <usename> <folder>





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</pre>





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h3. check the status of a job





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# ssh to the processing server





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# <pre>qstat -au YOUR_USER_NAME</pre>





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# will list your jobs





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h3. check which nodes are currently being used on processing machine





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<pre>





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qstat -an





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</pre>





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h3. check the status of each node on the cluster





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# spew a bunch of info about each of the nodes including status:





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<pre>





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pbsnodes





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</pre>





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# For a graphic version use the command ( remember to use -X with





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ssh to display it back to your computer):





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<pre>





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xpbsmon





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</pre>





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h3. kill a process





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# Log into the machine it is running on





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<pre>ssh fly</pre>





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# Look for processes with your user name





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<pre>ps -ef |grep [your_username]</pre>





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# Kill the process using the number in the first column after your username





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<pre>kill [process id]</pre>





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# If the process was a copy, remove the destination folder





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<pre>rm [destination folder]</pre>





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# list system stats





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<pre>top</pre>





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h3. submit a job to a job manager





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<pre>





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qsub <jobfilename>





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</pre>





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h3. Kill a job running through the job manager





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* use *qdel* <job number>





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h3. Start an interactive session on a node





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<pre>





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qsub -I





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</pre>





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* you can type in job file contents line by line and see results.





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h3. Check how much space is available on a data drive





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* cd to the drive (cd /ami/data00) and type:





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<pre>





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df -h .





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</pre>





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* to show disc usage status of all mounted systems:





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<pre>





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df -h





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</pre> 





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h3. see how large the files are in a directory





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<pre>





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du





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</pre>





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* Or for a more human readable command:





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<pre>





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du -sch *





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</pre>





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h3. See what groups a user belongs to





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<pre>





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id <username>





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</pre>





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* *note:* the user's umask should be set to 002 in their .cshrc file if they are not using the global one to make sure AMI group members can process their data.





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h3. Find the version of CentOS installed





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<pre>





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# cat /etc/*release*





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</pre>





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h3. Fix a *Stale NFS file handle.* error





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Do a lazy unmount followed by mount.





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<pre>





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umount -l <drive>





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mount <drive>





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</pre>