Useful shell commands » History » Version 19
Amber Herold, 11/15/2011 11:13 AM
1 | 1 | Amber Herold | h1. Useful shell commands |
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3 | 9 | Amber Herold | Link to "top 10 cheat sheets":http://www.cyberciti.biz/tips/linux-unix-commands-cheat-sheets.html. |
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5 | 7 | Amber Herold | |
6 | h3. make a folder writable |
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8 | <pre> chmod -R g+rw eman_recon14</pre> |
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10 | 1 | Amber Herold | h3. check the status of a job |
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12 | # ssh to the processing server |
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13 | # <pre>qstat -au YOUR_USER_NAME</pre> |
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14 | # will list your jobs |
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16 | 7 | Amber Herold | h3. check which nodes are currently being used on processing machine |
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18 | 7 | Amber Herold | <pre> |
19 | qstat -an |
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20 | </pre> |
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21 | 1 | Amber Herold | |
22 | 10 | Amber Herold | h3. check the status of each node on the cluster |
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24 | 18 | Amber Herold | # spew a bunch of info about each of the nodes including status: |
25 | <pre> |
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26 | pbsnodes |
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27 | </pre> |
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28 | # For a graphic version use the command ( remember to use -X with |
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29 | ssh to display it back to your computer): |
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30 | <pre> |
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31 | xpbsmon |
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32 | </pre> |
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33 | 1 | Amber Herold | |
34 | h3. kill a process |
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36 | # Log into the machine it is running on |
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37 | <pre>ssh fly</pre> |
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38 | # Look for processes with your user name |
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39 | <pre>ps -ef |grep [your_username]</pre> |
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40 | # Kill the process using the number in the first column after your username |
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41 | <pre>kill [process id]</pre> |
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42 | # If the process was a copy, remove the destination folder |
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43 | <pre>rm [destination folder]</pre> |
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44 | # list system stats |
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45 | <pre>top</pre> |
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46 | 2 | Amber Herold | |
47 | 5 | Amber Herold | h3. submit a job to a job manager |
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49 | <pre> |
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50 | qsub <jobfilename> |
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51 | </pre> |
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53 | 4 | Amber Herold | h3. Kill a job running through the job manager |
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55 | 3 | Amber Herold | * use *qdel* <job number> |
56 | 5 | Amber Herold | |
57 | h3. Start an interactive session on a node |
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59 | <pre> |
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60 | qsub -I |
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61 | </pre> |
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63 | 17 | Amber Herold | * you can type in job file contents line by line and see results. |
64 | 1 | Amber Herold | |
65 | 6 | Amber Herold | h3. Check how much space is available on a data drive |
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67 | 8 | Amber Herold | * cd to the drive (cd /ami/data00) and type: |
68 | 1 | Amber Herold | <pre> |
69 | df -h . |
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70 | </pre> |
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71 | 7 | Amber Herold | |
72 | * to show disc usage status of all mounted systems: |
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73 | <pre> |
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74 | df -h |
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75 | </pre> |
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76 | 6 | Amber Herold | |
77 | 11 | Amber Herold | h3. see how large the files are in a directory |
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79 | <pre> |
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80 | du |
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81 | 1 | Amber Herold | </pre> |
82 | 17 | Amber Herold | |
83 | * Or for a more human readable command: |
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85 | 12 | Amber Herold | <pre> |
86 | du -sch * |
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87 | </pre> |
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88 | 11 | Amber Herold | |
89 | 6 | Amber Herold | h3. See what groups a user belongs to |
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91 | <pre> |
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92 | id <username> |
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93 | </pre> |
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94 | 16 | Amber Herold | |
95 | 15 | Amber Herold | * *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. |