Useful shell commands » History » Revision 13
Revision 12 (Amber Herold, 11/15/2011 11:08 AM) → Revision 13/28 (Amber Herold, 11/15/2011 11:09 AM)
h1. Useful shell commands
Link to "top 10 cheat sheets":http://www.cyberciti.biz/tips/linux-unix-commands-cheat-sheets.html.
h3. make a folder writable
<pre> chmod -R g+rw eman_recon14</pre>
h3. check the status of a job
# ssh to the processing server
# <pre>qstat -au YOUR_USER_NAME</pre>
# will list your jobs
h3. check which nodes are currently being used on processing machine
<pre>
qstat -an
</pre>
h3. check the status of each node on the cluster
There's a couple ways you can check. One is using the command 'pbsnodes'.
That will spew a bunch of info about each of the nodes including status.
For a graphic version use the command xpbsmon ( remember to use -X with
ssh to display it back to your computer).
h3. kill a process
# Log into the machine it is running on
<pre>ssh fly</pre>
# Look for processes with your user name
<pre>ps -ef |grep [your_username]</pre>
# Kill the process using the number in the first column after your username
<pre>kill [process id]</pre>
# If the process was a copy, remove the destination folder
<pre>rm [destination folder]</pre>
# list system stats
<pre>top</pre>
h3. submit a job to a job manager
<pre>
qsub <jobfilename>
</pre>
h3. Kill a job running through the job manager
* use *qdel* <job number>
h3. Start an interactive session on a node
<pre>
qsub -I
</pre>
you can type in job file contents line by line and see results.
h3. Check how much space is available on a data drive
* cd to the drive (cd /ami/data00) and type:
<pre>
df -h .
</pre>
* to show disc usage status of all mounted systems:
<pre>
df -h
</pre>
h3. see how large the files are in a directory
<pre>
du
</pre>
Or for a more human readable command:
<pre>
du -sch *
</pre>
h3. See what groups a user belongs to
<pre>
id <username>
</pre>
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.