Appion

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.