Useful shell commands¶

Link to top 10 cheat sheets.

make a folder writable¶

 chmod -R g+rw eman_recon14

check the status of a job¶

1. ssh to the processing server

2. qstat -au YOUR_USER_NAME

3. will list your jobs

check which nodes are currently being used on processing machine¶

qstat -an

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).

kill a process¶

1. Log into the machine it is running on
   

   ssh fly

2. Look for processes with your user name
   

   ps -ef |grep [your_username]

3. Kill the process using the number in the first column after your username
   

   kill [process id]

4. If the process was a copy, remove the destination folder
   

   rm [destination folder]

5. list system stats
   

   top

submit a job to a job manager¶

qsub <jobfilename>

Kill a job running through the job manager¶

• use qdel <job number>

Start an interactive session on a node¶

qsub -I

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

Check how much space is available on a data drive¶

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

  df -h .
  

• to show disc usage status of all mounted systems:
  

  df -h
  

see how large the files are in a directory¶

du

• Or for a more human readable command:

du -sch *

See what groups a user belongs to¶

id <username>

• 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.