Useful shell commands¶

Link to top 10 cheat sheets.

make a folder writable¶

 chmod -R g+rw eman_recon14

change the owner of a folder and its contents¶

chown -R <usename> <folder>

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¶

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

   pbsnodes
   

2. For a graphic version use the command ( remember to use -X with
   ssh to display it back to your computer):
   

   xpbsmon
   

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.

Find user name from UID¶

awk -v val=UID -F ":" '$3==val{print $1}' /etc/passwd

Find the version of CentOS installed¶

# cat /etc/*release*

Fix a Stale NFS file handle. error¶

Do a lazy unmount followed by mount.

umount -l <drive>
mount <drive>

OR

On the file server:

exportfs -f

See what modules are available on a cluster¶

On Garibaldi at least:

1. display a list of all the installed modules that can be added to your .cshrc file.
   

   module avai
   

2. list all the modules that are currently loaded.
   

   module list