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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

ssh to the processing server

qstat -au YOUR_USER_NAME
  1. 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 `

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