Useful shell commands¶

check the status of a job¶

1. ssh to the processing server

2. qstat -au YOUR_USER_NAME

3. will list your jobs

make a folder writable¶

 chmod -R g+rw eman_recon14

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.