Basic Commands

Submitting/Viewing/Running/Canceling a job:

To submit a job in batch mode -- "qsub ./script_file.sh"
Give a "showq" to see what job you are running right now, you'll see a jobid (number)

"showq -r" to see active queue, it will also show you on which compute node users were assigned to

"showq -r -u user_id" to see on which node particular user is running his/her job

"showq -i" to see idle queue

"showstats -u user_id" to see a particular user's current and completed job number

"showstats" to see historical usage of cluster

If a job goes to idle mode, issue "showstart job_id" to see when it will go to active mode
"showgrid" then "showgrid <option>" to see various historical data on cluster
"canceljob job_id" command will cancel your job
If for some reason your job goes to idle mode instead of active mode, you can try running your job by "runjob jobid" command, if it do not run on that time, it will be in running mode after sometime when it can allocate nodes and processor
Command "pbsnodes -a" will show you the status (load ave., how many proecessor is busy, which job is running) of all compute nodes

"pbsnodes compute-i" where i=1/2/3/4 will show you particular node statistics

Based on these information you can ask for nodes and processors to validate your parallel computing toolbox / running fluent /starccm+ / Ls-dyna or parallel programmming

Viewing files:

Writing File in vi editor:

In SecureCRT type something like "vi myfile.sh"
It will create a new file (if there was no file as myfile.sh) and press "i"
You'll see "insert" in the bottom which means you can insert/type
Type the file the way you want
Press "Esc" and then press "shift + :" and press "w" then "q" and hit enter - which means write and quit

Reading a file in vi editor:

If you have an existing file named as "myfile.sh" you can type "vi myfile.sh" to view the file
After viewing you can quit the file using "Esc" the press "shift + :" then "q" and then hit enter
If you have edited the file somewhere un-intentionally and you do not want this changes, you can force quit by "q!" in the previous step which will let you exit the file without any change

Editing a file in vi editor:

If you have an existing file named as "myfile.sh" you can type "vi myfile.sh" to view the file
Press "i" and make the changes
Press "Esc" and then press "shift + :" and press "w" then "q" and hit enter - which means write and quit

Writing a file in gedit:

Make sure you are forwarding X-32 in SecureCRT and X server is on (guidline is provided in Access Information)
gedit exixting_file_name.sh_or_new_file_name.sh -- will open a GUI based editor, type, save and close it

Making a shell script file:

Whenever you are done with writing a file say myfile.sh, you can make it executable by "chmod 744 myfile.sh"

Copy, Move and Delete in Linux:

cp /home/au_user_id/test1/myfile.m /home/au_user_id/test2/ (copying from tes1 to test2)
cp /home/au_user_id/test1/* /home/au_user_id/test2/ (copy all contents from test1 to test2)
mv /home/au_user_id/test1/myfile.m /home/au_user_id/test2/ (moviing from tes1 to test2)
mv /home/au_user_id/test1/myfile.m /home/au_user_id/test1/ (renaming)
mv /home/au_user_id/test1/* /home/au_user_id/test2/ (moviing all content from tes1 to test2-- cut)
rm /home/au_user_id/test1/myfile.sh (delete a particular file)
rm /home/au_user_id/test1/* (delete all content from test1 folder)
rm -r /home/au_user_id/test1/ (if test1 folder has sub-folder, then delete the sub-folder and all the contents as well)

Last Updated: Oct 31, 2012