(shell script - qsub) wait for submitted job to complete before next command

Question

My shell script involves qsub job submission and then copying the file generated by that job to some other location. How does one do that?

Here is how my shell script looks like:

...
qsub synplify.csh
cp ./rev_1/netlist.vqm ~/sample
...

Here, synplify.csh job is submitted on server but not completed. And it clears way to execute second line. Thus second line is executed while first job is being processed. I want second line to be executed after the job is completed.

Answer 1

Use -sync y the option.

qsub -sync y synplify.csh
cp ./rev_1/netlist.vqm ~/sample

From the man page:

-sync y causes qsub to wait for the job to complete before exiting.

Answer 2

You can chain commands as described here:

https://unix.stackexchange.com/questions/63648/how-to-send-many-commands-to-shell-and-wait-for-the-command-behind-ends

Alternatively, you can submit separate scripts that use job dependencies (with afterok):

http://docs.adaptivecomputing.com/torque/6-0-2/adminGuide/help.htm#topics/moabWorkloadManager/topics/jobAdministration/jobdependencies.html