Making qsub block until job is done?

Question

Currently, I have a driver program that runs several thousand instances of a "payload" program and does some post-processing of the output. The driver currently calls the payload program directly, using a shell() function, from multiple threads. The shell() function executes a command in the current working directory, blocks until the command is finished running, and returns the data that was sent to stdout by the command. This works well on a single multicore machine. I want to modify the driver to submit qsub jobs to a large compute cluster instead, for more parallelism.

Is there a way to make the qsub command output its results to stdout instead of a file and block until the job is finished? Basically, I want it to act as much like "normal" execution of a command as possible, so that I can parallelize to the cluster with as little modification of my driver program as possible.

Edit: I thought all the grid engines were pretty much standardized. If they're not and it matters, I'm using Torque.

Corrody

Answer 1

You don't mention what queuing system you're using, but SGE supports the '-sync y' option to qsub which will cause it to block until the job completes or exits.

Lexington

Answer 2

In TORQUE this is done using the -x and -I options. qsub -I specifies that it should be interactive and -x says run only the command specified. For example:

qsub -I -x myscript.sh

will not return until myscript.sh finishes execution.

Unhand

Don't you lose the ability to store the output in output files? – Homovec

You lost the automatic storing of output this way, but you can log your terminal session and save the output that way. – Unhand

Answer 3

In PBS you can use qsub -Wblock=true <command>

Pritchett