Prologue and epilogue scripts on remote machine about clusterjob HOT 2 CLOSED

Hi, sorry for the delay, I went on leave for a few weeks and have only just come back to this.

That's really helpful, thank you. In the end I've "simplified" things by moving my pipeline off my laptop and onto a server that can bsub in it's own right, which is probably better in the long term. It's very helpful however to have the solution available; many thanks.

from clusterjob.

It is, indirectly, but only by defining a custom backend. Basically, you would have to subclass LsfBackend and overwrite all the cmd_ methods.

For example,

class MyCustomLsfBackend(LsfBackend)

    def cmd_submit(self, jobscript):
        return 'my_bsub_wrapper.sh "%s"' % jobscript.filename

You would then put the script my_bsub_wrapper.sh somewhere in your $PATH on the cluster login node. It would contains whatever you need to do to actually submit to the scheduler (i.e., source your setup script and then call bsub). You'll have to register MyCustomLsfBackend with JobScript.register_backend before using it. Sorry I haven't gotten around to writing the section on custom backends yet, but I hope you get the idea.

Does that solve your problem?

from clusterjob.