[Condor-users] Transfering directories structure using the Condor file transfer mechanisem

[Ajasja Ljubetič <ajasja.ljubetic@xxxxxxxxx>]

Dear Condor users,

When using the Condor file transfer mechanism, is there perhaps a way to transfer the directory structure (and the files as well, of course)?

Something akin perhaps to "--relative" switch of rsync?

I am planning to use Condor to run multiple NAMD MD simulations. There are a lot of input files for the simulations, which I have structured in many directories. (an example layout is attached to the end of the message).

Since Condor transfers all the files to the top execute directory I have to rename and edit a lot of scripts (and change all the analysis scripts as well..). 

Perhaps the easiest way is to just zip the whole directory structure, then specify the zip file as the input and write a wrapper that unzips the file with the directory structure intact, runs the simulation and at the end zips the right output directories.

But if I'm missing an (undocumented) switch somewhere, or if there is a better way to do this, then I'd really like to know.

Best regards,

Ajasja Ljubetič,

Young researcher,

Laboratory of biophysics,

Institute Jozef Stefan,

Ljubljana, Slovenia  

/My_sim (directory)
      submit.condor (the submit description file)
      namd (the executable)
      FF (directory)
          param (file)
          rtf (file)

log (directory)

* log files go here

out (dir)

min (dir)

* output files of minimization go here 

(these are also input files for equilibration)

equ (dir)

* output files of equilibration go here

(these are also input files for the run)

run (dir)

* output files of minimization go here

namd.conf (file)

      (various other conf files)