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[Condor-users] output and input files



I have a program the I want to run on condor for a user. 

but it has the following inbuilt file structure

/executable
/dependency1
/dependency2
/input/file1
/input/file2
/output/file1
/output/file2


my question has 2 parts

first this is on a shared file system so I don't want to really have to transfer input files. 

can I use the following submit file? well should I be able to ?

initialdir = /
executable = executable
transfer = no

But my second and main question is how do I get the output files back? 

If I set the job to run once, I can using the local file system get it to out put to the /output/file1,2 whichs is cool

but if I run the job twice it will over write the first output. 

What i really want is to use the condor submit file to somehow copy the output files back in to 

/output1/...
/output2/...
etc

so use shared file system for the input files, and then set the initialdir = output$(process)/ and get condor to copy any changed files back to here. 

but it seems if I do this for the output it mucks up the input, and if set the input right it mucks up the output!! 

is there a way to do this ? 

Cheers 

Aaron