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You could share the directory that the files are in on M1 to server M2 , thereby making them appear 'local' to M2 , or install an agent on M1 and run any jobs to access those files on that agent (read the file, copy the file to M2 etc).
Depending on the OS you're working on, you might try creating mounted directories on M2 which reference the directories containing the flat files on M1.
Alternatively, you should set up a stand-alone ODI agent on the remote machine (M1) which will be local to the flat files.
...It appears Alistair beat me to this :)
Edited by: _Phil on Sep 12, 2012 10:16 AM
From a previous forum discussion, here's another route utilizing FTP if that works in your environment:
You can add the server 1 file drive as a Network drive in Server2 where you have ODI.
then you can use as X:\<file Path> in your File Physical Schema directory in Topology Manager..
Edited by: KP on Sep 12, 2012 1:37 PM