The easiest is to check for the existence of a special file on a start-up if the file not exists create a temporary file and delete this file after the script has finished. Then you can decide to exit the script if the file already exists. This would be a problem if the first started script crashes without deleting a file. Maybe you want to do a double check if the file exists and the process perl.exe is running. This technique is pretty common for *nix utilities to prevent double execution as it is easy to implement but you should be aware this is not very reliable.

UPDATE: maybe you want to read about File locking and implement this in your script as you mentioned the problem comes from parallel access to the same file.

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