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I am running a process that is uploading a large file to Amazon S3 in a Linux screen (byobu). The programs outputs progress of the upload as it runs (s3cmd). Since the process is running remotely, and outputting to a screen on my local machine, will it run slower?

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It shouldn't (but it could). If all of the buffers between the process and your screen fill up, then it will pause the next time it goes to write data to the console, but that's usually not an issue unless it's absolutely flooding you with output.

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