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I would like to have a loop script run over two machines (with global IP), in which during the loop I have several scp command for exchanging the outputs of those executions. Do we have a way to avoid password prompt on every SCPs ? i.e., generating keys for scp, etc

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yes, you can use key pairs like you do for ssh (scp ist "the same")

http://ubuntuforums.org/showthread.php?t=938969

create a rsa key pair with no password, move/copy the public part to destination machine and enjoy!

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