Copying files
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One way to copy files to and from a machine is as follows:
To copy from the machine you are on
tar czf - dir1 dir2 dir3 | ssh tbalius@sgehead.bkslab.org "tar xzf - -C path/for/new/files "
To copy from a remote machine to the machine you are on
ssh tbalius@sgehead.uoft.bkslab.org "cd path/to/dir/you/want ; tar czf - diryouwant1 diryouwant2 " | tar xzf - -C where/it/goes/locally
This has advantages that it does not copy symbolic links. It also compresses the data while copying
Clear?