After logging on obtaining an account one of the things that you may wish to do is get data transferred to ( or from ) the HPC system. Two of the most widely available tools for secure file transfer are SCP (Secure Copy) and SFTP (Secure File Transfer Protocol) which utilize the SSH protocol to implement security. While SCP is a simple, non-interactive command line tool, it is often a more suitable choice when setting up unattended file transfers using scripts. Alternatively, SFTP is an interactive tool which offers features like remote file listing, copying, deleting, directory creation, etc.
While SCP and SFTP are available out of the box on Linux and Mac systems, ITS also offers downloads of Fetch (login required) for MacOS and WS_FTP Professional (login required) for Windows from the ITS Software Download Site - ITS Help Desk - Information Technology Services at The University of Iowa site. In addition, SecureCRT also has SFTP capability. Below are some basic examples showing syntax for both tools. Note that while the examples are specific to Helium, they are broadly applicable and will thus work for Neon as well, and both commands have extensive man pages available.
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Off-campus access to the default ssh/scp/sftp port of 22 has been blocked at the campus border. Therefore, users must specify an alternate port in order for these tools to work from off campus. Helium and Neon The ITS-RS HPC systems use port 40 for off campus, non-VPN access. Some examples below show port specification. |
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Duo dual factor authentication is required for SFTP and SCP to work. Ensure that you have a default request method for duo to authenticate. |
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| title | Non-interactive shell output |
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Your client software will first try to establish a non-interactive session on the server. It will fail with an error if the non-interactive portion of your shell's startup prints anything. For the common case of bash, your ~/.bashrc configures non-interactive sessions, so make sure it contains no modifications which cause output. It's safe to place such modifications in ~/.bash_profile which only configures interactive logins. |
SCP
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| title | Copy file from local to the HPC system (note alternate port specification) |
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[user@local ~]$ scp -P 40 file1 hawkid@heliumhawkid@argon.hpc.uiowa.edu:file1 |
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| title | Copy file from local to HPC system (note alternate port specification) |
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[user@local~]$ sftp -o port=40 hawkid@heliumhawkid@argon.hpc.uiowa.edu
Connecting to heliumargon.hpc.uiowa.edu...
sftp> put file1
Uploading file1 to /Users/hawkid/file1
file1 100% 840 0.8KB/s 00:00
sftp>
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| title | Copy directory from local to HPC system |
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[user@local~]$ sftp hawkid@heliumhawkid@argon.hpc.uiowa.edu
Connecting to heliumargon.hpc.uiowa.edu...
sftp> mkdir remote
sftp> put local/* remote/
Uploading local/file1
Uploading local/file2
Uploading local/file3
sftp> ls remote/
remote/file1
remote/file2
remote/file3
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This process is more involved in that one must create the directory remotely first and then transfer the contents from one to the other – wildcards are helpful for this. |
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