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HOWTO_transfer_files_to_HPC.md

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One-time setup (macbook)

Create a nickname'd entry in your .ssh/config file

Host tuftshpc
    User {YOUR_USERNAME_HERE}
    HostName login.cluster.tufts.edu
    ControlMaster auto
    ControlPath ~/.ssh/%r@%h:%p
    UseKeychain yes

This will let you cleanly refer to the remote filesystem as tuftshpc

Every time

Login to the cluster

Follow standard procedures to log into the cluster

  1. Open VPN and start a secure session

  2. Log into the tufts HPC via an SSH tunnel in a window of your terminal

$ ssh tuftshpc

Use scp to move files to/from the cluster

Open a fresh terminal. Keep the old window open (so the tunnel is open).

The scp works just like Unix's cp command, but over SSH tunnels

Setup the local path (on your laptop filesystem) and the remote path

REMOTE_PATH=/cluster/tufts/hugheslab/datasets/
LOCAL_PATH='/Users/mhughes/Desktop/

Send data to the cluster

scp $LOCAL_PATH/myfile.txt tuftshpc:$REMOTE_PATH

Copy data from the cluster

scp tuftshpc:$REMOTE_PATH/myfile.txt $LOCAL_PATH