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HPCC-NML Bioinformatics Computing Resource: 2. File transfer and remote login

Transfer files between local Computer and HPCC

Windows:

  • Open Filezilla
  • Type in the following on the Quickconnect bar:
    • Host: almaak.usc.edu, Username: your_USC_NetID, Password: your_USC_password, Port: 22
    • Click on Quickconnect

  • Navigate to the source folder with data files on your local computer (left side pane) and your HPCC project directory (right side pane)
  • Drag the data folder files from your local computer to your HPCC project directory.
  • You may also create a new folder in your HPCC project directory and transfer desired data files from your local computer to this folder.
  • You may follow similar steps to download results files from your HPCC project directory to your local computer.

 

Mac OS/Linux:

Mac/Linux users can use either Filezilla or command line scp or sftp to transfer files between local and remote computers

* To use Filezilla

  • Follow Windows instructions above

* To use command line scp or sftp:

  • First bring up a terminal window
    • Mac OS: Applications > Utilities > Terminal
    • Linux: Terminal location depending on system
  • Using scp (secure copy command)

scp syntax:

Examples of using scp to transfer files:

    • Upload a file named mydata.txt from your local computer to HPCC
      scp local-path-to-file/mydata.txt USCNetID@hpc-nml.usc.edu:remote-path
    • Download a file named output.txt from HPCC to your local computer
      scp USCNetID@hpc-nml.usc.edu:remote-path-to-file/output.txt local-path
  • Using sftp (secure FTP)

First log in to the remote host:

    • In the terminal window, type in the following:
      sftp USCNetID@hpc-nml.usc.edu
    • If successful, the terminal will display:
      sftp>

Examples of using FTP commands to transfer files:

    • Upload a file named mydata.txt from your local computer to HPCC:
      put local-path-to-file/mydata.txt remote-path
    • Download a file named output.txt from HPCC to your local computer:
      get remote-path-to-file/output.txt local-path

For further details using sftp, see instructions here

Connect to HPCC-NML Custom Condo

To use the HPCC-NML Bioinformatics Computing Resource, you must first log in to HPCC-NML head node following the instructions below:

Windows:

  • Open X-Win32 > Click on the pre-configured HPC-NML connection > Click "Launch"
  • If prompted, type in your USC NetID and password
  • An X-Win32 terminal window will be launched. 
  • The default location is your HPCC HOME Directory:
    [your_USC_NetID@hpc-nml ~]$

Mac OS/Linux:

  • Open a terminal window:
    • Mac OS: Applications > Utilities > Terminal
    • Linux: Terminal location depending on system
  • Connect to HPCC-NML using SSH:
    • In the terminal window, type in
      ssh -X your_USC_NetID@hpc-nml.usc.edu
    • If prompted to confirm the connection, type in
      yes
    • When prompted for password, type in your USC password
    • When successful, the terminal will display your HPCC HOME Directory location:
      [your_USC_NetID@hpc-nml ~]$