Chapter 2 Accessing Servers

Created on 2020 Aug 25 by Gregory Stewart.

Ported to bookdown on 2022 Jul 26 by Nathan Muncy.

2.1 LaBar Lab Shared Drive (keoki)

  1. Request LaBar lab whitelist permissions from the lab manager (can sometimes take 24 hours for the update to push through).
  2. Map the network drive
    • For Windows, go to My computer or This PC and map network drive. Choose a drive and enter \\ccn-keoki.win.duke.edu\experiments2\ to access the lab’s shared drive. Keep in mind that this is mapped to the specific PC you are using, so will need to remap it to other computers as needed.
    • For Mac OSx, open Finder and select go. Select connect to server and enter smb://ccn-keoki.win.duke.edu/experiments2/ to access the lab’s shared drive. Keep in mind that this is mapped to the specific PC you are using, so will need to remap it to other computers as needed.

2.2 BIAC Servers

This document contains information on installing and setting up the local software necessary to log into and transfer files to/from the BIAC servers. This is required in order to access any imaging data collected at BIAC. Remotely logging into the BIAC servers will also allow you to run scripts on the servers and use the various image analysis software packages installed there.

NOTE 1: BIAC recently (11/2015) began requiring Duke’s multi-factor authentication system in order to log into their servers. If you have not set this up already, see this web page for details.

NOTE 2: You will need a DHE account to fully log into the BIAC servers.

2.2.1 Mac OSx Users

Mac OSX comes with the software necessary to log into and transfer files from the BIAC servers; no additional installation is required.

2.2.1.1 Logging into the BIAC Servers

  1. Open a Terminal window. The Terminal application can be found in …/Applications/Utilities.
  2. Type ssh -o ServerAliveInterval=120 -o TCPKeepAlive=no -X <username>@hugin.biac.duke.edu (replacing “username” with your actual user name) into the Terminal window. After typing in your password when prompted and completing multi-factor authentication you will be logged into the BIAC servers. If you are presented with an “are you sure you want to connect” question, just type “yes”.

2.2.1.2 Copying Files from the BIAC Servers

  1. Open a Terminal window. The Terminal application can be found in …/Applications/Utilities.
  2. Use the scp command to copy files between the BIAC servers and your local computer.

2.2.1.3 Examples

Copy from BIAC to local:

scp <username>@hugin.biac.duke.edu:/path/to/file /localpath/

Copy from local to BIAC:

scp <-r> /localpath/ <username>@hugin.biac.duke.edu:/path/to/file

In the examples above, replace “username” with your user name, “path” with the full path to the desired directory on the BIAC server, “file” with the name of the file (including 3-character file extension), and “localpath” with the full path to the desired local directory. Note that the scp command has options for copying multiple files at once, for more info on scp, see here.

2.2.2 Windows Users

Two additional programs will need to be installed, one that handles logging into the BIAC servers and another that handles file transfer.

2.2.2.1 Logging into the BIAC Servers

  1. Download and install X-Win32. This can be done via Duke’s OIT
    site (Browse and Order Software).
  2. Set up X-Win32 to get to the BIAC servers. Follow the instructions here.
  3. Once X-Win is set up, select the hugin connection (or whatever you named it) and click “Launch”. Enter your password/multi-factor authenticate when prompted and you should end up with a BIAC server terminal window. If you receive an “are you sure you want to connect” question, just type “yes.”

2.2.2.2 Copying Files from the BIAC Servers

  1. Download and install WinSCP. This can be done from Duke’s OIT site (Browse and Order Software).

  2. Set up WinSCP to get to the BIAC servers. Create a new “Site” in WinSCP (this can be called whatever you want, but “BIAC” is a good suggestion) with the following values:

     File Protocol: SFTP
 Host name: nernst.biac.duke.edu
 Port number: 22
 User Name: (your user name)

  3. Once the new site is created, highlight it and click “Login”. After password/authentication prompts this should provide a graphical interface for transferring files, very similar in appearance and function to Windows Explorer.

2.2.3 After Succesful Login

The BIAC servers run linux. You’ll need to type linux commands at the command prompt in order to do anything. An introduction to this environment can be found here.

The BIAC servers also have a variety of image analysis software packages installed. In order to use any of them, you’ll need to enter “interactive” mode by simply typing “qinteract” into the command line. This may prompt another password/authentication request. The list of installed software can be found here.