Once you have an account on Quarry, you will need to do the following things. If none of this makes sense, visit the director and do everything together.
  1. Log onto Quarry using an ssh client. For example, PuTTY (for Windows machines) is freely available on the UITS website . On the other hand, you should be able simply to type the following in a Macintosh or Unix/Linux terminal window:
            $ ssh your_username@quarry.teragrid.iu.edu

    Note: If you have an X-server (such as Hummingbird's Exceed) running on your local Windows machine and want to forward graphics from Quarry to it, you may need to use 'ssh -X' to forward the display from Quarry to the local machine making this connection. There should be an X-server running whenever you connect from a Unix/Linux machine and from most Macintosh machines, and whether you need to use "ssh -X" or simply "ssh" will depend on how your local machine is configured.

    Note2: There is a free Windows X-server program call Xming that can be downloaded and installed on Windows machines. Running an X-server on your local Windows machine will make it much easier to interact with Quarry and it is strongly recommended that you install Xming or a similar X-server.

  2. The first time you log onto Quarry, you will be prompted to choose your shell (interface to the computer). Everything is guaranteed to work if you choose bash (choice 1) and should also work if you choose tcsh (choice 2).

  3. Copy the .soft file from the general cryoem area by typing the following on the command line: 
       $ cp /N/dcwan/projects/cryoem/Files/.soft ./
    This file creates a user-specific working environment (the system referred to as SoftEnv manages these working environments). In our case, we use SoftEnv to give access to image processing and manipulation programs and to other useful tools. The existing .soft file will look something like:
            # This is your SoftEnv configuration run control file.
		#
		#   It is used to tell SoftEnv how to customize your environment by
		#   setting up variables such as PATH and MANPATH.  To learn more
		#   about this file, do a "man softenv".
		#
		#
		+cryoem
		@intel-11.1.059-64
		@openmpi
		+lynx
		+R
		+local-utils
		+emacs
		+Matlab
		+gcc-4.2.2
		+gnuplot-4.2.2
		@quarry
  4. After you have copied the .soft file into your home area, type the following on the command line: 
            $ resoft
    This will apply any changes in the Softenv setup to your current session on Quarry. You will not need to do this the next time you log onto Quarry (it happens automatically whenever you login), but this "resoft" command is necessary to make changes happen without logging off and back on.

  5. Create a symbolic link between your login area and the area where the microscope stores images, EELS and EDX spectra, etc. by typing the following on the command line:
            $ ln -s /N/dcwan/projects/cryoem/Users ImageData
     or $ ln -s /N/dcwan/projects/cryoem/Users/your_lab ImageData
    NOTE: You can replace 'ImageData' with whatever name you want. In general, the "your_lab" designation will be something like "ZlotnickLab" or "DragneaLab". You can examine the currently available names by typing the following on the command line:
              $ ls -la /N/dcwan/projects/cryoem/Users
  6. Test that the symbolic link created in step 5 actually works by typing the following on the command line::
            $ cd ImageData

                changes from the current directory to the place where
                the 3200FS writes data (and errors will indicate that
                the symbolic link was not made properly) 

        $ ls -la
                
                lists everything in this directory (this will show all
                the folders (sub-directories) for the various people and
                labs who are using the 3200FS if you have chosen to make
                the link to the Users area and it will show almost nothing
                if you have chosen to make the link to your specific 
                lab's area);  the -la used here and above means show a 
                long listing of things in the directory and show all the
                files (including files such as . and .. that Windows would
                treat as "hidden file")
  7. You are now able to access the directory where your data will be written when using the 3200FS.

    NOTE: In order for the system to function properly, it will be necesary to save your data in a particular place each time you use the 3200FS.

  8. You will also need to be able to move your data to and from this area on Quarry. You will need a secure FTP client such as psft (obtained along with PuTTY) or WinSCP to do this from a Windows machine. Macintosh and Unix/Linux machines should have sftp available on the command line.