First Time Logins on Karst

Once you have an account on Karst, you will need to do the following things. If none of this makes sense, visit David Morgan and work through all this with him.

  1. Log onto Karst 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

    Note: If you have an X-server (such as Hummingbird's Exceed) running on your local Windows machine and want to forward graphics from Karst to it, you may need to use 'ssh -X' to forward the display from Karst 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 (semi) free Windows X-server program call Xming that can be downloaded (the Public Domain downloads are free whereas the others are available if you make a donation to the project) and installed on Windows machines. Running an X-server on your local Windows machine will make it much easier to interact with Karst and it is strongly recommended that you install Xming or a similar X-server.

  2. The first time you log onto Karst, 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 .modules file from the general cryoem area by typing the following on the command line:

       $ cp /N/dcwan/projects/cryoem/Files/.modules ./

    This file creates a user-specific working environment (the system referred to as Modules manages these working environments). In our case, we use Modules to give access to image processing and manipulation programs and to other useful tools. The .modules file will look something like:

            # Working example of a .modules file (May, 2013)
            # should not need to load these
            #module load core
            #module load quarry-default
            # these should be loaded by 'core' (and by default, but there is
            #       some wierdness caused by X-forwarding (ssh -X) ) and it
            #       currently seems best to do things this way...
            module load gcc/4.7.2 moab/7.1.1
            module load perl/5.16.2 python/2.7.3
            module load freetype2 motif xpdf
            module load cryoem
            module load gnuplot
            # for paralleljob and serialjob
            module load local-utils
            # NOTES:
            #       I was told that I shouldn't need to load core or quarry-default (and
            #            that quarry-default does not do anything), but when I try to
            #            leave them out, I need gcc.4.7.2 (which is loaded by core)
            #       xpdf depends on motif which depends on freetype2, so they MUST be
            #            loaded in the order shown above
  4. After you have copied the .modules file into your home area, type the following on the command line:

            $ source .modules

    This will apply any changes in the Modules setup to your current session on Karst. You will not need to do this the next time you log onto Karst (it happens automatically whenever you login), but this "source'ing" 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 Karst. You will need a secure FTP client such as psftp (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.