How to access see.engr.uga.edu

What is see.engr.uga.edu?

It is a powerful computer for numerical computations. "see" stands for Systems and Engineering Ecology. The computer has dual CPU's, and each CPU has four cores. It is practically a small 8-node cluster. The installed OS is Suse Linux 10.2. It is stored in the server room at Driftmier Engineering Center. We all access it remotely.

How can I use SEE?

First, you need to have an account. Please contact me to obtain an account.

You can access to see.engr.uga.edu from any platform, even from a high-tech cellphone. SEE runs linux, but this does not mean that you need to work in an un-userfriendly black shell. SEE has a nice graphical user interface, and a functional file manager, far superior to Explorer. It is called Konqueror. You can use it the way you use Windows or Macs; so when you click on a file, Konqueror opens the file with the appropriate software. You can also right-click and tell it which software to use.

You can store your files at SEE. It is also easy to transfer files back and forth between your computer and SEE.

From Windows:

  1. You need two software two connect to SEE: ssh-client and X-server (port of the Unix window system to MS Windows). Download and install them (Both are free).
  2. You should have a Start Menu item for XMing. Go ahead and start it. If you're using a firewall, it'll ask you if you want to unblock it. You don't need to. Look for the "X" icon in your system tray.
  3. First, open PuTTY. Then, put in your normal settings for connecting to SEE: under host name, put "your_username@see.engr.uga.edu". For "Port Number", please enter 4700.
  4. Then, on the left, click on the Connection/SSH/X11 sub-panel. It'll have a few options. Check "Enable X11 Forwarding", and in the "X display location", put "localhost:0:0" in the box. Leave the radio button on "MIT-Magic-Cookie-1".
  5. Now click back to the main "Session" panel on the left. Put a name (like "see") in the text box in the middle right below "Saved Sessions". Click the "Save" button. From now on, you can double click the connection in the list box when you want to connect to SEE; you don't need to do these settings every time.
  6. Press "Open" to start PuTTY. Put in your password or do whatever you do to authenticate. Now run the command "xclock &". You should get a clock. Better yet, type "konqueror &", which is the file manager and the internet browser. Click on the home icon to see your files and folders in your home directory.

From Mac:

  1. Open the X11 application found in the folder applications > utilities > x11.
  2. In the xterm window that pops up, type the following: "ssh -XC your_username@see.engr.uga.edu -p 4700"
  3. As an example, type "xclock &", a forwarded window showing an analog clock should pop up.

Once you are connected:

  1. In Linux, each use have a home directory. This belongs to you, and you can store your files and directories here. To see your home directory in a file manager, type konqueror& and then click on the home icon on the window that pops up.
  2. If you click on the text file named "simple", it will be opened in a text editor (kwrite).
  3. You can run kwrite from the command line, just enter: 

    kwrite simple &
If you would like to use the emacs editor, please install these free fonts.

What next?

What can you do at SEE? You can run PARTICLE TRACKING. Or you can write a very short script that can automatically run EcoNet (or a specific analysis of your own) through 40 different models stored in a directory... How?

For starters, there is a very simple model at your home directory called "simple". To run this model, type the following:

readmodel simple
runsim simple r 10 .01 40
showplot

The first command, "readmodel simple" makes sure that your model is well defined, then creates a directory named "data" and stores the initial conditions, flow coefficients and the model in separate files.

"runsim" performs the numerical solution and stores the result in various files in directory "data".

"showplot" reads the results and plots them in the file "timeCourse.gif".

If you type just "runsim", it will give you the available options. Now, to run the particle simulation, type: 

runsim simple p 100 1 40
The simulation result will be stored in files in the directory "data". To see these files, type 

ls data
You should see these files:

completed_paths.dat : Pathways of particles that dissipated from the system
current_paths.dat : Pathways of particles that are currently in the system
dissipated_particles.dat : Names (numbers) of dissipated particles
current_stocks.dat : Names of particles that are currently in the system
event_log.dat : log file of all flows

Here, names in the file "dissipated_particles.dat" correspond to the pathways in the file "completed_paths.dat". You can see the contents of any file by the command "cat ", or if you'd like to see the file in a text editor, type "kwrite " So, to see the event log, just type: 

cat data/event_log.dat
or 

kwrite data/event_log.dat
Now, to see particles that have been through node "2", simply type: 

cat data/completed_paths.dat | grep -cE "2"
Or, to find the number of particles that followed the path "0 -> 1 -> 2", type: 

cat data/completed_paths.dat | grep -cE "0+[[:space:]]+1+[[:space:]]+2"
You can always use "up" arrows to revisit the previous commands you type. When typing a command, or a file name, you can use the "tab" button to complete an incomplete command. Like, type "konq" ans press tab once, it should complete it to "konqueror". For future reference, here are a few short Linux/Unix tutorials:

http://www.tldp.org/LDP/gs/node5.html
http://www.fsid.cvut.cz/cz/U201/LINUX.HTML
http://gd.tuwien.ac.at/.vhost/tutorialbox.com/tutors/linux/LINUX.HTML

Please let me know if you have any questions, or experience any difficulties.
  • You can change your password using the command passwd
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