Junior is a High-Performance Computing Cluster, purchased by CCAS (Vassar’s Center for Collaborative Approaches to Science), thanks to funds from Vassar’s HHMI grant. Junior has 156 total processor cores, configured as follows:

• single twelve core cpu - 2.2GHz AMD Opteron™ Processor 6174
• 32 gig ram
• 2Tb local drive space
• 16Tb raid array shared across all nodes
• network to world - 2 gig ports bonded
• internal network 4 gig ports bonded

• 4 twelve core cpu - 2.2GHz AMD Opteron™ Processor 6174
• 64 gig ram
• 4Tb local drive space
• internal network 6 gig ether ports bonded together

• 64 bit linux kernel 2.6.32.x
• Grid Engine 6.2x
  
  

This semester we will run our programs on back-end node back2 of jr. To run your programs on back2, Greg has written a script for us. It’s called jrun, and if you type jrun at the command prompt on jr, you’ll get a full description of the command, including how it works, how to pronounce it, and the origins of how it was named.

Here is an example of how to use it:

If a student is in ~/bioinf/lab1 and has a script called myscript.pl, 
they would type at the command prompt:
 
    jrun perl myscript.pl
 
and jrun will execute the command:
 
    ssh back2 "cd ~/bioinf/lab1 ; perl myscript.pl"
 
Which should "do the right thing".

You can print to the printer in the Sci Vis lab from Jr, but you must issue the print command from the head node, not the back-end nodes. The print command is lpr, so, for example, to print a file named foo.txt, you would issue the command:

   mlsmith@ccas20:~/bioinf[hh:mm]$ lpr foo.txt

1. cd into your bioinf directory
   

1. Within your bioinf directory, create a directory named “project#”. For example:
   

mlsmith@ccas20:~/bioinf[hh:mm]$ mkdir project1

1. From jEdit, save your script to your bioinf/project# directory. Give the file the same name as the name of the directory.

1. From your bioinf directory, use the submit353 script to submit the project directory containing your file
   

   mlsmith@ccas20:~/bioinf[hh:mm]$ submit353 project1