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Printing and Queues

The UNIX print command on Ranger is lpr -P

You also need to specify to which printer your print job will be sent (that is the -P option, otherwise your print job will come out on the default printer in the RCR office), and of course the name of the file to be printed.

Taken all together it looks like this:

	lpr -P printername filename

Of course, you need to know the name of a network printer that is convenient for you to use. The command printers will give you a list of the currently available printers.

There is also a web page that has a list of printers available from Ranger

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Using the Batch Queue

UNIX has a variety of different ways to share resources among the various jobs running on a computer including interactive users and background processes. However, GCG has created something called a batch queue (a holdover from its orgins on VMS computers) for scheduling time consuming jobs.

The advantage of running a GCG program as a batch job is that you don't have to wait for the program to finish in order to continue with your work. Also, the system as a whole can better balance the workload of multiple users (such as when we are all working in the computer lab) if everyone makes use of the batch queue.

To run a GCG program in batch mode, type the program name followed by the -BAT modifier like this:

	> fasta -BAT

There are several GCG programs that can take a long time to complete - mostly these are database searches and phylogenetics, but also some of the more sophisiticated pattern searching algorithms. Here is a list of all of the programs that can be used with the -BAT command:

    fasta	frameaearch	  paupsearch
    tfasta	framealign	  pileup	
    fastx	profilesearch	  compare
    tfastx	stringsearch	  mfold
    blast	findpatterns	  prime
    ssearch	coilscan	  wordsearch

When your batch job is finished, the system will send you an e-mail that contains the messages that are ususally sent to the screen when you run that program (the "standard output"). The actual results file is stored in your home directory (or whatever sub-directory you were working in when you started the program).

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Using Computers for Molecular Biology: Queues
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@med.nyu.edu