BMDP

Introduction

BMDP facilitates the manipulation of statistical analysis which is incorporated into many Trinity courses. BMDP resides on a UNIX-based computer called "Shakti," which is accessible from both the Macintoshes and PCs in MCEC. These directions assume that one of the aforementioned computers is being used. This handout should provide all of the information needed to successfully create and submit a BMDP program.

Connecting to Shakti

All students should already have a UNIX and password to access BMDP on Shakti. Any student with an e-mail account also possesses an account on Shakti, from which BMDP can be used. To access, or logon, to the computer, follow the instructions below. Note: make sure that <Caps Lock> is NOT on.

From a Public Macintosh

* Open the folder "Information Services"

* Double-click on the icon "TCP3270"

* Select "shakti" from the list of servers and click "Connect"

Follow the directions below in the section "The Logon Procedure"

From a Public PC

* Open the "Standard Configuration" group

* Double-click on the icon "Telnet"

* Select "shakti" from the list of servers and click Ok.

Now follow the directions below for the logon procedure

The Logon Procedure

After the connection is established, "SunOS UNIX(shakti)" will appear on your monitor followed by the "login:" prompt. Type in your username and press the return key. Next a prompt for a password will appear. Type in the password and press the return key. If the username or password was misspelled a "login incorrect" message will appear, followed by another login prompt. Fill in the information again and give it another try. Continue this until access is gained. When the login information has be successfully entered, information about the computer, and your account will appear on the monitor, followed by a "bash$". This is the prompt and indicates that the computer is now ready for the entering of commands.

UNIX Commands

The commands listed below are the UNIX commands that may be needed to complete assignments. Each of the commands is printed in boldface and should be typed exactly as it appears below. The information printed in italics should be replaced by the actual name of a file located in the current UNIX account. For example, using the information below, to print a file called "myfile" to the MCEC laser printers, type

bash$ laser_dup myfile

at the prompt. (Remember that only the text in bold needs to be typed, the word "bash$" indicates the computer prompt)

ls lists the files contained in the current directory

pico filename edits the specified file

more filename displays the named file on a terminal, one page at a time. Press <Return> to see the next line, or press <Space> to view a screenful of text.

rm filename deletes the specified file

cp filename newname copies the specified file to another file specified by newname

laser_dup filename Prints the specifeid file to the MCEC laser printer, using duplex (front and back of the page) printing

laser_sim filename Prints the specifeid file to the MCEC laser printer, using simplex (front of the page only) printing

NOTE: Filenames in UNIX cannot contain spaces! UNIX is case sensitive and considers capital and small letters as unique. Therefore, the files named "myfile" and "Myfile" are separate documents.

Getting Class Data

The analysis for BMDP to run will depend upon data collected from experiments. This data is stored in a central location on "Shakti" and can be copied to your account using the Kopy command. First, obtain the name of the file to copy from your TA. Next, login to the UNIX account and type

kopy filename

to obtain a copy of the file to edit. (Note that after using the kopy command and type ls the new file will be listed among those that are in your directory. This is the file that will be edited to submit to BMDP)

Using Pico

Pico is one of many text editors in UNIX, it is also one of the easiest to use. BMDP programs are acutally just text files, so any text editor can be used to write one. In order to begin editing, Pico must be invoked with the filename of the file to be edited or created. For instance, to create a file called myfile, or to edit an existing file called myfile, type the following:

pico myfile

Once pico is running, there will no longer be a "bash$" prompt. Instead, a screen will open with a list of commands along the bottom of the screen. At this point, the text document is ready to be edited.

Use the arrow keys to move the cursor around the document. Insert text by moving the cursor to the desired location of the text and typing the new information. When editing a new file, start typing on the first line. New lines can be added by hitting the return key at the end of a line. Hitting the return in the middle of the line will split the text at the cursor point moving all information after the cursor to the newly created line.

Once all of the editing is completed, the document can be saved and Pico can be quit by pressing <Ctrl-x> (Hold down the Control key and press the "x" key). After exiting Pico, the "bash$" prompt will reappear, and the program is ready to submit.

Submitting BMDP Programs

The BMDP program file is now ready to be submitted for analysis. BMDP expects the file to contain both instructions and the data. When BMDP completes processing the submitted information, it will create a new file in the current directory that contains the output from the analysis. The name of the output file must be specified when the program is submitted. The command to submit a program should be entered with the following parameters:

bmdp program datafile outputfile

and is broken down in this way

bmdp invokes bmdp

program Should be replaced with the name of specific program required by

the assigned analysis

datafile The name of the file that was created with the instructions and data and bmdp

outputfile The name assigned to the output file

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Last Modified: 01/04/2011