Technical Help

This page describes the computer system at the Bioinformatics Research Center, software installed on the Sun cluster, and who to go to for technical help.

Stan Martin and Oliver Serang are responsible for administering our Windows workstations. Contact either Stan (help@statgen.ncsu.edu) or Oliver (orserang@unity.ncsu.edu.) for help with Microsoft Windows and PC hardware, software and printing.

If you have problems with the Unix machines (Solaris, Macintosh OS X, or Linux), contact Stan Martin at help@statgen.ncsu.edu or Chris Smith at chris@statgen.ncsu.edu.

1. Our main server (brooks.statgen.ncsu.edu) is a dual-processor Sunblade 1000 running Solaris 9. It handles mail, web, ftp and remote logins. It will probably be phased out in the near future in favor of a Macintosh OS X based server. It is aliased by statgen.ncsu.edu. The email address for user "username" on this machine is "username@statgen.ncsu.edu". This same user can set up a private web site in a subdirectory "public_html" that will show up as http://statgen.ncsu.edu/~username, but note that the directory must have a file "index.html" or "index.php" to work.
2. We have a Mac OS X based cluster comprised of ten dual processor Xserves. The cluster name and website is poole.statgen.ncsu.edu. Click on the link for more information.
3. There is a Linux based server for the use of students. It is called brc.statgen.ncsu.edu. You can run SAS batch jobs on it. Contact Chris Smith or Stan Martin if you want an account.

If you notice any irregularities or have any problems with the above machines, contact:

Stan Martin
Office: 1523 Partners II
Phone: 515-1934
Pager : 919-310-1716 (emergencies only, please.)
Email: help@statgen.ncsu.edu

Numerous programs are in the /usr/local and /opt partitions of the Sun cluster. Some of the installed software is listed below.

1. The TeX package includes:
   1. LaTeX2e (command: latex, or use pdflatex to produce pdf files)
   2. BiBTeX (command: bibtex)
   3. MetaFont (called automagically by dvips when new fonts are needed)
   4. dvips, a postscript translator for .dvi files
   5. xdvi, an OpenWindows previewer of .dvi files
2. Fortran (f77, f90), C (cc), C++ (CC) and Pascal (pc) compilers from SUN. Using optimization with the cc compiler can double the speed of your programs. Also, if your program does a lot of reading and writing, it is best to run it from a local /export directory.
3. Genetic data analysis software, including:
   1. Phylip 3.5, a DNA and protein analysis package from Joe Felsenstein
   2. ODEN, a sequence analysis package from Yasuo Ina
   3. mapmaker and qtl (MapMaker programs)
   4. QTLCartographer, a program package to map QTLs written by Chris Basten.
   5. GDA, Genetic Data Analysis
4. Most of the GNU software including:
   1. EMACS
   2. gcc, g++
   3. bison
   4. various utilities for text processing, compression, etc.
   5. ghostscript and ghostview, for viewing postscript files
   6. the gnu make utility
   7. gzip and gunzip, compression programs
   8. protoize and unprotoize can create or eliminate C function prototypes from your C code.
5. Statistical software including:
   1. R, a freeware Splus clone.
   2. SAS version 8. If in Openwindows, just type sas to start it. From a terminal, use sas -fsdevice ascii. You will also want to use the -work . option if it will be a big job.
   3. Splus
6. Maxima, a freeware version of Macsyma. This is a program that does symbolic math.
7. Maple and Matlab (both similar to Maxima).
8. Netscape, an OpenWindows interface to the World Wide Web.
9. xv, a program to display images in OpenWindows.
10. mpeg3play, is a player of mpeg movies.
11. a2ps, a program to translate text into postscript for printing.
12. gnuplot, an OpenWindows plotting package.
13. pine, for reading email.
14. Perl, a useful scripting language.

If you have questions about how to use any of this software, please contact Chris Smith at chris@statgen.ncsu.edu or Stan Martin at help@statgen.ncsu.edu.

Samba is installed on mcintyre.statgen.ncsu.edu to allow you to mount your unix home directory onto your Windows 2000. Your machine must have an IP address that begins with 152.14.14.

To use samba on Windows 2000 boxes, do the following.

1. You must send plain text passwords from Windows to brooks. To do this,
1. Download the file Win2000_PlainPassword.reg to your Windows machine, run it from the start menu and reboot. This only needs to be done ONE time.
2. The same subdirectory has similar files for other versions of Windows. Look at the directory for a full listing. (It is pub/w2k/registry on statgen.ncsu.edu.)
2. Now you can map your home drive from the statgen server. To do this,
1. Right click on the network places icon and select Map Network Drive.
2. If your statgen username is uname, then your samba-served drive is \\mcintyre.statgen.ncsu.edu\uname.
3. If your username is different on your Windows machine than on brooks.statgen.ncsu.edu, you will need to logon with a different username (click on underlined message).
4. When you click finish, you should be asked for your username and password. Give your statgen username and password. In a few seconds, your home directory should pop up in a window.

Six printers are available from our workstations. The default for most machines is WestWing, located near the kitchen area in the West Wing. For other available printers, see the /etc/printers.conf file on the Sun cluster.

You can print postscript files with the lpr command:

% lpr   some.postscript &

This is a postscript printer, so you should use a2ps to print text:

% a2ps   some.text &

The program dvips converts a .dvi file into postscript and prints.

% dvips   some.dvi &

To run a job in the background, use an ampersand '&' after the command. You may also want to redirect the standard error and standard output to a file.

%  command > file.comments &

Use nice if it is a long job:

%  nice command > file.comments &

Some problems that you may notice (contact Chris Smith at chris@statgen.ncsu.edu if they occur):

1. When you type the name of a command (e.g. xdvi), the shell says there is no such command. It may be that your path variable is not set correctly.
2. Mail doesn't go out, or mail that you expect doesn't come in. Inform Chris as soon as you notice the problem and he will try to fix it immediately. Send copies of mail to yourself to be on the safe side.
3. In the past, the Sun compilers would complain that the license server was down. The compilers are available to us through a site license. Each time you invoke one of these compilers, it tries to get permission from one of the license servers. If all license servers are down, you have to wait until they are back online. This problem has not occurred in a long time.