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.

MS-Windows Help

Stan Martin and Oliver Serang are responsible for administering our Windows workstations. Contact either Stan (help@statgen.ncsu.edu or pager 919-310-1716) or Oliver (orserang@unity.ncsu.edu.) for help with Microsoft Windows and PC hardware, software and printing.

If you have problems with the Sun Workstations or the Macintosh, contact Chris Basten at basten@statgen.ncsu.edu.

Hardware

The machines listed below are administered by Chris Basten. They are in the statgen.ncsu.edu domain and are running Solaris 8. Your email address is username@statgen.ncsu.edu.

1. brooks is an Ultra 10. It is our mail, web and ftp server. Please do not run computationally intensive programs on brooks. Also, it is the only machine that allows telnet connections from the outside world. You should telnet to it (telnet statgen.ncsu.edu) and then rlogin to any of the other machines. Better yet, use ssh to access brooks.
2. gaut is an Ultra 60 dedicated to the corn project. It runs Oracle and shouldn't be used for anything else unless you have permission from Charles Du.
3. kao is an Ultra 10 used by Dahlia Nielsen. You may run batch jobs on this machine, but be sure to nice them.
4. mcintyre is the cluster file server. Do not run jobs on it.
5. lewis is an UltraSparc 60 with two 300Mhz processors. You can use this for batch jobs.
6. poole, hernandez and ohta are SunBlade 1000's, each with two 750Mhz processors with 1GB of memory. You should use these for computing or for memory intensive applications. These are good machines to run SAS jobs on.
7. doerge is Greg Gibson's Ultra 5.

Six machines have local hard drive spaces that you can use. They are mcintyre, dodds, lewis, poole, kao and ohta. If your job does a lot of reading and writing, you might consider running it on the local space of those machines. Ask Chris Basten to make a directory for you. When made, you will have a directory in /export on the local machine for your own use. These spaces are meant as temporary program space; they are not backed up.

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

Chris Basten
Office: 1523 Partners II
Phone: 515-1934
Home Phone: 919-571-2677 (emergencies only, please.)
Email: basten@statgen.ncsu.edu

Sun Cluster Software

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 Basten.

Statgen Samba

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.
3. Printers served by samba do not seem to be working yet.

Printing

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 &

Backups

Chris Basten does full and incremental backups on a regular basis. If you accidentally delete a file, see Chris. He may be able to recover it for you.

Running Background Jobs

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 &

Problems

Some problems that you may notice (contact Chris Basten at basten@statgen.ncsu.edu or at 515-1934 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.