SGI IRIX
About this page
I wrote this page as a resource for myself and others interesting in learning IRIX with empahsis on biocomputing and molecular modeling. I also have some links above for commonly used programs.
What is IRIX?
IRIX is a flavor of UNIX that comes on Silcon Graphics hardware. It is a very robust operating system but very difficult to use if you are not familiar with UNIX of programming. The current version of IRIX that I work on is 6.5 with overlay 23. There is a limited GUI and a lot of configuration takes place with the UNIX SHELL. Common commands can be found here. One piece of advice if you are new to IRIX and are purchasing an SGI. Make sure it comes with the compilers you want for your programs. This can cost extra but it saves a lot of hassle. The common ones are cc, fortran (f77 and f90), and cpp among others.
 Getting on the internet
This was a lot more difficult than I had expected and will depend on your institution's network. We used a static IP and things seemed to work fine. If you go to tool chest and network configuration you see two options. I configured g10 (I'm not sure what the other one does). For this you will need the IP of the machine, the hostname (i.e. tezro.university.edu), the DNS server name, the netmask, and the gateway. Once you have this you can use the wizard to fill out the parameters. After a reboot you should be able to get online.
 Accelrys InsightII Installation
InsightII is a powerful molecular modeling package from Accelrys which runs on IRIX. The installation however, was tricky. First one is advised NOT to install under root and the instruction book has a typo. Go in and create a directory called /usr/accelrys and /usr/accelrys/I2000.1 with the command mkdir /usr/accelrys/ and mkdir /usr/accelrys/I2000.1.
Next switch to the directory /usr/accelrys then launch the installation of the program as shown in the manual. This makes it so the "root" is /usr/accelrys and the final installation path is under /usr/accelrys/I2000.1.
Wait you aren't yet! Some of InsightII's computation modules (CHARMm and Discover) require some fortran libraries to be installed. The directions for the installation can be found here.
The .cshrc file
This took me a while to understand but basically this is a file that executes everytime you open up a unix terminal. It is found in your home directory. You can get to your home directory by typing the symbol ~ It is pretty barebones if you look at it through nedit. You can do useful things like source directories or set environmental variables. I use InsightII a lot and VMD with the MSMS surface generation program so I added the following lines to my .cshrc file:
source /usr/accelrys/cshrc (this makes it so that all I have to type to get into insightII is "insightII". No need for sourcing the .cshrc script did it for us!
setenv MSMSSERVER /usr/local/lib/vmd/msms (this specifies the environmental variable MSMSSERVER that is used by the program VMD. Basically it tells the program VMD where the program MSMS is.
Making Icons in IRIX
In order to make an icon go to nedit in Applications and create a new text file. Simply add the commands you want to run. So say for example your program was in /usr/local/ and it was called adt. You would make a text file with the following line /usr/local/adt. That is the most basic form but you can add more commands. For example if you want to set an environmental variable before the program exits you can do that by setenv. Next you will need to go the the unix terminal and make the text file you just saved an executable. You do this by the following command:
chmod +x /directorywhereyourfileis/filename
You then click and drag this text file to your desktop and you have an executable icon!
FTP access through the UNIX terminal
There is a neat way to FTP through the UNIX terminal and I have found it very useful for transfering files around. Open a UNIX shell and type in ftp -n nameofsite.com (or whatever the ftp site is). The -n command is to make sure you don't have an auto login. Nex,t you will need to put in your username and password. Do this by executing the following commands:
user username
it will then prompt for password then you will have to type in your password. You can transfer files to the ftp site by the following command:
put localfilename remotefilename (make sure to specify the exact location of your file and the name of the file as it will appear on the remote server).
Other useful commands for the FTP utility can be found using the man ftp command.
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UNIX