SGI Systems Administration Helps
(Adapted from SGI Administrator's meeting May5, 1999)

Proceed With Caution: System Administrators are encouraged to take an active role in the management of their systems. To maximize your value not only to your Research Group at IU but to potential future employers as well, you should take the opportunity to learn as much about the system as possible. This requires you to spend some time logged in and exploring various options and analyzing the potential benefits and risks as they relate to the research needs of your group. Failure to do this is like driving a car but being afraid to adjust the mirrors, seats, and steering wheel - it'll still get you where you want to go but at the cost of reduced comfort and safety. Part of your job as System Administrator is determining which tasks you can and should perform yourself and which require additional support from the ITG or MolViz staff or other support channels.

NOTE:  Some of these procedures may change!  If there is any question, contact the ITG or MolViz staff.

Adding and Removing Users

Adding and removing users can best be performed using the Graphical User Interface at the console of the system on which the account is to be added or removed. To be sure you have all the information you will need to add an account, we recommend that a form (similar to those used for accounts on the departmental systems) be filled out by the user requesting the account. This also provides a convenient way to inform the users of their rights and responsibilities in using the accounts.

Add Procedure:

  1. Login as root
  2. Get the username and UID (User ID) from the person requesting the account or from IU addressbook.
    Note: It's not a bad idea to verify this info even if requestor gives it to you.
  3. From the Toolchest (usually the top left of the console), select System. For O2 Systems running IRIX 6.3, these additional steps must be added:
    1. Select System Manager
    2. Select Security
    3. Select Access Control
  4. Select User Manager
  5. Verify the username selected is not already used and then select Add
  6. Enter username and Full Name as requested and select OK
  7. Fill in as much additional info as possible on the next screen and select OK
    Note: Be sure to use the User ID determined in step 2 above and to assign a temporary password to the account. The 3 yes/no questions should all be left set to no.
Remove Procedure:
  1. Login as root and backup user's files if needed
  2. From the Toolchest (usually the top left of the console), select System
    For O2 Systems running IRIX 6.3, these additional steps must be added:
    1. Select System Manager
    2. Select Security
    3. Access Control
  3. Select User Manager
  4. Select account to delete
  5. Select Delete
  6. Specify whether or not to delete user's directory. Usually the answer is yes but occasionally the directory may still have value to other users.
To temporarily disable a user account without permanently removing it, edit the /etc/passwd file and replace the password (x on systems with shadow passwords) with an asterisk (*). This is often done when a user leaves and a final decision has not been made as to the value of any data in the user's account. It is also often used to prevent further damage when an account appears to have been compromised or hacked.

Performing Backups

Eventually, all computer disks get full and files must be removed. It is important to backup your files and remove them from the SGI workstations before the disk becomes 100% full and your SGI stops working. Also, the department charges for disk space on departmental SGI disks so you can reduce your charges by backing up your files and deleting the originals for files rarely needed. Finally, the department does NOT save your work. If you have important files, you MUST backup these files for the future.

DAT.floater1 is available on all SGIs. This program is started by typing DAT.floater1 at the prompt in a UNIX window. The DAT.floater1 program allows you to use the DAT tape drive on floater1 (room A421) to write files and directories to a new tape or, with appropriate caution, to append files and directories to a tape. You can also read files from tape and list the "table of contents" of the tape. A 'help' option is available which describes what can and cannot be specified when reading and writing files and directories. This program can be run by any user on all SGI workstations in the Chemistry Department. The program can archive a single file, the contents of a directory, or an entire disk. Thus, each user has the opportunity to write important files to tape and remove these files from the SGI disk. A 'system backup' option exists for research SGI system administrators. For more information, type 'man tar'. To understand these scripts, type more /remote/server/bin/DAT.floater1. This is a typical C-shell script written by Marty. You can write similar scripts to perform other operations.

A similar program, DAT.nmrsg1 is also available on all SGIs to allow users to read and write DAT tapes using the tape drive on nmrsg1 (root C237). DAT.splatter, DAT.colossus, and DAT.iumsc3 are similar programs that are available ONLY on splatter, colossus, and iumsc3, respectively, for users who have accounts on those systems and want to use the tape drive on splatter, colossus, and iumsc3, respectively.

DAT.inorganic3 accesses inorganic3's DAT drive. It is 'hardwired' to perform a backup in background so you can start the backup and then logout. DAT.pooh and similar scripts on jwz1 and jwz2 also run this way, but it uses the DAT drive on nmrsg1.

Contact Marty if you need a customized DAT backup script.

Other programs exist that help you use tape drives. However, DAT.floater1 has more options, is customized for our SGI network, and (most importantly) it is the only program that the department supports at this time.

DAT tapes have a capacity of 2 GBytes, cost less than $20, and are available .t the IU Bookstore. The floater1 tape drive may be used by SGI users at any time. If you use a tape drive, please place the "WARNING!!! Drive in use!" sign (which sits in a box on the shelf above floater1) on top of the drive. Please check on the progress of the backup and remove your tape and the sign as soon as possible after completion so others may use it.

Before we move on to other options, we would like to make a recommendation and offer a bit of reassurance concerning use of the DAT backups. The recommendation is that you should always label your tape before putting it into the drive so you don't get confused and use the wrong tape in the future, possibly overwriting valuable data. The reassurance is that when your backup is complete using DAT.floater1 or the various customizations of it mentioned above it is automatically ejected from the drive so it cannot be accidentally overwritten by another user unless someone physically re-inserts the tape into the drive. This does not protect you from intentional damage, but does provide some degree of protection from accidental damage to your tape. Please take the time to verify the tape by removing some moderately-sized text file, then restore it from the tape and compare the 2 files by typing diff renamed_file file_restored_from_tape

We have recently purchased a 25/50 GByte tape backup system for backing up our UNIX systems within the department. Once that is working reliably, we plan to offer a weekly backup service option to groups who are willing to share in the cost of maintenance and support for that device.

The NMR Facility has a CD Recorder and is willing to share that on a limited basis for making more permanent backups of critical data, such as a permanent backup of a user's account when they are leaving IU and need to take their data with them. This would need to be scheduled at a time not likely to interfere with normal usage by regular users of the NMR Facility. For NMR users to backup their NMR data there is no charge except for the media required. A fee of $5 per CD will be assessed for all other usage. For additional information, contact the staff of the NMR Facility.

Monitoring the System

UNIX contains a variety of commands to aid in determining the status of the system. This is often done in analyzing unexpected behavior on a system or in attempting to recover from and prevent repeating a crash. For more detail with using a particular command, consult the online manual (or man) pages. For example, typing man du will show how to use the du command. A few of the more common system monitoring commands and what they do: 
     date           show date and time
     df             show disk space usage (by file system) in blocks (512 bytes)
     df -k          show disk space usage (by file system) in KBytes
     du             show disk space usage (by subdirectory) in blocks (512 bytes)
     du -k          show disk space usage (by subdirectory) in Kbytes
     du -ks         show disk space usage summary (lower level directories not displayed) in Kbytes
     finger         show info about a user
     gr_osview      show system usage dynamically and graphically
     history        show commands recently issued in current shell
     last           show last login of users and terminals
     lpq            show print queue status
     lpstat         show printer status  
     man            show syntax and usage of the indicated command
     man -k         show list and brief description of commands related to specified topic
     netstat        show network status
     nslookup       show IP number and name (from DNS tables) based on lookup for either one
     osview         show system usage dynamically in text form
     printenv       show current environment settings
     ps             show status of processes
     ps -ef         show status of many more processes along with more detail about each
     uptime         show system load and time since last boot
     versions       show installed software including version number
     who            show all users currently logged on
     whoami         show user in the current shell
     more /var/spool/lpr/lpr.log      show log of printer access
For additional information about these or other commands, type man command_name (for example, man df) or consult your favorite UNIX book. Some systems (floater1) also have Insight installed for menu-based help on a variety of topics. Man is great if you know the command name but aren't sure how to use it, but Insight lets you find answers to less specific questions.

Maintaining Documentation

The more documentation you have, the more fondly your successor and your users will think of you. You as well as your successor will be able to more quickly identify and correct problems if there is adequate information to show any unique characteristics of your system. Examples of items to maintain in your documentation files are user account request forms, list of applications installed along with their version numbers and vendor contact information, any problems encountered and the solutions found for those problems. Include dates as well as detailed descriptions as appropriate.

Keeping a 3-ring binder with notes applicable to users is highly recommended. This should contain a supply of blank account request forms, a brief description of the applications your users are likely to be running, common user-solvable problems and solutions, notes about available printers and procedures for accessing them, and a statement on how you are to be contacted with problems and questions (phone, Email, note on desk, or whatever works best for you). You may also want to create a web page with this information available for your users on-line so they can consult it even if they are logging in remotely rather than at the console.

If there is some current information you feel your users should be made aware of, UNIX has provided a very simple process for doing this. There is a file, /etc/motd.your_machine_name (/etc/motd.nmrsg1, for example), which gets displayed each time a new shell is opened. This is a good place to announce things such as application upgrades, scheduled downtimes and backups, times you will be unavailable and an alternate contact, and impending problems such as disk filling up. Unfortunately, most of us have seen enough worthless messages displayed in these areas that we no longer pay attention to them, so if you use this vehicle be sure you only include truly important messages and only for an appropriate amount of time. If you login to upgrade the OS and see a message telling you the system has just been upgraded to the previous version, you are probably leaving the messages there too long.

Care and Cleaning of the Hardware

The electronics inside the case of any computer generates a great deal of heat. The systems are usually designed with a fan to circulate air for minimizing this heat. Unfortunately, the same fan that pulls air into the case also pulls dust into it and this dust can accumulate either on the ventilation openings of the case or on the components inside the case, preventing adequate air circulation and eventually causing failure of power supply, disk drive, or other components due to the heat buildup. This problem is further complicated if the computer sits on the floor where dust is stirred up each time someone walks near the system. All systems should be checked on a regular basis to assure that this problem is not occurring. If dust is accumulating on the ventilation openings, it probably is also accumulating on the components inside. In any case, the system should be shutdown and cleaned with a vacuum cleaner and/or air blower (cautiously used to avoid excessive dust all over). My preference is to use a vacuum cleaner to clean as much of the dust as possible and then use an air compressor to blow out the dust that can't be reached by the vacuum cleaner. There is a vacuum cleaner available in the NMR Facility, which can be checked out for this purpose.

The following is a few more recommendations for extending the life of your equipment and making it more inviting to your users:

  1. Clean the screen with a damp cloth - avoid KimWipes or any kind of abrasive materials
  2. Keep your mouse and mouse pad clean for smoother, more precise operation
  3. Clean the keyboard
  4. Make sure all cables are properly installed (not kinked or stretched and protected from damage from feet, etc...)
  5. Provide a safe storage area for all media and be sure it is used religiously
  6. Store documentation in an organized, easily accessible area
  7. Be extremely cautious with the CrystalEyes Glasses - the foam boxes they are shipped in is an ideal place to keep them when they are not in use

Customizing User Accounts

If users want to customize their accounts, they can do this by editing the default setup files in their home directory. The most commonly modified setup files are .cshrc and .login. The .login file typically sets the terminal type and defines general environmental characteristics and other tasks to be performed once at login time. The .cshrc file sets aliases, paths, umask values, prompt string, history characteristics and other features each time a new shell is opened.

As we try to maintain some degree of compatibility between systems, it is essential that local System Administrators do not modify the default cshrc files in the /etc directory. Local System Administrators may choose to add features to the /etc/cshrc.local files, but should consult with eithe Marty or Ken before removing existing features or making extensive modifications. However, it would be a useful learning experience to look at those files as an example of the kinds of customization that can be done. Likewise, many applications installed on the systems are run using scripts or shell wrapper files in the /remote/server/bin directory and may be worth looking at to see how to provide customization needed for a specific application without consuming unneeded resources when the application is not running.

The desktop tool menus can be customized so applications such as pcmodel and insightII appear as icons.

Finding more information

If you need additional information, please feel free to contact the MolViz Facility staff. We are available to assist with any specific problems you may have or to help you understand any general concepts which may seem at first confusing. We also have several excellent books which we can loan to you or recommend for purchase. In addition, the Internet is full of information ranging from sites with online UNIX manuals to newsgroups which discuss far more about UNIX than any of us have the time to read. Any major search engine such as Alta-vista or Infoseek can be used to find specific topics of interest.

The Molecular Visualization Facility Website, is a resource which provides a great deal of information about the SGIs, including the topic "where to get help" and should be consulted regularly. There is a section on System Administration as well as a link on each page to send Email to the MolViz Staff with any comments or requests for additional information.

Responsibilities of the Molecular Visualization Staff

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Last updated: 01/23/2001