System Administration Varian NMR Spectrometer Systems With VNMR 6.1C Software Pub. No. 01-999166-00, Rev. C0503 System Administration Varian NMR Spectrometer Systems With VNMR 6.1C Software Pub. No. 01-999166-00, Rev. C0503 Revision history: A0800 – Initial release for VNMR 6.1C A1001 – Corrected errors on pg 120, general edit B0202 – Updated AutoTest B0602 – Added additional Autotest sections including VNMRJ update B1002 – Updated Solaris patch information and revised section 21.7, Autotest C0503 – Add additional Autotest sections including cryogenic probes Applicability: Varian NMR spectrometer systems with Sun workstations running Solaris 2.x and VNMR 6.1C software By Rolf Kyburz ([email protected]) Varian International AG, Zug, Switzerland, and Gerald Simon ([email protected]) Varian GmbH, Darmstadt, Germany Additional contributions by Frits Vosman, Dan Iverson, Evan Williams, George Gray, Steve Cheatham Technical writer: Mike Miller Technical editor: Dan Steele Copyright 2001, 2002, 2003 by Varian, Inc., NMR Systems 3120 Hansen Way, Palo Alto, California 94304 1-800-356-4437 http://www.varianinc.com All rights reserved. Printed in the United States. The information in this document has been carefully checked and is believed to be entirely reliable. However, no responsibility is assumed for inaccuracies. Statements in this document are not intended to create any warranty, expressed or implied. Specifications and performance characteristics of the software described in this manual may be changed at any time without notice. Varian reserves the right to make changes in any products herein to improve reliability, function, or design. Varian does not assume any liability arising out of the application or use of any product or circuit described herein; neither does it convey any license under its patent rights nor the rights of others. Inclusion in this document does not imply that any particular feature is standard on the instrument. UNITYINOVA, MERCURY, Gemini, GEMINI 2000, UNITYplus, UNITY, VXR, XL, VNMR, VnmrS, VnmrX, VnmrI, VnmrV, VnmrSGI, MAGICAL II, AutoLock, AutoShim, AutoPhase, limNET, ASM, and SMS are registered trademarks or trademarks of Varian, Inc. Sun, Solaris, CDE, Suninstall, Ultra, SPARC, SPARCstation, SunCD, and NFS are registered trademarks or trademarks of Sun Microsystems, Inc. and SPARC International. Oxford is a registered trademark of Oxford Instruments LTD. Ethernet is a registered trademark of Xerox Corporation. VxWORKS and VxWORKS POWERED are registered trademarks of WindRiver Inc. Other product names in this document are registered trademarks or trademarks of their respective holders. Overview of Contents SAFETY PRECAUTIONS .................................................................................. 17 Disclaimer ......................................................................................................... 21 Foreword ........................................................................................................... 21 Acknowledgments ........................................................................................... 21 Conventions in This Manual ........................................................................... 22 Chapter 1. Sun Hardware ................................................................................ 23 Chapter 2. Software Installation ..................................................................... 39 Chapter 3. VNMR-Related System Administration ....................................... 61 Chapter 4. Output Devices, Terminals, Serial Ports ..................................... 85 Chapter 5. Software Operating Levels .......................................................... 93 Chapter 6. Disk Organization ....................................................................... 105 Chapter 7. Files, Permissions, and Owners ................................................ 119 Chapter 8. UNIX Commands ......................................................................... 131 Chapter 9. Text Editing ................................................................................. 141 Chapter 10. Using Tapes and Floppy Disks ................................................ 149 Chapter 11. Periodic Maintenance and Troubleshooting .......................... 163 Chapter 12. File Security, Repair, and Archiving ........................................ 175 Chapter 13. UNIX System Customization .................................................... 183 Chapter 14. A Quick Guide to C ................................................................... 189 Chapter 15. Shell Scripts .............................................................................. 205 Chapter 16. Tcl/Tk .......................................................................................... 219 Chapter 17. Networking via Ethernet ........................................................... 221 Chapter 18. X Window System Operation ................................................... 249 Chapter 19. Other Networking Options ....................................................... 261 Chapter 20. Solaris 2.x vs. SunOS 4.1.x ...................................................... 267 Chapter 21. Calibration Tests and Shimming ............................................. 269 Chapter 22. Magnet and Spectrometer Maintenance ................................. 317 Annotated Bibliography ................................................................................ 329 Glossary of UNIX, Sun, and VNMR Terms ................................................... 337 Index ................................................................................................................ 397 01-999166-00 C0503 System Administration 3 4 System Administration 01-999166-00 C0503 Table of Contents SAFETY PRECAUTIONS .................................................................................. 17 Disclaimer ......................................................................................................... 21 Foreword ........................................................................................................... 21 Acknowledgments ........................................................................................... 21 Conventions in This Manual ........................................................................... 22 Chapter 1. Sun Hardware ................................................................................ 23 1.1 How Does a Workstation Work? ................................................................................ 23 CPU Module .................................................................................................... 24 CPU Chip ......................................................................................................... 24 Random-Access Memory ................................................................................ 25 Graphics Controller ......................................................................................... 25 System Interconnect ........................................................................................ 26 PCI Bus / SBus ................................................................................................ 26 EBus ................................................................................................................ 27 Other CPU Board Components ....................................................................... 27 SCSI Bus ......................................................................................................... 27 1.2 Sun Workstations—An Overview .............................................................................. 28 CPU Type, Performance .................................................................................. 29 Expansion Options, I/O Ports. ......................................................................... 29 1.3 Data Storage Options ................................................................................................. 29 Hard Disk Drives ............................................................................................. 29 Floppy Disk Drives .......................................................................................... 31 CD-ROM Drives ............................................................................................. 32 Tape Drives ...................................................................................................... 33 Read/Write Optical Disk Drives, WORM Drives ........................................... 35 1.4 Installing the Hardware .............................................................................................. 35 1.5 Adding a Disk (Hardware) ......................................................................................... 35 Adding an Internal Disk .................................................................................. 35 Adding an External Hard Disk ........................................................................ 36 Checking the SCSI Address ............................................................................ 36 Hints on Adding SCSI Devices ....................................................................... 37 Chapter 2. Software Installation ..................................................................... 39 2.1 Installing Solaris ........................................................................................................ 39 Swap Space .....................................................................................................