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UNIX at Fermilab
Detailed Table of Contents
Chapter 1:
- Introduction
1.1
- The UNIX at Fermilab Manual
1.1.1
- Conventions Used in this Manual
1.1.2
- Summary of Chapters and Appendices
1.2
- About UNIX
1.2.1
- A Brief History
1.2.2
- A Word About Features and Components
1.2.3
- The Advantages of UNIX
1.3
- The Fermi UNIX Environment
1.4
- UNIX OS Support at Fermilab
1.5
- The Central Fermilab UNIX Resource: FNALU
1.5.1
- Getting an Account on FNALU
1.5.2
- Intended Uses of the FNALU Cluster
1.6
- Additional Documents and Information
1.6.1
- Fermilab Documents
1.6.2
- Useful URLs
1.6.3
- Commercially Available Texts
Chapter 2:
- Getting Started on a UNIX System
2.1
- Logging In
2.1.1
- C Shell Family
2.1.2
- Bourne Shell Family
2.2
- Logging Out
2.2.1
- C Shell Family
2.2.2
- Bourne Shell Family
2.3
- The UNIX Prompt
2.4
- Special Keys
2.5
- Special Characters (Metacharacters)
2.6
- File Systems: Standard UNIX and AFS
2.7
- Information Distribution System: NIS
2.8
- Changing Your Password
2.8.1
- Standard UNIX Password
2.8.2
- Kerberos (AFS) Password
Chapter 3:
- Information Resources
3.1
- UNIX On-Line Help
3.1.1
- man Pages
3.1.2
- Finding the Right Command
3.1.3
- Vendor Product Documentation
3.2
- The Internet
3.2.1
- The World Wide Web (WWW or "the Web")
3.2.2
- UNIX Help on WWW
3.2.3
- Newsgroups
3.3
- The Info Utility
3.4
- Other Users: WWW Directories, finger and who
3.5
- The Fermilab Helpdesk
Chapter 4:
- Shells
4.1
- Introduction to Shells
4.1.1
- Determining Your Current Shell
4.1.2
- Starting a Shell
4.1.3
- Exiting a Shell
4.2
- Features of Available Shells
4.3
- Supported/Recommended Shells at Fermilab
4.4
- Shell Scripts
4.5
- Other Interpretive Programming Languages
Chapter 5:
- Important UNIX Concepts
5.1
- Processing Environment
5.1.1
- Programs, Commands and Processes
5.1.2
- Command Interpretation by the Shell
5.2
- Command Entry
5.2.1
- Command Format
5.2.2
- Miscellaneous Command Line Features
5.3
- Command Recall
5.4
- Important Concepts
5.4.1
- Path
5.4.2
- Standard Input and Output Redirection
5.4.3
- Pipes
5.4.4
- Filters
5.4.5
- Regular Expressions
5.5
- Job Control
5.5.1
- Priority
5.5.2
- Background, Foreground, and Suspended Jobs
5.5.3
- Scheduling Jobs: at and cron
Chapter 6:
- The UNIX File System
6.1
- Directory Structure
6.1.1
- Pathnames
6.1.2
- The Home Directory
6.1.3
- Command Line Directory Shortcuts
6.1.4
- Directories and Executables
6.2
- Files
6.2.1
- Filenames
6.2.2
- Filename Expansion and Wildcard Characters
6.3
- Manipulating Files
6.3.1
- List Directory Contents: ls
6.3.2
- List File Contents: cat, less, more, head, and tail
6.3.3
- Copy a File: cp
6.3.4
- Move (Rename) a File: mv
6.3.5
- Reference a file: ln
6.3.6
- Remove a File: rm
6.3.7
- Copy to/Restore from Archive or Tape: tar
6.3.8
- Compress or Expand a File: gzip, gunzip
6.4
- Information About Files
6.4.1
- Find a File: find
6.4.2
- Search for a Pattern: grep
6.4.3
- Count a File: wc
6.4.4
- Dump a File: od
6.4.5
- Determine File Type: file
6.5
- Manipulating Directories
6.5.1
- Print Working Directory: pwd
6.5.2
- List Directory Contents: ls
6.5.3
- Change Directory: cd
6.5.4
- Make a Directory: mkdir
6.5.5
- Copy a Directory
6.5.6
- Move (Rename) a Directory: mv or mvdir
6.5.7
- Remove a Directory: rmdir
6.6
- File and Directory Permissions
6.6.1
- File Access Permissions
6.6.2
- Directory Permissions
6.7
- Temporary Directories
Chapter 7:
- The AFS File System
7.1
- Introduction to AFS
7.2
- How to Determine if AFS is Installed on your System
7.3
-
7.3.1
- Authentication in AFS
7.3.2
- Kerberos (AFS) Password
7.3.3
- Standard UNIX Password on an AFS System
7.3.4
- Managing your Token
7.4
- AFS File System Commands and man Pages
7.5
- AFS Volumes and Quota
7.6
- File and Directory Permissions
7.6.1
- File Permissions
7.6.2
- Directory Permissions via Access Control Lists (ACLs)
7.7
- AFS Protection Groups
7.7.1
- Permissions for Performing Group-Related Tasks
7.7.2
- Listing Information about Groups
7.7.3
- Modifying Group Characteristics
7.8
- Implications of ACLs and Examples
7.8.1
- Protecting your Subdirectories
7.8.2
- Protecting your Home Directory
7.9
- AFS in Translator Mode
7.10
- File Locking in AFS
7.11
- Frequently Asked Questions
7.11.1
- Lost Access to Files
7.11.2
- AFS and the UNIX Command "find"
7.11.3
- Error Messages
7.11.4
- Retrieving Old Files
7.11.5
- Link Failure
Chapter 8:
- Printing
8.1
- The FUE Print Command: flpr
8.2
- Pre-Printing Options
8.2.1
- Convert ASCII to PostScript: a2ps
8.2.2
- Print Multiple Pages per Sheet: psnup
8.2.3
- Set Duplex Mode
8.3
- Other Print Utilities
Chapter 9:
- Working Environment
9.1
- Shell Variables and Environment Variables
9.1.1
- C Shell Family
9.1.2
- Bourne Shell Family
9.2
- Some Important Variables
9.3
- The Alias Command
9.3.1
- C Shell Family
9.3.2
- Bourne Shell Family
9.4
- Tailoring Your Environment
9.4.1
- C Shell Family Fermi Files
9.4.2
- Bourne Shell Family Fermi Files
9.4.3
- Storing Customized Code
9.5
- X Terminal Support
9.5.1
- Configuration
9.5.2
- Connecting to Host Computers
9.6
- Multimedia File Support
9.7
- Terminal Characteristics
Chapter 10:
- Accessing Software Products
Notice of Upcoming Changes
10.1
- Finding Information about Available Software
10.2
- Accessing Installed UPS Products
10.2.1
- Get Information About Products Installed on Your System
10.2.2
- Setup a Product Instance
10.2.3
- Unsetup a Product Instance
10.2.4
- Invoke the Product
10.3
- Obtaining Products from KITS
10.3.1
- Steps for Installing a Product
10.3.2
- UPD Menu Interface Operations
10.4
- Using Anonymous ftp to Download a Product
10.4.1
- Access Anonymous ftp
10.4.2
- Select a Product Instance Tar File
10.4.3
- Copy the Tar File
Chapter 11:
- Editors
11.1
- The Available Editors
11.2
- Comparison of Editors
11.3
- Getting Started with the Editors
11.3.1
- vi
11.3.2
- emacs and xemacs
11.3.3
- NEdit
11.3.4
- nu/TPU
11.3.5
- fermitpu
11.3.6
- EDT+
Chapter 12:
- UNIX Mail Systems
Notice of Upcoming Changes
12.1
- Mail Forwarding
12.1.1
- The Fermilab Mail Server: FNAL
12.1.2
- Forwarding on File-Sharing UNIX "Clusters"
12.1.3
- Recommended Forwarding Procedure
12.2
- Overview of Mail Systems Available at Fermilab
12.2.1
- pine
12.2.2
- MH Graphical Interface: exmh
12.2.3
- MH Line-Mode Interface: mh
12.2.4
- Berkeley Mail
12.3
- The exmh and mh Mail Handlers
12.3.1
- Run Setup and Invoke the Application
12.3.2
- Compose and Send Messages
12.3.3
- Incorporate and Read Incoming Messages
12.3.4
- Reply to Messages
12.3.5
- Forward Messages
12.3.6
- Print Messages
12.3.7
- Extract Messages
12.3.8
- Remove Messages
12.3.9
- Create, Change and Remove Folders
12.3.10
- Refile Messages
12.3.11
- Search for Messages
12.4
- Basic Configuration for MH
12.4.1
- Configuration Files
12.4.2
- MH Mail Folders
12.4.3
- Incorporation of Incoming Mail into Folders
12.4.4
- Signature Lines
12.4.5
- Mail Aliases
12.4.6
- Folder Order and Header Display (exmh)
12.5
- Berkeley Mail
12.5.1
- Send Messages and Files
12.5.2
- Read Messages
Chapter 13:
- Connecting to Remote Systems
13.1
- Transferring Files
13.1.1
- ftp
13.1.2
- rcp
13.1.3
- The .rhosts File
13.2
- Logging in to Other Systems
13.2.1
- telnet
13.2.2
- rlogin
13.3
- Executing Commands Remotely: rsh
Chapter 14:
- Batch Processing Environment
14.1
- The Standard Batch System at Fermilab: LSF
14.1.1
- Job Queues
14.1.2
- Load Monitoring on Hosts
14.1.3
- Host Selection
14.1.4
- Job Priority
14.2
- Local Interface to LSF: fbatch
14.2.1
- View Host Information
14.2.2
- View Queue Information
14.2.3
- Submit a Batch Job
14.2.4
- Monitor Submitted Batch Jobs
14.2.5
- Control Submitted Batch Jobs
14.3
- Related Software Components
Chapter 15:
- Tape Handling
15.1
- Operator Communications Software (OCS)
15.1.1
- OCS Basics
15.1.2
- The OCS X Interfaces
15.1.3
- Using Provided Examples to Get Started
15.2
- Raw Buffered I/O (RBIO)
15.3
- DAta From Tape (DAFT)
15.4
- Fermi Tape Tools (FTT)
15.5
- Fermi Modular Backup (FMB)
Chapter 16:
- Software Development
16.1
- Overview of Programming Languages and Tools
16.2
- Introduction to C and FORTRAN on UNIX
16.2.1
- The C Compiler: cc
16.2.2
- The FORTRAN Compiler: f77
16.2.3
- C and FORTRAN Compiling Basics
16.2.4
- Linking Order
16.2.5
- Displaying Active Options
16.2.6
- Option Passing
16.3
- Introduction to C++ on UNIX
16.4
- C and FORTRAN Compiler Options
16.4.1
- Commonly-Used Options
16.4.2
- Recommended Options for General Use
16.4.3
- Debugging Option
16.4.4
- Portability Option for AIX
16.4.5
- ABI Options Under IRIX 6
16.4.6
- Speed Optimization Options
16.4.7
- Load Map Option
16.4.8
- Special FORTRAN Compiler Options
16.5
- FORTRAN Programming
16.5.1
- External Reference and Entry Point Names
16.5.2
- Separate Compilation of FORTRAN Subprograms: fsplit
16.5.3
- AIX-Specific Issues
16.5.4
- Loading Block Data Modules
16.5.5
- Program Control
16.5.6
- Future FORTRAN Enhancements
16.6
- Obsolete Programming Features
16.7
- C and FORTRAN I/O
16.7.1
- Records
16.7.2
- Tapes
16.7.3
- Standard Input and Output
16.8
- Performance Tuning for C and FORTRAN
16.8.1
- Optimization
16.8.2
- Word Length
16.8.3
- Feedback
16.8.4
- Inlining
16.9
- C and FORTRAN Mixed Programming
16.9.1
- Variable Types
16.9.2
- Array Indexing
16.9.3
- External Names
16.9.4
- Arguments
16.9.5
- Commons
16.9.6
- I/O
16.9.7
- Linking
16.10
- Executing a Program
16.11
- Debugging
16.11.1
- FORTRAN Source Code Analyzer: FLINT
16.11.2
- dbx
16.11.3
- gdb
16.11.4
- purify
16.11.5
- CASEVision
Chapter 17:
- The make Utility
17.1
- An Overview of the make Utility
17.2
- The Makefile and its Components
17.2.1
- Macros
17.2.2
- Targets
17.2.3
- Suffix Rules
17.2.4
- Suffix Declarations
17.2.5
- Control Files within a Makefile
17.3
- Running make
17.3.1
- General Usage
17.3.2
- Usage without Specifying Target
17.3.3
- Usage without a Makefile
17.4
- "Housekeeping" Targets
17.5
- Portability
17.6
- make's Built-in Rules
17.7
- A Few Caveats...
Chapter 18:
- Code Management
18.1
- CVS
18.1.1
- Accessing CVS and Obtaining the Manual
18.1.2
- Basic CVS Commands
18.2
- UCM
18.2.1
- Accessing UCM and Obtaining the Manual
18.2.2
- Basic UCM Commands
Appendix A.
- VMS Migration for the Impatient
A.1
- The Two Necessary Commands
A.2
- OK, What's the Catch?
A.3
- Whoa! Too Fast!
Appendix B.
- UNIX Product Support (UPS) Overview
Notice of Upcoming Changes
B.1
- Introduction
B.2
- The UPS Environment
B.3
- UPS Products
B.4
- UPS Databases
B.5
- UPS Product Files
B.6
- Product Versions
B.7
- UNIX Operating System Flavors
B.7.1
- What is "Flavor"?
B.7.2
- Simple Flavors
B.7.3
- Extended Flavors
B.8
- Instances
B.9
- Flavor Specification
B.10
- Chains
B.11
- Product Dependencies (Use and Build Requirements)
B.12
- Notes on Setup and Unsetup
Appendix C.
- Fermi Login Files
C.1
- C Shell Family
C.1.1
- .cshrc
C.1.2
- fermi.cshrc
C.1.3
- setpath.csh
C.1.4
- setups.csh
C.1.5
- .login
C.1.6
- fermi.login
C.2
- Bourne Shell Family
C.2.1
- .profile
C.2.2
- fermi.profile
C.2.3
- setpath.sh
C.2.4
- .shrc
C.2.5
- fermi.shrc
C.2.6
- setups.sh
Appendix D.
- awk's Programming Model
Appendix E.
- VMS to UNIX Command Reference
E.1
- UNIX Equivalents for Many VMS Commands
E.2
- Shell Scripts for Copying/Renaming Multiple Files
E.3
- Unpacking VMS Backup Save-sets
Appendix F.
- mh and exmh Customization
F.1
- Forwarding and Notification
F.1.1
- Forwarding Address
F.1.2
- Mail Notification
F.2
- Files Used to Customize mh and exmh
F.2.1
- .mh_profile
F.2.2
- components
F.2.3
- replcomps
F.2.4
- forwcomps
F.2.5
- scan-form and inc-form
F.2.6
- .maildelivery
F.3
- Automatic Reply to Incoming Mail
F.4
- Unattended Autoincorporation
F.4.1
- In Standard UNIX Environment
F.4.2
- In AFS Environment
Appendix G.
- mh Command Reference
Appendix H.
- Mail Conversion from VMS
H.1
- Preparation for Conversion
H.2
- Choosing the Process to Use
H.3
- Using the Semi-Automatic Process
H.4
- Using the Automatic Process
Appendix I.
- Programming Examples
I.1
- Interfacing C and FORTRAN
I.2
- Makefiles and the make Process
I.2.1
- A Simple make Process
I.2.2
- A Physics Makefile
Index
UNIX at Fermilab - 10 Apr 1998
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