NCSA TeraGrid IA-64 Linux Cluster User Documentation

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Table of Contents

1. Technical Summary
2. Allocations and Access
1. The Allocation Process
2. Encryption Software
3. Connecting to NCSA Systems
   1. NCSA HPC Systems
   2. Archival Storage System
4. NCSA Dial-up
3. Account Management
   1. Managing your Account
   1. Passwords
   2. Your shell
   3. Managing your "dot" files
   4. Forwarding your mail
   2. Managing your Allocation
   1. Adding/removing users
   2. Charging Algorithms
   3. Verifying Your Account Balance
   4. Changing Projects for Charging
   5. Refunds
   6. Account Termination, Renewals, and Extensions
4. File Systems and Storage
   1. Directories
      1. Home Directories
      2. Scratch Directories
      3. /tmp, /usr/tmp, and /var/tmp Directories
      4. Reserved Project Space
      5. TeraGrid Environment Variables
   2. Permanent File Storage
   3. File Transfer Options
5. Managing Your Environment (SoftEnv)
6. Programming Environment
1. Compilers
1. Introduction
2. Compiler Commands
3. Intel Compiler Documentation
4. Useful Intel Compiler/Linker Options
5. Notes
2. Message Passing Libraries
1. Introduction
2. MPICH-GM
3. Virtual Machine Interface (VMI)
4. MPICH Softenv Keys
5. MPICH Compiler Commands
3. Intel Math Kernel Library
4. Hierarchical Data Format (HDF) Library
7. Running Jobs
1. Interactive Use
2. Running MPI Programs
3. Batch System (Torque)
1. Queues, Resources, and Limits
2. Commands
1. qsub
2. qsub -I
3. qstat
4. qhist
5. qdel
3. Sample Batch Script
8. Debugging
1. Overview
2. Classic serial debuggers
   1. gdb
   2. ddd
   3. idb
   4. idb -gui
   5. TotalView
3. Parallel debuggers
   1. TotalView
4. Memory allocation debuggers
   
   1. Electric Fence
   2. MALLOC_CHECK_
5. MPI specific debugging tools
   1. Marmot MPI check libraries MPICH2 & gdb
6. General purpose tools and techniques
   1. Floating point exceptions
   2. Source code analysis tools
   3. strace
   4. ltrace
   5. ssh_pbs.pl & ~consult/debug/gdbwhere.pl
7. References