NCSA TeraGrid IA-64 Linux Cluster User Guide

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Data
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Allocations
Consulting
Training
Strategic Applications Program

 

Table of Contents

1. Allocations and Account Management
1. The Allocation Process
2. Access
1. Standard Password
2. X.509 Certificate
3. Managing your Account
1. Changing Your Password
2. Your shell
3. Email
4. Managing your Allocation
1. Charging Algorithm
2. Checking Your Account Balance
2. Managing your Environment (SoftEnv)
3. Filesystems and Storage
1. Directories
1. Home Directories
2. Scratch Directories
3. User Project Directories
4. TeraGrid Environment Variables
2. Permanent Storage
3. Transferring Files
4. 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
5. 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
6. 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