NCSA SGI Altix 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. Vendor Documentation
4. Useful Compiler/Linker Options
2. Libraries and Application Software
1. Intel's Math Kernel Library (MKL)
2. SGI's Scientific Computing Software Library (scsl)
3. Locally Installed Software
4. Hierarchical Data Format (HDF) Library
7. Running Jobs
   1. Overview
   2. Interactive Use
   3. Queues
   4. Batch Commands
      1. qsub
         1. qsub -I
      2. qstat
      3. qhist
      4. qhosts
      5. qpeek
      6. qps
      7. qdel
   5. Sample Batch Script
   6. Managing Batch Scripts
   7. Disk Space for Batch Jobs
   8. Automated Saving of Files from Batch Jobs
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
2. MPICH2 & gdb
6. General purpose tools and techniques
1. Floating pointexceptions
2. Source code analysis tools
3. strace
7. References
9. Timing and Profiling
   1. Timing Codes
   1. time
   2. gprof
   2. Profiling
   1. gprof
   2. PerfSuite