NCSA Xeon 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
         1. Xeon Linux Cluster (tungsten)
         2. SGI Altix (cobalt)
         3. Intel 64 Linux Cluster (abe)
      3. /tmp, /usr/tmp, and /var/tmp Directories
      4. Reserved Project Space
   2. Permanent File Storage
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. Locally Installed Software
3. Hierarchical Data Format (HDF) Library
7. Running Jobs
   1. Overview
   2. Running MPI Programs
   3. Queues
   4. Disk Space for Batch Jobs
   5. LSF batch Commands
      1. bsub
         1. bsub for Interactive Jobs
      2. bjobs
      3. bhist
      4. bkill
      5. bacct
      6. bpeek
   6. Sample Batch Script
   7. Managing Batch Scripts
   8. LSF Documentation
8. Debugging
1. Overview
2. Classic serial debuggers
   1. gdb
   2. ddd
   3. idb
   4. idb -gui
   5. TotalView
3. Parallel debuggers
   1. TotalView
   2. cmpirun -gdb [-idb]
   3. cmpirun & MSTI_PRINT
4. Memory allocation debuggers
   1. Valgrind
   2. Electric Fence
   3. MALLOC_CHECK_
   4. Purify
5. MPI specific debugging tools
   1. Marmot MPI check libraries
   2. 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
9. Timing and Profiling
1. Timing
1. time
2. gprof
2. Profiling
1. gprof
2. Perfsuite