NCSA Intel 64 Cluster User Documentation

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Strategic Applications Program

 

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. Compiler Commands
2. Vendor Documentation
3. Useful Compiler/Linker Options
2. Libraries and Application Software
1. Intel's Math Kernel Library (MKL)
2. Locally Installed Software
7. Running Jobs
   1. Interactive Use
   2. Running Programs
   3. Batch System (Torque)
   1. Scheduling Policies
   2. Queues
   3. Batch Commands
   1. qsub
   2. qsub -I
   3. qstat
   4. qhist
   5. qdel
   4. Sample Batch Scripts
   5. Disk Space for Batch Jobs
   6. Automated Saving of Files from Batch Jobs
   4. Notes
8. Debugging
   1. Overview
      
   2. Classic serial debuggers
      gdb
      ddd
      idb
      TotalView
      
   3. Parallel debuggers
      TotalView
      
   4. Memory allocation debuggers
      Valgrind
      MALLOC_CHECK_
      
   5. MPI specific debugging tools
      Marmot MPI check libraries
      MVAPICH2 & gdb
   6. General purpose tools and techniques
      Floating point exceptions
      Source code analysis tools
      strace
      ltrace
      ssh_pbs.pl & ~consult/debug/gdbwhere.pl
      
   7. References
9. Timing and Profiling
1. Timing
   
2. Profiling