Next:
Introduction
User Guide to the HECToR Service
(Version 2.0)
Introduction
Architecture Overview
The HECToR system
Processors, Caches and Memory
X2 Vector Processors
Communication Networks
Data I/O and storage
Operating system
Getting started
Logging in
User Resource Management
What resources do I have - time?
What resources do I have - storage?
Diskspace
The HECToR Administration Web Site
Using the
module
environment
Information on the modules
Loading, unloading and swapping modules
Things to watch out for
Compilation
Compiling for Quadcore
Compiling for XT Nodes
Compiling Fortran code
Compiling C code
Compiling C++ code
Selecting compiler suites and compiler versions
Compiling MPI code
Compiling OpenMP code
Useful compiler options
Compiling for X2 Nodes
Useful compiler options
Compiling for the frontend nodes
File Management.
Filesystems
home
filesystem
work
filesystem
Obtaining information on quota usage
Allocating quotas to specific groups and users
File permissions and security
Transferring data to and from HECToR
Performance considerations
Sharing data with other HECToR users
Sharing data between systems
Guidelines
Data archiving
Use of
/tmp
Backup policies
Standard Output, Standard Error and Lost Files
Porting Codes
Compilers and Modules
MPI
Timers
Environment variables
Batch Processing
Using PBS
The
qsub
command
The
qstat
command
The
qdel
command
Output from PBS jobs
Serial Queues
Example Serial Job Submission Script
Example Serial Job Submission Script for Visualisation Software
Running Jobs on the XT Nodes
Problems with serial commands in parallel job scripts
Parallel job launcher
aprun
for XT jobs
Job submission scripts for parallel jobs using MPI on the XT nodes
Job submission scripts for parallel jobs using OpenMP on the XT4 nodes
Job submission scripts for hybrid parallel jobs using MPI and OpenMP (Mixed Mode) on the XT nodes
Checking the health of compute nodes
Running Jobs on the X2 Vector Nodes
Parallel job launcher
aprun
for jobs on the X2 nodes
Job submission scripts for parallel MPI jobs on the X2 nodes
Job submission scripts for parallel OpenMP jobs on the X2 nodes
Batch System Layout and Limits
Tools
Performance Analysis and Debugging Tools
Performance Analysis Tools: CrayPAT, Apprentice2
Debugging Tools: Totalview debugger
Visualization Tools
Paraview
Usage
Example Paraview Batch Scripts
Using the Paraview GUI on HECToR
Libraries
XT-Libraries (Opteron based system)
XT-LibSci
Usage
Linear algebra: BLAS and LAPACK
BLACS
ScaLAPACK
SuperLU
Iterative Refinement Toolkit
AMD Core Math Library - ACML
Usage
Cray FFT interface
Random Number Generators
PGI OpenMP issue
HDF5
NetCDF
FFTW
PETSc
NAG Fortran Library, Mark 21
NAG SMP Library, Mark 21
NAG Parallel Library, Release 3
X2 Libraries (Vector System)
libsci
FFTs
Optimisation
Single Processor Optimisation
Use the Right Algorithms
Use the Performance Libraries
Use the Compiler Flags
Optimise use of Cache
I/O Optimisation
Lustre File System Performance
MPI
MPI in general.
Optimizing MPI on HECToR
More information about MPI on the Cray XT.
Scaling
Third Party Packages
Grid.
References and Further Reading
Online Documentation and Resources
MPI Programming
OpenMP Programming
Parallel Programming
Programming Languages
Programming Skills
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