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HPC | Software & System Specifications

System Hardware Specifications

The AU HPC System provides high-speed parallel/distributed data processing and research-dedicated storage with high input-output capabilities. Hardware includes a head node (Dell R710); blade chassis (Dell M1000E: PowerEdge M610 Blade Server); 15 blades each housing 2 Intel hexacore X5650 processors (12 cores each), 24 GB of memory, and a 160 GB SATA hard drive; one node with an Nvidia graphics processing unit (Tesla 2050); Infiniband interconnect; 25 TB 5-node Isilon IQ5400S Network Attached Storage cluster.

 

Results of LINPACK Benchmarking

T/V N NB P Q Time Gflops
WR03R2R4 200000 240 12 15 3165.20 1.685e+03
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=  0.0017584 ...... PASSED
Finished 1 tests with the following results:
1 tests completed and passed residual checks,
0 tests completed and failed residual checks,
0 tests skipped because of illegal input values.
End of Tests.

Rpeak (theoretical) (180 cores @ 10.664 Gf per core) = 1919.52 Gf
Rmax (actual) = 1685 Gf (87.78% efficiency)

 

System Software, Related Documents, and Links

Open Source

C++
http://www.cplusplus.com/

 

CUDA
http://www.nvidia.com/object/cuda_home_new.html

 

Enthought Python Distributed
http://www.enthought.com/products/epd.php

 

Fortran

 

MEGA (Molecular Evolutionary Genetics Analysis)
http://www.megasoftware.net/

 

MrBayes
http://mrbayes.csit.fsu.edu/

MrBayes Manual (3.1, PDF)
 

Muscle
http://www.drive5.com/muscle/
Muscle User Guide
(3.8, PDF)

 

Octave
http://www.gnu.org/software/octave/

 

OpenBUGS (Bayesian inference Using Gibbs Sampling)
http://www.openbugs.info/w/

 

Perl
http://www.perl.org/

 

R Project
http://www.r-project.org/
R Intro (Version 2.13.0, PDF)


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Licensed Software

Load Sharing Facility (LSF)
LSF AU User Guide (PDF)
LSF Commands (PDF)
LSF Submitting Jobs (PDF) 

 

Matlab Distributed
http://www.mathworks.com/products/distriben/
Matlab AU User Guide
(PDF)


Mathematica
Please (free) installation/licensing via CAS at
Mathematica Software

 

Stata MP
http://www.stata.com/statamp/