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HPC Awareness Day |
KFUPM High Performance Computing Awareness Day
Tuesday 27th January 2009 |
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>> more info |
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HPC Orientation Workshop |
| Last week of February |
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>> more info |
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Available Software on HPC Cluster
The HPC@KFUPM offers a variety of
applications and codes that are installed on the cluster.
The software presently available are:
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Gaussian with Linda: Gaussian 03 is used
by chemists, chemical engineers, biochemists, physicists and others for
research in established and emerging areas of chemical interest. Starting
from the basic laws of quantum mechanics, Gaussian predicts the energies,
molecular structures, and vibrational frequencies of molecular systems,
along with numerous molecular properties derived from these basic
computation types. It can be used to study molecules and reactions under a
wide range of conditions, including both stable species and compounds which
are difficult or impossible to observe experimentally such as short-lived
intermediates and transition structures. Gaussian with Linda is the HPC
version of Gaussian 03 software with parallel capabilities to run jobs in
parallel on HPC clusters.
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MPICH: It is a freely available, portable
implementation of
MPI, a standard for message-passing for distributed-memory applications
used in
parallel computing. MPICH is free
software and is available for most flavors of
Unix (including
Linux and
Mac OS X)
and
Microsoft Windows. Moreover, MPICH is a developed program library.
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Microsoft MPI SDK: It is the Microsoft's
implementation of MPI and its accompanying Software Developer Kit which is
used on Windows HPC Server 2008 to develop parallel programs.
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OpenMP: The OpenMP Application Program Interface
(API) supports multi-platform shared-memory parallel programming in C/C++
and Fortran on all architectures, including Unix platforms and Windows NT
platforms. Jointly defined by a group of major computer hardware and
software vendors, OpenMP is a portable, scalable model that gives
shared-memory parallel programmers a simple and flexible interface for
developing parallel applications for platforms ranging from the desktop to
the supercomputer.
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DL_POLY: It is a
general purpose serial and parallel molecular dynamics simulation package
developed at Dares bury Laboratory by W. Smith, T.R. Forester and I.T.
Todorov. The original package was developed by the Molecular Simulation
Group (now part of the Computational Chemistry Group,
MSG) at Dares
bury
Laboratory under the auspices of the Engineering and Physical Sciences
Research Council (EPSRC) for the EPSRC's Collaborative Computational Project
for the Computer Simulation of Condensed Phases (
CCP5). The package is the property of the Central Laboratory of the
Research Councils.
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Octave: GNU Octave is a
high-level language, primarily intended for numerical computations. It
provides a convenient command line interface for solving linear and
nonlinear problems numerically, and for performing other numerical
experiments using a language that is mostly compatible with Matlab. It may
also be used as a batch-oriented language. Octave has extensive tools for
solving common numerical linear algebra problems, finding the roots of
nonlinear equations, integrating ordinary functions, manipulating
polynomials, and integrating ordinary differential and
differential-algebraic equations. It is easily extensible and customizable
via user-defined functions written in Octave's own language, or using
dynamically loaded modules written in C++, C, Fortran, or other languages.
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EGSnrc: The EGSnrc system is a package for the
Monte Carlo (MC) simulation of coupled electron-photon transport. Its
current energy range of applicability is considered to be 1keV - 10 GeV.
EGSnrc is an extended and improved version of the EGS4 package originally
developed at SLAC. It incorporates many improvements in the implementation
of the condensed history technique for the simulation of charged particle
transport and better low energy cross sections.
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BEAMnrc: BEAMnrcMP is a general purpose Monte Carlo
simulation system for modeling radiotherapy sources which is based on the
EGSnrcMP code system for modeling coupled electron and photon transport.
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GROMACS:GROMACS is a versatile package to perform
molecular dynamics, i.e. simulate the Newtonian equations of motion for
systems with hundreds to millions of particles.
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Intel® C++ Compiler Professional Edition for
Linux: The Intel® C++ Compiler Professional
Edition delivers rapid development and winning performance for the full
range of Intel® processor-based platforms. The Professional Edition not only
comes with the compiler’s breadth of advanced optimization, multi-threading,
and processor support, including automatic processor dispatch,
vectorization, and loop unrolling, it also has highly optimized C++
templates for parallelism, math processing, and multimedia libraries.
Following software will also be made
available to the faculty and students in the near future.
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