This cluster incorporates CPUs and graphics processing units (GPUs). This technology greatly enhances the speed with which computer systems process information and represents an important development in supercomputing. Nationally, GPU-accelerated supercomputers have enabled new research projects in areas as diverse as bioinformatics, climatology, and molecular and materials modeling. HPC resources enable researchers to move beyond the limitations of traditional research to produce new understandings of problems and meaningful results that have far-reaching interdisciplinary impact. Part of the focus of HPC is to expand the reach of “big computing” by addressing system-level questions in social, economic, and cultural research. With its advanced computing and communications resources, HPC is helping to create the virtual organizations, virtual worlds, and immersive environments that will continue to transform and globalize higher education in the twenty-first century.

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running .

MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. Typical uses include:

• Math and computation
• Algorithm development
• Modeling, simulation, and prototyping
• Data analysis, exploration, and visualization
• Scientific and engineering graphics
• Application development, including Graphical User Interface building

TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Available ASAP .

Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics. It was conceived by Stephen Wolfram and is developed by Wolfram Research of Champaign, Illinois. The Wolfram Language is the programming language used in Mathematica. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Mathematica Tutorial .

The Message Passing Interface Standard (MPI) is a message passing library standard based on the consensus of the MPI Forum, which has over 40 participating organizations, including vendors, researchers, software library developers, and users. The goal of the Message Passing Interface is to establish a portable, efficient, and flexible standard for message passing that will be widely used for writing message passing programs. As such, MPI is the first standardized, vendor independent, message passing library. The advantages of developing message passing software using MPI closely match the design goals of portability, efficiency, and flexibility. MPI is not an IEEE or ISO standard, but has in fact,become the "industry standard" for writing message passing programs on HPC platforms. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Message Passing Interface (MPI) .

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. For examples of LAMMPS simulations, see the Publications page of the LAMMPS Site. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• LAMMPS Molecular Dynamics Simulator .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

DL POLY 4 is a general purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith and I.T. Todorov. The DL POLY project was developed 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 Computational Chemistry and Advanced Research Computing Groups (CCG & ARCG) at Daresbury Laboratory and the Natural Environment Research Council (NERC) for the NERC’s eScience project Computational Chemistry in the Environment (eMinerals), directed by M.T. Dove. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• DL_POLY Interface .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

Gaussian G09 is a software package for molecular dynamics. Gaussian G09 is installed on Linux Cluster for serial (single-processor) and for parallel (multi-processor, shared memory) use within a single compute node, and for distributed (multi-processor, distributed memory) use on different compute nodes. TORQUE, also known by its historical name, Portable Batch System (PBS), is the Job scheduler or resource manager on the HPC at Shahid Beheshti University. PBS manages jobs that users submit to queues on the system.

Full Examples from source code to sample output:

• Running a Gaussian Job .

This guide will explain how to begin using HPC resources. It will provide information on how to apply for a HPC account and how to log in to the system and begin working with the HPC environment. Applying for an HPC Account You must be a SBU faculty or staff member to receive an HPC account and use HPC facilities. In order to apply for a new HPC account, please complete the account application at SBU Vice Chancellor for Research. For additional information on applying for a HPC account, please contact us. After you get account, you can log in to the HPC Linux cluster by ssh-ing to 192.168.220.100. This head nodes should only be used for editing, compiling and submitting jobs. Computing should be done on the compute nodes. Jobs executed on the head nodes are subject to termination. The Linux cluster resource runs the CentOS 6.5 operating system.

How to:

• Login

• File Transferring