SFHG

From HP-SEE Wiki

Contents 1 General Information 2 Short Description 3 Problems Solved 4 Scientific and Social Impact 5 Collaborations 6 Beneficiaries 7 Number of users 8 Development Plan 9 Resource Requirements 10 Technical Features and HP-SEE Implementation 11 Usage Example 12 Infrastructure Usage 13 Running on Several HP-SEE Centres 14 Achieved Results 15 Publications 16 Foreseen Activities

General Information

• Application's name: Self Avoiding Hamiltonian Walk on Gaskets
• Application's acronym: SFHG
• Virtual Research Community: Computational Physics Applications
• Scientific contact: Sreten Lekic, slekic@blic.net
• Technical contact: Sreten Lekic, slekic@blic.net
• Developers: Sreten Lekic, Faculty of Mech. Engineering, University of Banja Luka (UoBL), Bosnia - Herzegovina
• Web site: http://wiki.hp-see.eu/index.php/SFHG

Short Description

Hamiltonian self avoiding walks on fractals (Sierpinsky gaskets) are one of perspective models for long polymers (DNA, RNA and other bio polymers) behavior description.

We have developed a program for counting self-avoiding Hamiltonian walks to run on multiple processors in a parallel mode. We study Hamiltonian walks (HWs) on the family of two-dimensional modified Sierpinski gasket fractals, as a simple model for compact polymers in nonhomogeneous media in two dimensions. We apply an exact recursive method which allows for explicit enumeration of extremely long Hamiltonian walks of different types: closed and open, with end-points anywhere in the lattice, or with one or both ends fixed at the corner sites. The leading term n is characterized by the value of the connectivity constant 1, which depends on fractal type, but not on the type of HW.

Problems Solved

Initial parallelization of process, partitioning.

Scientific and Social Impact

Collaborations

Beneficiaries

Number of users

3

Development Plan

• Concept: 2012-06-01
• Start of alpha stage: 2012-11-01
• Start of beta stage: 2013-01-01
• Start of testing stage: 2013-04-01
• Start of deployment stage: 2013-05-01
• Start of production stage: 2013-06-01

Resource Requirements

• Number of cores required for a single run: 64
• Minimum RAM/core required: <1GB
• Storage space during a single run: <10GB
• Long-term data storage: <40GB
• Total core hours required: <32000

Technical Features and HP-SEE Implementation

• Primary programming language: FORTRAN
• Parallel programming paradigm: MPI
• Main parallel code: .
• Pre/post processing code: .
• Application tools and libraries: .

Usage Example

Infrastructure Usage

• Home system: PARADOX
  • Applied for access on: 2010-09-01
  • Access granted on: 2010-09-01
  • Achieved scalability: .
• Accessed production systems: .

1. .
   • Applied for access on: .
   • Access granted on: .
   • Achieved scalability: .

• Porting activities: .
• Scalability studies: .

Running on Several HP-SEE Centres

• Benchmarking activities and results: .
• Other issues: .

Achieved Results

Publications

Foreseen Activities