SFHG
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Hamiltonian self avoiding walks on fractals (Sierpinsky gaskets) are one of perspective models for long polymers (DNA, RNA and other bio polymers) behavior 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 == | == Problems Solved == | ||
| Line 30: | Line 30: | ||
== Number of users == | == Number of users == | ||
| + | 3 | ||
== Development Plan == | == Development Plan == | ||
| - | * Concept: | + | * Concept: 2012-06-01 |
| - | * Start of alpha stage: | + | * Start of alpha stage: 2012-11-01 |
| - | * Start of beta stage: | + | * Start of beta stage: 2013-01-01 |
| - | * Start of testing stage: | + | * Start of testing stage: 2013-04-01 |
| - | * Start of deployment stage: | + | * Start of deployment stage: 2013-05-01 |
| - | * Start of production stage: | + | * Start of production stage: 2013-06-01 |
== Resource Requirements == | == Resource Requirements == | ||
| - | * Number of cores required for a single run: '' | + | * Number of cores required for a single run: ''64'' |
| - | * Minimum RAM/core required: ''1GB'' | + | * Minimum RAM/core required: ''<1GB'' |
| - | * Storage space during a single run: ''10GB'' | + | * Storage space during a single run: ''<10GB'' |
| - | * Long-term data storage: ''40GB'' | + | * Long-term data storage: ''<40GB'' |
| - | * Total core hours required: '' | + | * Total core hours required: ''<32000'' |
== Technical Features and HP-SEE Implementation == | == Technical Features and HP-SEE Implementation == | ||
| Line 61: | Line 62: | ||
== Infrastructure Usage == | == Infrastructure Usage == | ||
| - | * Home system: '' | + | * Home system: ''PARADOX'' |
| - | ** Applied for access on: '' | + | ** Applied for access on: ''2010-09-01'' |
| - | ** Access granted on: '' | + | ** Access granted on: ''2010-09-01'' |
** Achieved scalability: ''.'' | ** Achieved scalability: ''.'' | ||
* Accessed production systems: ''.'' | * Accessed production systems: ''.'' | ||
Revision as of 11:07, 11 September 2012
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: .
- .
- 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: .
