SFHG

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	** Achieved scalability: ''8''		** Achieved scalability: ''8''
	* Accessed production systems: ''.''		* Accessed production systems: ''.''
-	# ''.''	+	# ''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: ''8''
-	* Porting activities: ''.''	+	# ''Pecs SC''
-	* Scalability studies: ''.''	+	#* Applied for access on: ''2013-01-18''
		+	#* Access granted on: ''2013-01-21''
		+	#* Achieved scalability: ''48''
		+	# ''Szeged SC''
		+	#* Applied for access on: ''2013-01-18''
		+	#* Access granted on: ''2013-01-21''
		+	#* Achieved scalability: ''24''
		+	* Porting activities: ''Emulated implementation of OpenMP functions not implemented in older versions of gcc/libgomp''
		+	* Scalability studies: ''Scalability studies performed at PARADOX (up to 8 CPU cores), BA-01-ETFBL (up to 16 CPU cores) and Pecs SC (up to 48 CPU cores). Detailed results available in Deliverable D8.4.''
	== Running on Several HP-SEE Centres ==		== Running on Several HP-SEE Centres ==

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Revision as of 11:19, 23 January 2013

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, Igor Sevo, Mihajlo Savic Faculty of Electrical 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

New serial C++ code produced. Parallelization of serial C++ code done in OpenMP.

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: 2013-01-15
• Start of deployment stage: 2013-02-15
• Start of production stage: 2013-03-01

Resource Requirements

• Number of cores required for a single run: up to 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: C/C++
• Parallel programming paradigm: OpenMP
• Main parallel code: Nested OpenMP
• Pre/post processing code: N/A
• Application tools and libraries: libgomp, gcc, gprof

Usage Example

Infrastructure Usage

• Home system: PARADOX
  • Applied for access on: 2010-09-01
  • Access granted on: 2010-09-01
  • Achieved scalability: 8
• Accessed production systems: .

1. PARADOX
   • Applied for access on: 2010-09-01
   • Access granted on: 2010-09-01
   • Achieved scalability: 8
2. Pecs SC
   • Applied for access on: 2013-01-18
   • Access granted on: 2013-01-21
   • Achieved scalability: 48
3. Szeged SC
   • Applied for access on: 2013-01-18
   • Access granted on: 2013-01-21
   • Achieved scalability: 24

• Porting activities: Emulated implementation of OpenMP functions not implemented in older versions of gcc/libgomp
• Scalability studies: Scalability studies performed at PARADOX (up to 8 CPU cores), BA-01-ETFBL (up to 16 CPU cores) and Pecs SC (up to 48 CPU cores). Detailed results available in Deliverable D8.4.

Running on Several HP-SEE Centres

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

Achieved Results

Publications

Foreseen Activities