SFHG
From HP-SEE Wiki
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== Beneficiaries == | == Beneficiaries == | ||
| + | Faculty of Science. Dept of Physics | ||
== Number of users == | == Number of users == | ||
| Line 35: | Line 36: | ||
* Concept: 2012-06-01 | * Concept: 2012-06-01 | ||
| - | * Start of alpha stage: 2012- | + | * Start of alpha stage: 2012-10-01 |
* Start of beta stage: 2013-01-01 | * Start of beta stage: 2013-01-01 | ||
| - | * Start of testing stage: 2013- | + | * Start of testing stage: 2013-01-15 |
| - | * Start of deployment stage: 2013- | + | * Start of deployment stage: 2013-02-15 |
| - | * Start of production stage: 2013- | + | * Start of production stage: 2013-03-01 |
== Resource Requirements == | == Resource Requirements == | ||
| Line 45: | Line 46: | ||
* Number of cores required for a single run: ''up to 64'' | * Number of cores required for a single run: ''up to 64'' | ||
* Minimum RAM/core required: ''<1GB'' | * Minimum RAM/core required: ''<1GB'' | ||
| - | * Storage space during a single run: ''< | + | * Storage space during a single run: ''<1GB'' |
| - | * Long-term data storage: ''< | + | * Long-term data storage: ''<1GB'' |
* Total core hours required: ''<32000'' | * Total core hours required: ''<32000'' | ||
== Technical Features and HP-SEE Implementation == | == Technical Features and HP-SEE Implementation == | ||
| - | * Primary programming language: '' | + | * Primary programming language: ''C/C++'' |
* Parallel programming paradigm: ''OpenMP'' | * Parallel programming paradigm: ''OpenMP'' | ||
| - | * Main parallel code: '' | + | * Main parallel code: ''Nested OpenMP'' |
| - | * Pre/post processing code: '' | + | * Pre/post processing code: ''N/A'' |
| - | * Application tools and libraries: '' | + | * Application tools and libraries: ''libgomp, gcc, gprof'' |
== Usage Example == | == Usage Example == | ||
| Line 67: | Line 68: | ||
** 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 == | ||
| - | * Benchmarking activities and results: ''.'' | + | Application is currently running at PARADOX, Pecs SC and Szeged SC. |
| - | * Other issues: ''.'' | + | |
| + | * Benchmarking activities and results: ''Performed scalability study for D8.4. Achieved 207k Walks/s for level 8 and 132k Walks/s for level 9.'' | ||
| + | * Other issues: ''Issues with incomplete or missing support for specific OpenMP features with Open64 and Portland Group compilers.'' | ||
== Achieved Results == | == Achieved Results == | ||
| + | *We have calcualted exact number of walks for previously unavailable levels 8 and 9 for all needed types of walks. | ||
| + | *We have created a novel approach to solution of the problem without resorting to brute-force walk counting. | ||
== Publications == | == Publications == | ||
| Line 86: | Line 99: | ||
== Foreseen Activities == | == Foreseen Activities == | ||
| + | * Optimization of parallelization approach to tasks - partially completed. | ||
| + | * Creating MPI code. | ||
| + | * Creating hybrid MPI+OpenMP code. | ||
| + | * Performing all types of walks at the same time (most likely via MPI). | ||
Latest revision as of 09:40, 5 March 2013
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
Faculty of Science. Dept of Physics
Number of users
3
Development Plan
- Concept: 2012-06-01
- Start of alpha stage: 2012-10-01
- 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: <1GB
- Long-term data storage: <1GB
- 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: .
- PARADOX
- Applied for access on: 2010-09-01
- Access granted on: 2010-09-01
- Achieved scalability: 8
- Pecs SC
- 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
Application is currently running at PARADOX, Pecs SC and Szeged SC.
- Benchmarking activities and results: Performed scalability study for D8.4. Achieved 207k Walks/s for level 8 and 132k Walks/s for level 9.
- Other issues: Issues with incomplete or missing support for specific OpenMP features with Open64 and Portland Group compilers.
Achieved Results
- We have calcualted exact number of walks for previously unavailable levels 8 and 9 for all needed types of walks.
- We have created a novel approach to solution of the problem without resorting to brute-force walk counting.
Publications
Foreseen Activities
- Optimization of parallelization approach to tasks - partially completed.
- Creating MPI code.
- Creating hybrid MPI+OpenMP code.
- Performing all types of walks at the same time (most likely via MPI).
