AMR PAR

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: Parallel algorithm and program for the solving of continuum mechanics equations using Adaptive Mesh Refinement
• Application's acronym: AMR_PAR
• Virtual Research Community: VRC "Computational Physics"
• Scientific contact: Boris RYBAKIN, rybakin@math.md
• Technical contact: Nicolai ILIUHA, nick@renam.md
• Developers: Dr. habil. Boris RYBAKIN,Institute of Mathematics and Computer Science, Laboratory of Mathematical Modelling, Republic of Moldova
• Web site: http://www.math.md/en/

Short Description

Many complex problems of continuum mechanics are numerically solved on structured or unstructured grids. To improve the accuracy of the calculations is necessary to choose a sufficiently small grid (with a small cell size). This leads to the drawback of a substantial increase of computation time. Therefore, for the calculations of complex problems in recent years the method of Adaptive Mesh Refinement (AMR) is applied. That is, the grid refinement is performed only in the areas of interest of the structure, where e.g. the shock waves are generated, or a complex geometry or other such features exist. Thus, the computing time is greatly reduced. In addition, the execution of the application on the resulting sequence of nested, decreasing nets can be parallelized. For the arrays with dimension up to 128x128x128 the application AMR_PAR can still be executed in Grid. For higher-dimensional arrays, which are of practical interest, the delays in sending messages is greatly increasing the run time of the application, and the use of the HPC solution becomes mandatory.

Problems Solved

We consider a continuum mechanics problem, such as the problem of modeling the explosion of a supernova type II and, for this example, create an algorithm using the method of AMR and build a parallel program. Then the results of the calculation of specified problem of blast are visualized.

Scientific and Social Impact

This method can be applied to any other nowaday problem of continuum mechanics - to calculate the aerodynamics of aircraft, the calculations of the air flow of cars, a large number of other problems of mathematical modeling - calculation of the flow of blood through the vessels, the calculations of the heart valves, etc. Hence, the practical use – the calculation of complex problems in a reasonable time. In all these cases, at the beginning of the problem we define a way to highlight areas in which need to construct the grid, then the program builds a sequence of grids and makes a decision on them. The social impact depends on the problem to be solved, the use of AMR_PAR being of interest for heavy industry (e.g. car body design and development, aircraft aerodynamics), or for healthcare industry.

Collaborations

• SIISI RAS, Moscow, Russia

Beneficiaries

• Main beneficiaries are research groups in Computational Mathematics and Computational Astrophysics.

Number of users

5

Development Plan

• Concept: The concept was done before the project started
• Start of alpha stage: M01. Construction of an algorithm. Creating of the program.
• Start of beta stage: M6. Parallelization and Debugging of the application.
• Start of testing stage: M8. Testing on multiprocessor platforms.
• Start of deployment stage: M10. Performing calculations, debugging of part for results virtualization. Preparing for deployment on a remote sites.
• Start of production stage: .

Resource Requirements

• Number of cores required for a single run: from 4 to up to 32
• Minimum RAM/core required: 1 Gb
• Storage space during a single run: 1-110 Gb
• Long-term data storage: 500 Gb
• Total core hours required: Unknown

Technical Features and HP-SEE Implementation

• Primary programming language: Intel Fortran 11.0
• Parallel programming paradigm: Open MP
• Main parallel code: Open MP
• Pre/post processing code: Own developer
• Application tools and libraries: OpenMP, Intel MKL10.1

Usage Example

Infrastructure Usage

• Home system: SGI UltraViolet 1000 supercomputer at NIIFI, located in Pecs, Hungary
  • Applied for access on: 10.2011
  • Access granted on: 10.2011
  • Achieved scalability: 8 cores
• Accessed production systems:

1. SGI UltraViolet 1000 supercomputer at NIIFI, located in Pecs, Hungary
   • Applied for access on: 10.2011
   • Access granted on: 10.2011
   • Achieved scalability: 8 cores
2. ...
   • Applied for access on: ...
   • Access granted on: ...
   • Achieved scalability: ... cores

• Porting activities: ...
• Scalability studies: ...

Running on Several HP-SEE Centres

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

Achieved Results

...

Publications

• RYBAKIN, B.; SIDER, N. Numerical modeling of multidimensional problems of gravitational gas dynamics with high resolution schemes. Buletinul AŞM, ser. Matematica. 2010, nr. 1, 92-102. ISSN 1024-7696.
• ...

Foreseen Activities

• Application scalable problems were found during tests.
• The work is further proceeds on two directions: the first - the developers modify application algorithm to create a new version of scalable OpenMP AMR_PAR application; the second - try to make changes to an existing version of the application to achieve the desired scalability. The current available for submission version is a lightweight model for testing applications - without withdrawal of large volumes of information;
• For remotely collaborative work organization with application were done the following preparation actions: a terminal server with software for creating and debugging applications under Windows; the virtual machine running CentOS 6.2 and Intel ® Parallel Studio XE 2011 for debugging application in Linux;