Limits...
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets.

Scharfe M, Pielot R, Schreiber F - BMC Bioinformatics (2010)

Bottom Line: We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties.The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units.We discuss several CBE-based optimisation methods and compare our results to standard solutions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.

ABSTRACT

Background: Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks.

Results: We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de.

Conclusions: The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.

Show MeSH

Related in: MedlinePlus

Listing 5: This code fragment illustrates a fourfold unrolling of a typical nested loop.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2821319&req=5

Figure 7: Listing 5: This code fragment illustrates a fourfold unrolling of a typical nested loop.

Mentions: The technique of loop unrolling provides significant performance improvements, as compilers can automatically schedule operations and optimise computations, if the algorithm consist of many independent operations [15,21]. In particular nested loops have been unrolled manually to gain a considerably better performance. It seems to be useful to try several levels of unrolling in order to find an optimal usage of the SPE's large register file. An example of a fourfold unrolled nested loop is shown in program listing 5 (Figure 7).


Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets.

Scharfe M, Pielot R, Schreiber F - BMC Bioinformatics (2010)

Listing 5: This code fragment illustrates a fourfold unrolling of a typical nested loop.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2821319&req=5

Figure 7: Listing 5: This code fragment illustrates a fourfold unrolling of a typical nested loop.
Mentions: The technique of loop unrolling provides significant performance improvements, as compilers can automatically schedule operations and optimise computations, if the algorithm consist of many independent operations [15,21]. In particular nested loops have been unrolled manually to gain a considerably better performance. It seems to be useful to try several levels of unrolling in order to find an optimal usage of the SPE's large register file. An example of a fourfold unrolled nested loop is shown in program listing 5 (Figure 7).

Bottom Line: We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties.The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units.We discuss several CBE-based optimisation methods and compare our results to standard solutions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.

ABSTRACT

Background: Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks.

Results: We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de.

Conclusions: The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.

Show MeSH
Related in: MedlinePlus