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ffnamespace:performance [2014/08/31 02:29] aldinuc |
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| - | ===== Bowtie2 ===== | + | ===== Applications and Performances ===== |
| + | ==== NGS tools (Bowtie2, BWA) ==== | ||
| + | Bowtie2.0.6, Bowtie-2.2.1, and BWA compared in performance against their porting onto the FastFlow library. Tested on | ||
| + | * Intel 4-socket 8-core Nehalem (64 HT) @2.0GHz, 72MB L3, 64 GB mem, Linux x86_64 | ||
| + | * Intel 2-socket 8-core Sandy Bridge (32 HT) @2.2GHz, 40MB L3, 64 GB mem, Linux x86_64 | ||
| - | |{{:ffnamespace:bowtie2-speedup.png?200|}}|{{:ffnamespace:bowtie-bwa-maxspeedup.png?200|}}| | + | More details in: |
| + | |||
| + | * C. Misale, “Accelerating Bowtie2 with a lock-less concurrency approach and memory affinity,” in Proc. of Intl. Euromicro PDP 2014: Parallel Distributed and network-based Processing, Torino, Italy, 2014. doi:10.1109/PDP.2014.50 [[http://calvados.di.unipi.it/storage/paper_files/2014_pdp_bowtieff.pdf|PDF]] | ||
| + | * C. Misale, G. Ferrero, M. Torquati, and M. Aldinucci, “Sequence alignment tools: one parallel pattern to rule them all?,” BioMed Research International, 2014. doi:10.1155/2014/539410 [[http://downloads.hindawi.com/journals/bmri/2014/539410.pdf|PDF]] | ||
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| + | |{{:ffnamespace:bowtie2-speedup.png?300|}}|{{:ffnamespace:bowtie-bwa-maxspeedup.png?300|}}| | ||
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| </note> | </note> | ||
| - | ===== Applications and Performances ===== | + | |
| We have been developing several applications using FastFlow and FastFlow accelerator. The complexity of them ranges from simple micro-benchmarks to quite complex scientific and business applications. Clearly, our main business consists in developing FastFlow itself more than any big or complex application. However, we believe that developing and running applications is the only effective way to demonstrate that FastFlow is a viable and convenient way to high-level parallel programming for multi-core. For this, each application is carefully chosen in order to demonstrate a particular aspect of feature of FastFlow, and we try make them timeliness available to third-parties with all the information needed to understand the code and reproduce the experiments we did. We also try to publish a Technical Report for each significant advance. Said that, we are also very interested to support independent programmers, scientists, and industries that would like to try FastFlow on their own applicative domains. If you interested just write us. | We have been developing several applications using FastFlow and FastFlow accelerator. The complexity of them ranges from simple micro-benchmarks to quite complex scientific and business applications. Clearly, our main business consists in developing FastFlow itself more than any big or complex application. However, we believe that developing and running applications is the only effective way to demonstrate that FastFlow is a viable and convenient way to high-level parallel programming for multi-core. For this, each application is carefully chosen in order to demonstrate a particular aspect of feature of FastFlow, and we try make them timeliness available to third-parties with all the information needed to understand the code and reproduce the experiments we did. We also try to publish a Technical Report for each significant advance. Said that, we are also very interested to support independent programmers, scientists, and industries that would like to try FastFlow on their own applicative domains. If you interested just write us. | ||
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ffnamespace/performance.txt · Last modified: 2014/08/31 02:52 by aldinuc
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