{"title":"NAMD分子动力学非键合力场在小区宽带引擎处理器上的实现","authors":"Guochun Shi, V. Kindratenko","doi":"10.1109/IPDPS.2008.4536470","DOIUrl":null,"url":null,"abstract":"We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E. processor. The non-bonded force-field kernel, as implemented in the NAMD SPEC 2006 CPU benchmark, has been implemented. Both single-precision and double-precision floating-point kernel variations are considered, and performance results obtained on the Cell/B.E., as well as several other platforms, are reported. Our results obtained on a 3.2 GHz Cell/B.E. blade show linear speedups when using multiple synergistic processing elements.","PeriodicalId":162608,"journal":{"name":"2008 IEEE International Symposium on Parallel and Distributed Processing","volume":"153 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2008-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"15","resultStr":"{\"title\":\"Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor\",\"authors\":\"Guochun Shi, V. Kindratenko\",\"doi\":\"10.1109/IPDPS.2008.4536470\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E. processor. The non-bonded force-field kernel, as implemented in the NAMD SPEC 2006 CPU benchmark, has been implemented. Both single-precision and double-precision floating-point kernel variations are considered, and performance results obtained on the Cell/B.E., as well as several other platforms, are reported. Our results obtained on a 3.2 GHz Cell/B.E. blade show linear speedups when using multiple synergistic processing elements.\",\"PeriodicalId\":162608,\"journal\":{\"name\":\"2008 IEEE International Symposium on Parallel and Distributed Processing\",\"volume\":\"153 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2008-04-14\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"15\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2008 IEEE International Symposium on Parallel and Distributed Processing\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/IPDPS.2008.4536470\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2008 IEEE International Symposium on Parallel and Distributed Processing","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/IPDPS.2008.4536470","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor
We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E. processor. The non-bonded force-field kernel, as implemented in the NAMD SPEC 2006 CPU benchmark, has been implemented. Both single-precision and double-precision floating-point kernel variations are considered, and performance results obtained on the Cell/B.E., as well as several other platforms, are reported. Our results obtained on a 3.2 GHz Cell/B.E. blade show linear speedups when using multiple synergistic processing elements.
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