Parallelization of general-linkage analysis problems - PubMed (original) (raw)
. 1994 May-Jun;44(3):127-41.
doi: 10.1159/000154205.
Affiliations
- PMID: 8039796
- DOI: 10.1159/000154205
Parallelization of general-linkage analysis problems
S Dwarkadas et al. Hum Hered. 1994 May-Jun.
Abstract
We describe a parallel implementation of a genetic-linkage analysis program that achieves good speed improvement, even for analyses on a single pedigree and with a single starting recombination fraction vector. Our parallel implementation has been run on three different platforms: an Ethernet network of workstations, a higher-bandwidth asynchronous transfer mode (ATM) network of workstations, and a shared-memory multiprocessor. The same program, written in a shared-memory programming style, is used on all platforms. On the workstation networks, the hardware does not provide shared memory, so the program executes on a distributed shared memory system that implements shared memory in software. These three platforms represent different points on the price/performance scale. Ethernet networks are cheap and omnipresent, ATM networks are an emerging technology that offers higher bandwidth, and shared-memory multiprocessors offer the best performance because communication is implemented entirely by hardware. On 8 processors and for the longer runs, we achieve speedups between 3.5 and 5 on the Ethernet network and between 4.8 and 6 on the ATM network. On the shared-memory multiprocessor, we achieve speedups in the 5.5-6.5 range for all runs.
Similar articles
- Experience with PACS in an ATM/Ethernet switched network environment.
Pelikan E, Ganser A, Kotter E, Schrader U, Timmermann U. Pelikan E, et al. IEEE Trans Inf Technol Biomed. 1998 Mar;2(1):26-9. doi: 10.1109/4233.678532. IEEE Trans Inf Technol Biomed. 1998. PMID: 10719509 - Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology.
Miller PL, Nadkarni P, Gelernter JE, Carriero N, Pakstis AJ, Kidd KK. Miller PL, et al. Comput Biomed Res. 1991 Jun;24(3):234-48. doi: 10.1016/0010-4809(91)90046-y. Comput Biomed Res. 1991. PMID: 1868693 - Fast computation of genetic likelihoods on human pedigree data.
Goradia TM, Lange K, Miller PL, Nadkarni PM. Goradia TM, et al. Hum Hered. 1992;42(1):42-62. doi: 10.1159/000154045. Hum Hered. 1992. PMID: 1555846 - [Series: Medical Applications of the PHITS Code (2): Acceleration by Parallel Computing].
Furuta T, Sato T. Furuta T, et al. Igaku Butsuri. 2015;35(3):264-8. Igaku Butsuri. 2015. PMID: 27125134 Review. Japanese. - High-performance computing, high-speed networks, and configurable computing environments: progress toward fully distributed computing.
Johnston WE, Jacobson VL, Loken SC, Robertson DW, Tierney BL. Johnston WE, et al. Crit Rev Biomed Eng. 1992;20(5-6):315-54. Crit Rev Biomed Eng. 1992. PMID: 1486779 Review.
Cited by
- MLIP: using multiple processors to compute the posterior probability of linkage.
Govil M, Segre AM, Vieland VJ. Govil M, et al. BMC Bioinformatics. 2008 May 28;9 Suppl 6(Suppl 6):S2. doi: 10.1186/1471-2105-9-S6-S2. BMC Bioinformatics. 2008. PMID: 18541055 Free PMC article. - A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. Carriero N, et al. J Am Med Inform Assoc. 2005 Jan-Feb;12(1):90-8. doi: 10.1197/jamia.M1571. Epub 2004 Oct 18. J Am Med Inform Assoc. 2005. PMID: 15492032 Free PMC article. - Genetic linkage of familial granulomatous inflammatory arthritis, skin rash, and uveitis to chromosome 16.
Tromp G, Kuivaniemi H, Raphael S, Ala-Kokko L, Christiano A, Considine E, Dhulipala R, Hyland J, Jokinen A, Kivirikko S, Korn R, Madhatheri S, McCarron S, Pulkkinen L, Punnett H, Shimoya K, Spotila L, Tate A, Williams CJ. Tromp G, et al. Am J Hum Genet. 1996 Nov;59(5):1097-107. Am J Hum Genet. 1996. PMID: 8900239 Free PMC article. - Localization of a novel locus for autosomal recessive early-onset parkinsonism, PARK6, on human chromosome 1p35-p36.
Valente EM, Bentivoglio AR, Dixon PH, Ferraris A, Ialongo T, Frontali M, Albanese A, Wood NW. Valente EM, et al. Am J Hum Genet. 2001 Apr;68(4):895-900. doi: 10.1086/319522. Epub 2001 Mar 7. Am J Hum Genet. 2001. PMID: 11254447 Free PMC article. - Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers.
Silberstein M, Tzemach A, Dovgolevsky N, Fishelson M, Schuster A, Geiger D. Silberstein M, et al. Am J Hum Genet. 2006 Jun;78(6):922-35. doi: 10.1086/504158. Epub 2006 May 1. Am J Hum Genet. 2006. PMID: 16685644 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Research Materials
Miscellaneous