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Apus

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Dieter Thomas Tietze – One of the best experts on this subject based on the ideXlab platform.

  • molecular phylogeny of old world swifts aves apodiformes apodidae Apus and tachymarptis based on mitochondrial and nuclear markers
    Molecular Phylogenetics and Evolution, 2012
    Co-Authors: Martin Packert, Jochen Martens, Michael Wink, Anna Feigl, Dieter Thomas Tietze

    Abstract:

    Abstract We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b , 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda , (2) African-Asian clade of A. caffer , A. batesi , A. horus , A. affinis and A. nipalensis , (3) African-Palearctic clade of eight currently accepted species among which sequences of A. Apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus , Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus , A. barbatus , A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome- b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis / A. nipalensis and A. Apus / A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results.

Issam Said – One of the best experts on this subject based on the ideXlab platform.

  • evaluation of successive cpus Apus gpus based on an opencl finite difference stencil
    Parallel Distributed and Network-Based Processing, 2013
    Co-Authors: Henri Calandra, Romain Dolbeau, Pierre Fortin, Jean-luc Lamotte, Issam Said

    Abstract:

    The AMD APU (Accelerated Processing Unit) architecture, which combines CPU and GPU cores on the same die, is promising for GPU applications which performance is bottlenecked by the low PCI Express communication rate. However the first APU generations still have different CPU and GPU memory partitions. Currently, the APU integrated GPUs are also less powerful than discrete GPUs. In this paper we therefore investigate the interest of Apus for scientific computing by evaluating and comparing the performance of two successive AMD Apus (family codename Llano and Trinity), two successive discrete GPUs (chip codename Cayman and Tahiti) and one hexa-core AMD CPU. For this purpose, we rely on a 3D finite difference stencil, that is optimized and tuned in OpenCL. We detail the most interesting optimizations for each architecture and show very good performance in OpenCL: up to 500 Gflops on Tahiti. Finally, our results show that APU integrated GPUs outperform CPUs, and that integrated GPUs of upcoming Apus may match discrete GPUs for problems with high communication requirements.

  • Evaluation of Successive CPUs/Apus/GPUs Based on an OpenCL Finite Difference Stencil
    2013 21st Euromicro International Conference on Parallel Distributed and Network-Based Processing, 2013
    Co-Authors: Henri Calandra, Romain Dolbeau, Pierre Fortin, Jean-luc Lamotte, Issam Said

    Abstract:

    The AMD APU (Accelerated Processing Unit) architecture, which combines CPU and GPU cores on the same die, is promising for GPU applications which performance is bottlenecked by the low PCI Express communication rate. However the first APU generations still have different CPU and GPU memory partitions. Currently, the APU integrated GPUs are also less powerful than discrete GPUs. In this paper we therefore investigate the interest of Apus for scientific computing by evaluating and comparing the performance of two successive AMD Apus (family codename Llano and Trinity), two successive discrete GPUs (chip codename Cayman and Tahiti) and one hexa-core AMD CPU. For this purpose, we rely on a 3D finite difference stencil, that is optimized and tuned in OpenCL. We detail the most interesting optimizations for each architecture and show very good performance in OpenCL: up to 500 Gflops on Tahiti. Finally, our results show that APU integrated GPUs outperform CPUs, and that integrated GPUs of upcoming Apus may match discrete GPUs for problems with high communication requirements.

  • Assessing the relevance of APU for high performance scientific computing
    , 2012
    Co-Authors: Henri Calandra, Romain Dolbeau, Pierre Fortin, Jean-luc Lamotte, Issam Said

    Abstract:

    Fusion Apus eliminate the PCI Express bus which bottlenecks many GPU applications. However, integrated GPUs in Apus are less powerful than discrete GPUs, and while the upcoming Apus will rely on a unified memory, the first Apus still have a distinct GPU memory partition. Hence, it is worthwhile to investigate the applications, as well as problem sizes, for which the GPU part of an APU may outperform a discrete GPU. In this talk we assess the relevance of Llano and Trinity Apus for scientific HPC via hardware and applicative OpenCL micro-benchmarks. We present detailed measurements of CPU-GPU data transfers and performance tests of highly optimized 3D finite difference stencils (a synthetic one and a more realistic and complex one for wave propagation simulations) depending on the frequency of snapshot retrieval. Our results show that integrated GPUs of upcoming Apus can outperform discrete high-end GPUs for medium sized problems with high communication requirements.

Martin Packert – One of the best experts on this subject based on the ideXlab platform.

  • molecular phylogeny of old world swifts aves apodiformes apodidae Apus and tachymarptis based on mitochondrial and nuclear markers
    Molecular Phylogenetics and Evolution, 2012
    Co-Authors: Martin Packert, Jochen Martens, Michael Wink, Anna Feigl, Dieter Thomas Tietze

    Abstract:

    Abstract We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b , 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda , (2) African-Asian clade of A. caffer , A. batesi , A. horus , A. affinis and A. nipalensis , (3) African-Palearctic clade of eight currently accepted species among which sequences of A. Apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus , Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus , A. barbatus , A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome- b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis / A. nipalensis and A. Apus / A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results.