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CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms.
Lee D, Dinov I, Dong B, Gutman B, Yanovsky I, Toga AW. Lee D, et al. Comput Methods Programs Biomed. 2012 Jun;106(3):175-87. doi: 10.1016/j.cmpb.2010.10.013. Epub 2010 Dec 15. Comput Methods Programs Biomed. 2012. PMID: 21159404 Free PMC article.
This paper presents optimization strategies for compute- and memory-bound algorithms for the CUDA architecture. For compute-bound algorithms, the registers are reduced through variable reuse via shared memory and the data throughput is increased through heavier thre …
This paper presents optimization strategies for compute- and memory-bound algorithms for the CUDA architecture. For compute-bound …
Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors.
Hines ML, Eichner H, Schürmann F. Hines ML, et al. J Comput Neurosci. 2008 Aug;25(1):203-10. doi: 10.1007/s10827-007-0073-3. Epub 2008 Jan 23. J Comput Neurosci. 2008. PMID: 18214662 Free PMC article.
Splitting cells is useful in attaining load balance in neural network simulations, especially when there is a wide range of cell sizes and the number of cells is about the same as the number of processors. For compute-bound simulations load balance results in almost …
Splitting cells is useful in attaining load balance in neural network simulations, especially when there is a wide range of cell sizes and t …
SWPepNovo: An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis.
Li C, Li K, Li K, Xie X, Lin F. Li C, et al. Int J Biol Sci. 2019 Jul 3;15(9):1787-1801. doi: 10.7150/ijbs.32142. eCollection 2019. Int J Biol Sci. 2019. PMID: 31523183 Free PMC article.
Moreover, three optimization strategies, including vectorization, double buffering and memory access optimizations, have been employed to overcome both the compute-bound and the memory-bound bottlenecks in the parallel PSMs algorithm. ...
Moreover, three optimization strategies, including vectorization, double buffering and memory access optimizations, have been employed to ov …
Concurrent query processing in a GPU-based database system.
Li H, Tu YC, Zeng B. Li H, et al. PLoS One. 2019 Apr 16;14(4):e0214720. doi: 10.1371/journal.pone.0214720. eCollection 2019. PLoS One. 2019. PMID: 30990851 Free PMC article.
To that end, system-level resource management mechanisms are needed to fully unleash the computing power of GPUs in large data processing, and there were some researches focusing on it. In our previous work, we explored the single compute-bound kernel modeling on GP …
To that end, system-level resource management mechanisms are needed to fully unleash the computing power of GPUs in large data processing, a …
Hybrid-Basis Close-Coupling Interface to Quantum Chemistry Packages for the Treatment of Ionization Problems.
Marante C, Klinker M, Corral I, González-Vázquez J, Argenti L, Martín F. Marante C, et al. J Chem Theory Comput. 2017 Feb 14;13(2):499-514. doi: 10.1021/acs.jctc.6b00907. Epub 2017 Jan 6. J Chem Theory Comput. 2017. PMID: 28058835
Whereas quantum chemistry packages (QCP) implementing sophisticated methods to compute bound electronic molecular states are well-established, comparable tools for the continuum are not widely available yet. ...
Whereas quantum chemistry packages (QCP) implementing sophisticated methods to compute bound electronic molecular states are w …
Negative Ion Resonance States: The Fock-Space Coupled-Cluster Way.
Basumallick S, Sajeev Y, Pal S, Vaval N. Basumallick S, et al. J Phys Chem A. 2020 Dec 17;124(50):10407-10421. doi: 10.1021/acs.jpca.0c09148. Epub 2020 Dec 2. J Phys Chem A. 2020. PMID: 33327725
The existing Fock-space coupled-cluster (FSCC) and the equation-of-motion coupled-cluster (EOM-CC) approaches that compute bound states are redesigned for the direct and simultaneous determination of both the kinetic energy of the free electron at which the electron …
The existing Fock-space coupled-cluster (FSCC) and the equation-of-motion coupled-cluster (EOM-CC) approaches that compute bound …
Performance Modeling in CUDA Streams - A Means for High-Throughput Data Processing.
Li H, Yu D, Kumar A, Tu YC. Li H, et al. Proc IEEE Int Conf Big Data. 2014 Oct;2014:301-310. doi: 10.1109/BigData.2014.7004245. Proc IEEE Int Conf Big Data. 2014. PMID: 26566545 Free PMC article.
Specifically, we explore the connection between performance and resource occupancy of compute-bound kernels and develop a model that can predict the performance of such kernels. ...
Specifically, we explore the connection between performance and resource occupancy of compute-bound kernels and develop a mode …
Global segmentation and curvature analysis of volumetric data sets using trivariate B-spline functions.
Soldea O, Elber G, Rivlin E. Soldea O, et al. IEEE Trans Pattern Anal Mach Intell. 2006 Feb;28(2):265-78. doi: 10.1109/TPAMI.2006.36. IEEE Trans Pattern Anal Mach Intell. 2006. PMID: 16468622
This paper presents a method to globally segment volumetric images into regions that contain convex or concave (elliptic) iso-surfaces, planar or cylindrical (parabolic) iso-surfaces, and volumetric regions with saddle-like (hyperbolic) iso-surfaces, regardless of the value of th …
This paper presents a method to globally segment volumetric images into regions that contain convex or concave (elliptic) iso-surfaces, plan …
Computer ray tracing speeds.
Robb P, Pawlowski B. Robb P, et al. Appl Opt. 1990 May 1;29(13):1933-9. doi: 10.1364/AO.29.001933. Appl Opt. 1990. PMID: 20563112
The results indicate that the latest generation of workstations, using CPUs based on RISC (Reduced Instruction Set Computer) technology, are as fast or faster than mainframe computers in compute-bound situations....
The results indicate that the latest generation of workstations, using CPUs based on RISC (Reduced Instruction Set Computer) technology, are …