Distributed-memory parallelization of an explicit time-domain volume integral equation solver on Blue Gene/P

Two distributed-memory schemes for efficiently parallelizing the explicit marching-on in-time based solution of the time domain volume integral equation on the IBM Blue Gene/P platform are presented. In the first scheme, each processor stores the time history of all source fields and only the computationally dominant step of the tested field computations is distributed among processors. This scheme requires all-to-all global communications to update the time history of the source fields from the tested fields. In the second scheme, the source fields as well as all steps of the tested field computations are distributed among processors. This scheme requires sequential global communications to update the time history of the distributed source fields from the tested fields. Numerical results demonstrate that both schemes scale well on the IBM Blue Gene/P platform and the memory efficient second scheme allows for the characterization of transient wave interactions on composite structures discretized using three million spatial elements without an acceleration algorithm

Scaling of a Fast Fourier Transform and a pseudo-spectral fluid solver up to 196608 cores

In this paper we present scaling results of a FFT library, FFTK, and a pseudospectral code, Tarang, on grid resolutions up to $8192^3$ grid using 65536 cores of Blue Gene/P and 196608 cores of Cray XC40 supercomputers. We observe that communication dominates computation, more so on the Cray XC40. The computation time scales as $T_\mathrm{comp} \sim p^{-1}$, and the communication time as $T_\mathrm{comm} \sim n^{-\gamma_2}$ with $\gamma_2$ ranging from 0.7 to 0.9 for Blue Gene/P, and from 0.43 to 0.73 for Cray XC40. FFTK, and the fluid and convection solvers of Tarang exhibit weak as well as strong scaling nearly up to 196608 cores of Cray XC40. We perform a comparative study of the performance on the Blue Gene/P and Cray XC40 clusters

Comparative transcriptional profiling-based identification of raphanusanin-inducible genes

<p>Abstract</p> <p>Background</p> <p>Raphanusanin (Ra) is a light-induced growth inhibitor involved in the inhibition of hypocotyl growth in response to unilateral blue-light illumination in radish seedlings. Knowledge of the roles of Ra still remains elusive. To understand the roles of Ra and its functional coupling to light signalling, we constructed the Ra-induced gene library using the Suppression Subtractive Hybridisation (SSH) technique and present a comparative investigation of gene regulation in radish seedlings in response to short-term Ra and blue-light exposure.</p> <p>Results</p> <p>The predicted gene ontology (GO) term revealed that 55% of the clones in the Ra-induced gene library were associated with genes involved in common defence mechanisms, including thirty four genes homologous to <it>Arabidopsis </it>genes implicated in R-gene-triggered resistance in the programmed cell death (PCD) pathway. Overall, the library was enriched with transporters, hydrolases, protein kinases, and signal transducers. The transcriptome analysis revealed that, among the fifty genes from various functional categories selected from 88 independent genes of the Ra-induced library, 44 genes were up-regulated and 4 were down-regulated. The comparative analysis showed that, among the transcriptional profiles of 33 highly Ra-inducible genes, 25 ESTs were commonly regulated by different intensities and duration of blue-light irradiation. The transcriptional profiles, coupled with the transcriptional regulation of early blue light, have provided the functional roles of many genes expected to be involved in the light-mediated defence mechanism.</p> <p>Conclusions</p> <p>This study is the first comprehensive survey of transcriptional regulation in response to Ra. The results described herein suggest a link between Ra and cellular defence and light signalling, and thereby contribute to further our understanding of how Ra is involved in light-mediated mechanisms of plant defence.</p

Medical Literary Messenger (Vol. 2, No. 1, Fall 2014)

Quiet Please Sickness / Cathleen Calbert -- Helping a seven year old with inoperable brain cancer write a poem for her sister / Kate Peterson -- Asking My Liver for Forgiveness / Rob Cook -- Synesthesia 2 / Catherine Harnett -- Tic / Molly Lazer -- The Bridge / Alexander Schloe -- Mother’s Milk and Cystic Fibrosis / Lizabeth Berkeley -- Fanny Brawne / William Miller -- artwork / Venus -- Cure / Anne Spollen -- Gene / Kate Peterson -- The Love Song of Elliot Blue / Jacqueline Kirkpatrick -- “Next” / Michael P. Stevens -- Structures / C.I.L. -- Autoclave: 1960 / Claude Clayton Smith -- Waiting / dl mattila -- Burning a Hypothetical Helianthus Annuus / Sea Sharp -- Shot straight in, -- Joanna White -- Clinic in Olanchito / Michael P. Stevens

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method

Benchmark timings are presented for the fragment molecular orbital method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 basis functions, using second order perturbation theory and an augmented and polarized double-ζ basis set, takes ∼7 min on 131 072 cores

Medical School Watercooler Newsletter - August 18, 2019

This is the August 18, 2019 edition of the Frederick P. Whiddon College of Medicine\u27s Newsletter - Watercooler. Contents Include: USA Health honors retiring reproductive endocrinology staff September Med School Café to focus on gene therapy for sickle cell disease Mark Your Calendar: Game Day 2019 Four students at USA College of Medicine awarded Blue Cross and Blue Shield scholarship