Search Results - "Gunnels, J."

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 by Acharya, A, Agarwal, R, Baker, M. B, Baudry, J, Bhowmik, D, Boehm, S, Byler, K. G, Chen, S. Y, Coates, L, Cooper, C. J, Demerdash, O, Daidone, I, Eblen, J. D, Ellingson, S, Forli, S, Glaser, J, Gumbart, J. C, Gunnels, J, Hernandez, O, Irle, S, Kneller, D. W, Kovalevsky, A, Larkin, J, Lawrence, T. J, LeGrand, S, Liu, S.-H, Mitchell, J.C, Park, G, Parks, J.M, Pavlova, A, Petridis, L, Poole, D, Pouchard, L, Ramanathan, A, Rogers, D. M, Santos-Martins, D, Scheinberg, A, Sedova, A, Shen, Y, Smith, J. C, Smith, M. D, Soto, C, Tsaris, A, Thavappiragasam, M, Tillack, A. F, Vermaas, J. V, Vuong, V. Q, Yin, J, Yoo, S, Zahran, M, Zanetti-Polzi, L

“…We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking…”
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A flexible class of parallel matrix multiplication algorithms by Gunnels, J., Lin, C., Morrow, G., van de Geijn, R.

“…This paper explains why parallel implementation of matrix multiplication, a seemingly simple algorithm that can be expressed as one statement and three nested…”
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Perplexing pleural effusion by Gunnels, J J

“…Twenty-seven patients with perplexing pleural effusion were studied to determine clinical outcome. The value of performing pleuroscopic examination or open…”
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PLAPACK: high performance through high-level abstraction by Baker, G., Gunnels, J., Morrow, G., Riviere, B., van de Geijn, R.

“…Coding parallel algorithms is generally regarded as a formidable task. To make this task manageable in the arena of linear algebra algorithms, we have…”
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Shifting tuberculosis care to the general hospital by Gunnels, J J, Bates, J H

“…Control of tuberculosis infection within the hospital is of major importance to general hospitals that assume the responsibility for providing tuberculous…”
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Characterization and mycobacteriophage typing of Mycobacterium xenopi by Gunnels, J J, Bates, J H

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Extending stability beyond CPU millennium: a micron-scale atomistic simulation of Kelvin-Helmholtz instability by Glosli, J. N., Richards, D. F., Caspersen, K. J., Rudd, R. E., Gunnels, J. A., Streitz, F. H.

“…We report the computational advances that have enabled the first micron-scale simulation of a Kelvin-Helmholtz (KH) instability using molecular dynamics (MD)…”
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Infectivity of sputum-positive tuberculous patients on chemotherapy by Gunnels, J J, Bates, J H, Swindoll, H

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MPI Collective Communications on The Blue Gene/P Supercomputer: Algorithms and Optimizations by Faraj, A., Kumar, S., Smith, B., Mamidala, A., Gunnels, J.

“…The IBM Blue Gene/P (BG/P) system is a massively parallel supercomputer succeeding BG/L, and it comes with many machine design enhancements and new…”
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Toward real-time modeling of human heart ventricles at cellular resolution: Simulation of drug-induced arrhythmias by Mirin, A. A., Richards, D. F., Glosli, J. N., Draeger, E. W., Chan, B., Fattebert, J., Krauss, W. D., Oppelstrup, T., Rice, J. J., Gunnels, J. A., Gurev, V., Changhoan Kim, Magerlein, J., Reumann, M., Hui-Fang Wen

“…We have developed a highly efficient and scalable cardiac electrophysiology simulation capability that supports groundbreaking resolution and detail to…”
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No change in complication rate using spring-loaded gun compared to traditional percutaneous renal allograft biopsy techniques by Kovalik, E C, Schwab, S J, Gunnells, J C, Bowie, D, Smith, S R

“…The previous methods to biopsy renal allografts at our institution involved the use of the Franklin-Silverman or Tru-Cut needles. Unfortunately they had a…”
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Beyond homogeneous decomposition: scaling long-range forces on Massively Parallel Systems by Richards, D. F., Glosli, J. N., Chan, B., Dorr, M. R., Draeger, E. W., Fattebert, J.-L., Krauss, W. D., Spelce, T., Streitz, F. H., Surh, M. P., Gunnels, J. A.

“…With supercomputers anticipated to expand from thousands to millions of cores, one of the challenges facing scientists is how to effectively utilize this…”
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Parallel implementation of BLAS: general techniques for Level 3 BLAS by Chtchelkanova, Almadena, Gunnels, John, Morrow, Greg, Overfelt, James, van de Geijn, Robert A.

“…In this paper, we present straightforward techniques for a highly efficient, scalable implementation of common matrix–matrix operations generally known as the…”
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Genetic algorithms and simulated annealing for gene mapping by Gunnels, J., Cull, P., Holloway, J.L.

“…Ordering genes on a chromosome is similar to the traveling salesman problem (TSP), but with some extra information. This extra information prompted us to…”
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Unlocking the Performance of the BlueGene/L Supercomputer by Almasi, George, Chatterjee, Siddhartha, Gara, Alan, Gunnels, John, Gupta, Manish, Henning, Amy, Moreira, Jose E., Walkup, Bob

“…The BlueGene/L supercomputer is expected to deliver new levels of application performance by providing a combination of good single-node computational…”
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PLAPACK Parallel Linear Algebra Package Design Overview by Alpatov, P., Baker, G., Edwards, H.C., Gunnels, J., Morrow, G., Overfelt, J., van de Geijn, R.

“…The Parallel Linear Algebra Package (PLAPACK) is a maturing fourth generation linear algebra infrastructure which uses a application-centric view of vector and…”
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A high-performance SIMD floating point unit for BlueGene/L: architecture, compilation, and algorithm design by Bachega, L., Siddhartha Chatterjee, Dockser, K.A., Gunnels, J.A., Manish Gupta, Gustavson, F.G., Lapkowski, C.A., Liu, G.K., Mendell, M.P., Wait, C.D., Ward, T.J.C.

“…We describe the design, implementation, and evaluation of a dual-issue SIMD-like extension of the PowerPC 440 floating-point unit (FPU) core. This extended FPU…”
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An overview of the BlueGene/L Supercomputer by Adiga, NR, Almasi, GS, Aridor, Y, Barik, R, Beece, D, Bhanot, G, Bickford, R, Blumrich, M, Bright, AA, Brunheroto, J, Caşcaval, C, Castaños, J, Chan, W, Ceze, L, Coteus, P, Chatterjee, S, Chen, D, Cipolla, TM, Crumley, P, Desai, KM, Deutsch, A, Domany, T, Donath, W, Eleftheriou, M, Erway, C, Esch, J, Gagliano, J, Gara, A, Germain, R, Giampapa, ME, Gopalsamy, B, Gunnels, J, Gupta, M, Gustavson, F, Hall, S, Haring, RA, Heidel, D, Heidelberger, P, Herger, LM, Hoenicke, D, Jackson, RD, Kopcsay, GV, Krevat, E, Kurhekar, MP, Lanzetta, AP, Lieber, D, Liu, LK, Lu, M, Mendell, M, Misra, A, Moatti, Y, Mok, L, Moreira, JE, Nathanson, BJ, Newton, M, Ohmacht, M, Oliner, A, Pandit, V, Pudota, RB, Rand, R, Regan, R, Ruehli, A, Rus, S, Sahoo, RK, Sanomiya, A, Schenfeld, E, Sharma, M, Shmueli, E, Singh, S, Song, P, Steinmacher-Burow, BD, Strauss, K, Surovic, C, Swetz, R, Takken, T, Tremaine, RB, Tsao, M, Umamaheshwaran, AR, Verma, P, Wazlowski, M, Barrett, W, Engel, C, Drehmel, B, Hill, D, Kasemkhani, F, Krolak, D, Li, CT, Liebsch, T, Muff, A, Okomo, A, Rouse, M, Tubbs, M, Ulsh, G, Wittrup, J, Bae, M, Dockser, K, Kissel, L, Seager, MK, Vetter, JS, Yates, K

“…This paper gives an overview of the BlueGene/L Supercomputer. This is a jointly funded research partnership between IBM and the Lawrence Livermore National…”
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Fault-tolerant high-performance matrix multiplication: theory and practice by Gunnels, J.A., Katz, D.S., Quintana-Orti, E.S., Van de Gejin, R.A.

“…We extend the theory and practice regarding algorithmic fault-tolerant matrix-matrix multiplication, C=AB, in a number of ways. First, we propose low-overhead…”
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Juxtaglomerular apparatus tumor: a rare but curable cause of secondary hypertension by Jordan, J M, Gunnells, J C

“…We have reported our experience at Duke University Medical Center with juxtaglomerular apparatus tumor, a rare but remediable cause of significant…”
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