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Drosophila affords a genetically well-defined system to study apoptosis in vivo. It offers a powerful extension to in vitro models that have implicated a requirement for cytochrome c in caspase activation and apoptosis. We found that an overt alteration in cytochrome c anticipates programmed cell death (PCD) in Drosophila tissues, occurring at a time that(More)
—This paper presents a performance modeling and optimization analysis tool to predict and optimize the performance of sparse matrix-vector multiplication (SpMV) on GPUs. We make the following contributions: (1) We present an integrated analytical and profile-based performance modeling to accurately predict the kernel execution times of CSR, ELL, COO, and(More)
Currently, numerically simulated synthetic seismograms are widely used by seismologists for seismological inferences. The generation of these synthetic seismograms requires large amount of computing resources, and the maintenance of these observed seismograms requires massive storage. Traditional high-performance computing platforms is inefficient to handle(More)
LSQR (Sparse Equations and Least Squares) is a widely used Krylov subspace method to solve large-scale linear systems in seismic tomography. This paper presents a parallel MPI-CUDA implementation for LSQR solver. On CUDA level, our contributions include: (1) utilize CUBLAS and CUSPARSE to compute major steps in LSQR; (2) optimize memory copy between host(More)
We examined post-eclosion elimination of the Drosophila wing epithelium in vivo where collective "suicide waves" promote sudden, coordinated death of epithelial sheets without a final engulfment step. Like apoptosis in earlier developmental stages, this unique communal form of cell death is controlled through the apoptosome proteins, Dronc and Dark,(More)
With its rapid development, cloud computing has been increasingly adopted by scientists for large-scale scientific computation. Compared to the traditional computing platforms such as cluster and supercomputer, cloud computing is more elastic in the support of real-time computation and more powerful in the management of large-scale datasets. This paper(More)
A central problem of seismology is the inversion of regional waveform data for models of earthquake sources. In regions such as Southern California, preliminary 3-D earth structure models are already available, and efficient numerical methods have been developed for 3-D anelastic wave-propagation simulations. We describe an automated procedure that utilizes(More)
In flies and mammals, critical regulators of cell death function by antagonizing Inhibitor of Apoptosis Proteins (IAPs), which themselves directly block caspase action. The three currently known IAP antagonists in Drosophila map to the H99 genomic interval required for all programmed cell death. Here we describe a fourth member of this genetic group, sickle(More)
Least Squares with QR-factorization (LSQR) method is a widely used Krylov subspace algorithm to solve sparse rectangular linear systems for tomographic problems. Traditional parallel implementations of LSQR have the potential, depending on the non-zero structure of the matrix, to have significant communication cost. The communication cost can dramatically(More)
Keywords: LSQR algorithm Tomographic inversion MPI Computational seismology Inverse problems Parallel scientific computing a b s t r a c t The LSQR algorithm developed by Paige and Saunders (1982) is considered one of the most efficient and stable methods for solving large, sparse, and ill-posed linear (or linearized) systems. In seismic tomography, the(More)