Vipin Sachdeva

Vipin Sachdeva
Roivant · High-Performance Computing

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39
Publications
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461
Citations

Publications

Publications (39)
Preprint
Full-text available
Targeted protein degradation (TPD) has recently emerged as a powerful approach for removing (rather than inhibiting) proteins implicated in diseases. A key step in TPD is the formation of an induced proximity complex where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI a...
Preprint
3D FFTs are used to accelerate MD electrostatic forces computations but are difficult to parallelize due to communications requirements. We present a distributed OpenCL 3D FFT implementation on Intel Stratix 10 FPGAs for grids up to {\boldmath $128^3$}. We use FPGA hardware features such as HBM2 memory and multiple 100 Gbps links to provide scalabl...
Conference Paper
Full-text available
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but with much of the work shared by the host CPU; or prototype demonstrations, e.g., using OpenCL, that neither impl...
Preprint
Full-text available
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but with much of the work shared by the host CPU; or prototype demonstrations, e.g., using OpenCL, that neither impl...
Article
Full-text available
Background De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, result...
Article
Full-text available
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by 4 million mesoscopic particles --- using a single shared memory commodity workstation. To achieve this, we invented an adaptive...
Article
With recent advances in high throughput sequencing platforms, it is possible to sequence RNA obtained from biological samples more cost-effectively and comprehensively. Due to the ubiquity of the technology, massive volumes of RNA sequence data are now being generated, and as a result the need for more efficient analysis software has become an urge...
Article
This paper details a distributed-memory implementation of Chrysalis, part of the popular Trinity workflow used for de novo transcripto me assembly. We have implemented changes to Chrysalis, which was previously multi-threaded for shared-memory architectures, to change it to a hybrid implementation which uses both MPI and OpenMP. With the new hybrid...
Patent
Mechanisms for performing all-to-all comparisons on architectures having limited storage space are provided. The mechanisms determine a number of data elements to be included in each set of data elements to be sent to each processing element of a data processing system, and perform a comparison operation on at least one set of data elements. The co...
Article
The IBM Blue Gene®/Q platform presents scientists and engineers with a rich set of hardware features such as 16 cores per chip sharing a Level 2 cache, a wide SIMD (single-instruction, multiple-data) unit, a five-dimensional torus network, and hardware support for collective operations. An especially important feature is that the cores have four “h...
Article
Full-text available
We report on a demonstration of loose multiphysics coupling between a basin modeling code and a seismic code running on a large parallel machine. Multiphysics coupling, which is one critical capability for a high performance computing (HPC) framework, was implemented using the MOAB open-source mesh and field database. MOAB provides for code couplin...
Article
Full-text available
With the right software infrastructure, clouds can provide scientists with "as a service" access to high-performance computing resources. An award-winning prototype framework transforms the Blue Gene/P system into an elastic cloud to run a representative HPC application.
Conference Paper
Full-text available
Algorithms are described for the resolution of shared vertices and higher-dimensional interfaces on domain-decomposed parallel mesh, and for ghost exchange between neighboring processors. Performance data is given for large (up to 64M tet and 32M hex element) meshes on up to 16k processors. Shared interface resolution for structured mesh is also de...
Article
Full-text available
In recent years, significant progress in processor and system technologies has led to the appearance of many-core processors, such as the Tilera 100 core [1] and mega-core systems [2]. It is desirable to exploit such computing
Conference Paper
MATLAB® and its open-source implementation Octave have proven to be one of the most productive environments for scientific computing in recent years. There have been multiple efforts to develop an efficient parallel implementation of MATLAB including by Mathworks® (Parallel Computing Toolbox), MIT Lincoln Labs (pMatlab) and several other organizati...
Conference Paper
Full-text available
This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that overr...
Conference Paper
Full-text available
The Jaccard/Tanimoto coefficient is an important workload, used in a large variety of problems including drug design fingerprinting, clustering analysis, similarity web searching and image segmentation. This paper evaluates the Jaccard coefficient on three platforms: the Cell Broadband EngineTMprocessor Intel ®Xeon ®dual-core platform and Nvidia ®8...
Article
Full-text available
In this paper, we propose BIOPERF, a definitive benchmark suite of representative applications from the biology and life sciences community, where the codes are carefully selected to span a breadth of algorithms and performance characteristics. The BIOPERF suite is available from www.bioperf. org and includes benchmark source code, input datasets o...
Conference Paper
Full-text available
This paper examines several mechanisms to improve the performance of life science applications on high-performance computer architectures typically designed for more traditional supercomputing tasks. In particular, we look at the detailed performance characteristics of some of the most popular sequence alignment and homology applications on the POW...
Conference Paper
This paper evaluates the performance of bioinformatics applications on the Cell Broadband Engine (Cell/B.E.) recently developed at IBM. In particular we focus on three highly popular bioinformatics applications – FASTA, ClustalW, and HMMER. The characteristics of these bioinformatics applications, such as small critical time-consuming code size, re...
Article
Full-text available
The exponential growth in the amount of genomic data has spurred growing interest in large scale analysis of genetic information. Bioinformatics applications, which explore computational methods to allow researchers to sift through the massive biological data and extract useful infor-mation, are becoming increasingly important computer workloads. T...
Conference Paper
We are evaluating the performance of bioinformatics applications on the CBE recently developed at IBM. The characteristics of pairwise alignment, critical to bioinformatics applications, makes it uniquely suitable for the Cell processor. We have implemented two different strategies for pairwise alignment on Cell. We analyze the bottlenecks for each...
Conference Paper
Full-text available
The exponential growth in the amount of genomic data has spurred growing interest in large scale analysis of genetic information. Bioinformatics applications, which explore computational methods to allow researchers to sift through the massive biological data and extract useful information, are becoming increasingly important computer workloads. Th...
Conference Paper
Full-text available
Advances in experimental techniques have transformed biology into a data-intensive science, with a rapid explosion of data at the genomic and proteomic level. Few comprehensive suites of computationally-intensive life science applications are available to the computer science community for optimization of current high-performance architectures spec...
Article
Full-text available
BioSPLASH is a suite of representative applications that we have assembled from the com-putational biology community, where the codes are carefully selected to span a breadth of algorithms and performance characteristics. The main results of this paper are the assembly of a scalable bioinformatics workload with impact to the DARPA High Produc-tivit...
Article
Full-text available
The maximum flow problem is a combinatorial problem of significant importance in a wide variety of research and commercial applications. It has been extensively studied and implemented over the past 40 years. The push-relabel method has been shown to be superior to other methods, both in theoretical bounds and in experimental implementations. Our s...
Article
"December, 2005." Thesis (M.S.)--University of New Mexico, 2005. Includes bibliographical references (leaves 204-212).

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