Sasha Ames


Email: sasha@llnl.gov
Phone: 925-424-4644


Sasha Ames is a postdoctoral researcher in the Center for Applied Scientific Computing at the Lawrence Livermore National Laboratory.  He works for Maya Gokhale on application analysis and evaluation of the DI-MMAP runtime for the DCA LDRD effort.  He also works for Jonathan Allen on the "Metagenomics Search" LDRD where he is primarily responsible for the framework to create searchable genome reference database.  As part of this project, he co-manages the software development and release efforts for the Livermore Metagenomics Analysis Toolkit (LMAT).

Sasha received his PhD from UC Santa Cruz in 2011 while working at LLNL as part of the Lawrence Scholar Program (since 2008) with Prof. Carlos Maltzahn.   This work was part of the SISC and PerMA LDRD efforts, in which he developed the QUASAR query language and QMDS file system software prototype.  Previously, he earned a B.A. in computer science from Columbia University, spent several years in industry, working on a financial web application and intrusion detection software, and received a M.S. from UCSC, prior to working at LLNL.  

Publications:

Sasha Ames, Jonathan E. Allen, David A. Hysom, G. Scott Lloyd and Maya B. Gokhale. "Design and Optimization of a Metagenomics Analysis Workflow for NVRAM." 13th IEEE International Workshop on High Performance Computational Biology. May 2014

Brian Van Essen, Henry Hsieh, Sasha Ames, Roger Pearce, Maya Gokhale. “DI-MMAP—a scalable memory-map runtime for out-of-core data-intensive applications.” Cluster Computing (online), October 2013

Sasha K. Ames, David A. Hysom, Shea N. Gardner, G. Scott Lloyd, Maya B. Gokhale, Jonathan E. Allen. "Scalable metagenomic taxonomy classification using a reference genome database.” Bioinformatics,  29 (18) July 2013, 2253-2260.
 
Brian Van Essen, Henry Hsieh, Sasha Ames, Maya Gokhale, “DI-MMAP: A High Performance Memory Map Runtime for Data-Intensive Applications,” Data intensive scalable computing systems workshop at SC12, November 2012.
 
Brian Van Essen, Roger Pearce, Sasha Ames, Maya Gokhale:  “On the role of NVRAM in data intensive HPC architectures: an Evaluation” in Proceedings of the 26th IEEE International Parallel & Distributed Processing Symposium.  May 2012
 
Sasha Ames
, Maya B. Gokhale, Carlos Maltzahn.  "QMDS: a file system metadata management service supporting a graph data model-based query language." International Journal of Parallel, Emergent, and Distributed Systems,  28 (9), 2013 159-183.

Sasha Ames, Maya B. Gokhale, Carlos Maltzahn.QMDS: A File System Metadata Management Service Supporting a Graph Data Model-based Query Language.  in Procedenings of the 2011 IEEE Conference on Networking, Architecture, and Storage (NAS 2011). Dalian, China, July 2011. LLNL-CONF-45494

Jonathan Koren, Yi Zhang, Sasha Ames, Andrew Leung, Carlos Maltzahn, Ethan L. Miller. Searching and Navigating Petabyte Scale File Systems Based on Facets. Proceedings of the 2007 ACM Petascale Data Storage Workshop (PDSW 07), November 2007.

Sasha Ames, Nikhil Bobb, Kevin Greenan, Owen Hofmann, Mark W. Storer, Carlos Maltzahn, Ethan L. Miller, Scott A. Brandt. LiFS: An attribute-rich file system for storage class memories. Proceedings of the 23rd IEEE / 14th NASA Goddard~ Conference on Mass Storage Systems and Technologies, May 2006.

Ames, A., Bobb , N., Brandt, S.A., Hiatt, A., Maltzahn, C., Miller, E. L., Neeman, A., Tuteja, D.: "Richer File System Metadata Using Links and Attributes", in Proceedings of the 13th NASA Goddard Conference on Mass Storage Systems and Technologies (MSST '05)