Dan Bonachea's Home Page

me

Dan Bonachea
(PGP key)

575 Soda Hall
Berkeley, CA 94720
(510) 642-9583

I'm a graduate student researcher in the U.C. Berkeley CS Department, advised by Prof. Kathy Yelick. I earned my Masters degree in Spring 2000 and am currently working on my Ph.D. in parallel programming languages, networking and runtime systems support.
me

Current Research     Past Projects     Publications     Fun Stuff     Links

Current Research

GASNet High-Performance Communication System
    I'm the primary designer and developer for this communication system.


Titanium - A High-Performance Parallel Dialect of Java
    I'm one of the graduate student researchers on the Berkeley Titanium Project working with Kathy Yelick

UPC - Unified Parallel C
    I'm also doing runtime systems research on the UPC programming language with the Berkeley UPC compiler development effort at LBNL

SafeTP Project 
   SafeTP: Find out how to transparently secure your FTP connections!


Past Projects

AMMPI: Active Messages over MPI
   A portable implementation of the AM-2 lightweight messaging layer over MPI 1.1

AMUDP: Active Messages over UDP
   A portable implementation of the AM-2 lightweight messaging layer over UDP

AMLAPI: Active Messages over LAPI
   An implementation of AM-2 for IBM SP systems, using IBM LAPI

Microarray Optimal Oligo Selection Engine (MOOSE)
   A parallel engine for selecting the best oligonucleotide sequences for genetic microarray testing

Automatic Memory Management
   Feudal C: Automatic memory management through a static type system

Computer Vision on a Vector Processor
    Image Segmentation on IRAM

Traveling Salesman Problem - A Genetic Approach
    An Improved Adaptive Multi-Start Algorithm for Finding Near-Optimal Solutions to the Euclidean Traveling Salesman Problem


Publications

D. Bonachea, P. Hargrove, M. Welcome, K. Yelick. Porting GASNet to Portals: Partitioned Global Address Space (PGAS) Language Support for the Cray XT, Cray User Group (CUG), 2009. (Acrobat pdf) (Presentation pdf)

R. Nishtala, P. Hargrove, D. Bonachea, K. Yelick. Scaling Communication-Intensive Applications on BlueGene/P Using One-Sided Communication and Overlap, 23rd International Parallel & Distributed Processing Symposium (IPDPS), 2009. (Acrobat pdf)

W. Chen, D. Bonachea, C. Iancu, K. Yelick. Automatic Nonblocking Communication for Partitioned Global Address Space Programs International Conference on Supercomputing (ICS), 2007 (Acrobat pdf)

K. Yelick, P. Hilfinger, S. Graham, D. Bonachea, J. Su, A. Kamil, K. Datta, P. Colella, T. Wen. Parallel Languages and Compilers: Perspective From the Titanium Experience International Journal of High Performance Computing Applications, Vol. 21, No. 3, 266-290 (2007) (Acrobat pdf)

Shivali Agarwal, Rajkishore Barik, Dan Bonachea, Vivek Sarkar, Rudrapatna K. Shyamasundar and Katherine Yelick. Deadlock-Free Scheduling of X10 Computations with Bounded Resources
19th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), 2007. (Acrobat pdf)

C. Bell, D. Bonachea, R. Nishtala, K. Yelick. Optimizing Bandwidth Limited Problems Using One-Sided Communication and Overlap Lawrence Berkeley National Lab Tech Report LBNL-59207 (Acrobat pdf)
    Also in 20th International Parallel & Distributed Processing Symposium (IPDPS), 2006. (Acrobat pdf)

Hung-Hsun Su, Dan Bonachea, Adam Leko, Hans Sherburne, Max Billingsley III, Alan D. George GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming Models Lawrence Berkeley National Lab Tech Report LBNL-61659, 2006. (Acrobat pdf)

Adam Leko, Dan Bonachea, Hung-Hsun Su, and Alan D. George GASP: A Performance Analysis Tool Interface for Global Address Space Programming Models, Specification Version 1.5 Lawrence Berkeley National Lab Tech Report LBNL-61606, Sep 14 2006. (Acrobat pdf)

K. Datta, D. Bonachea, K. Yelick. Titanium Performance and Potential: an NPB Experimental Study Languages and Compilers for Parallel Computing (LCPC), 2005. (Acrobat pdf)
    Also in Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, Volume 4339/2006, pp 200-214, 2006.

UPC Consortium. UPC Language Specifications, v 1.2 Lawrence Berkeley National Lab Tech Report LBNL-59208, May 2005. (Acrobat pdf)

C. Bell, W. Chen, D. Bonachea and K. Yelick, Evaluating Support for Global Address Space Languages on the Cray X1 International Conference of Supercomputing, 2004. (Acrobat pdf)

W. Chen, D. Bonachea, J. Duell, P. Husbands, C. Iancu, K. Yelick, A Performance Analysis of the Berkeley UPC Compiler International Conference of Supercomputing, 2003. (Acrobat pdf) (PostScript ps) (Presentation ppt)

K. Yelick, D. Bonachea and C. Wallace, A Proposal for a UPC Memory Consistency Model, v1.0 (May 5, 2004) Lawrence Berkeley National Lab Tech Report LBNL-54983, 2004. (Acrobat pdf) (PostScript ps)

P. Hilfinger, D. Bonachea et al, Titanium Language Reference Manual UC Berkeley Tech Report UCB/EECS-2005-15, 2005. (Acrobat pdf)
    Also see the current version.

D. Bonachea and J. Duell, Problems with using MPI 1.1 and 2.0 as compilation targets for parallel language implementations 2nd Workshop on Hardware/Software Support for High Performance Scientific and Engineering Computing, SHPSEC-PACT03 , 2003. (Acrobat pdf) (PostScript ps) (Presentation ppt)
Journal version: Int. J. High Performance Computing and Networking, Vol. 1, Nos. 1/2/3, pp.91-99, 2004. (Acrobat pdf)

C. Bell, D. Bonachea, A New DMA Registration Strategy for Pinning-Based High Performance Networks, Workshop on Communication Architecture for Clusters (CAC'03), 2003. (Acrobat pdf)
    Also see my UPC web page.

C. Bell, D. Bonachea, et al. An Evaluation of Current High-Performance Networks, International Parallel and Distributed Processing Symposium (IPDPS'03), 2003.

Bonachea, Dan. GASNet Specification, v1.1 , UCB Tech Report CSD-02-1207, November 2002. (Acrobat pdf)
    For the latest version, see the GASNet web page.

Bonachea, D., Dickens, P. and Thakur, R. "High-Performance File I/O in Java: Existing Approaches and Bulk I/O Extensions," Concurrency and Computation:Practice and Experience , Vol 13, Issue 9, June 28, 2001. (PostScript ps)
    Also see my Bulk I/O in Java web site.

Bonachea, Dan. "Bulk File I/O Extensions to Java," Proceedings of the ACM Java Grande 2000 Conference, June 3-4, 2000. (Acrobat pdf) (gzipped-PostScript ps.gz)
    (This copy is posted by permission of ACM and may not be redistributed. The definitive version of this paper is located here.)
    Also see my
Bulk File I/O in Titanium web site.

Bonachea, D., Ingerman, E., Levy, J., and McPeak, S., "An Improved Adaptive Multi-Start Approach to Finding Near-Optimal Solutions to the Euclidean TSP," Genetic and Evolutionary Computation Conference (GECCO-2000), July 2000. (Acrobat pdf) (PostScript ps)
    Also see my TSP web site.

Bonachea, D., Fisher, K., Rogers, A., and Smith, F. "Hancock: A Language for Processing Very Large-Scale Data," Proceedings of the 2nd Conference on Domain-Specific Languages, October 1999. Also appeared in ACM SIGPLAN Notices, Volume 35, Number 1, January 2000. (Acrobat pdf) (PostScript ps)
    Also see the Hancock web site.

Bonachea, Dan and McPeak, Scott. " SafeTP: Transparently Securing FTP Network Services", UCB Tech Report CSD-01-1152, February 2001. (Acrobat pdf)
    Also see the SafeTP web site.

Bonachea, Dan and McPeak, Scott. " Protocol Negotiation Extensions to Secure FTP", Internet draft (draft-bonachea-sftp-*.txt) updating RFC 2228.
    Note: As with all internet drafts, this is considered a work-in-progress.
    Comments and suggestions are welcomed and appreciated.


Fun Stuff

Accordian Solitaire
    Here's a somewhat different solitaire game for windows that I wrote...


Links

Polly   Christian   Rich   Brian   Scott   Jen   Ben   C.T.  
    My buds... (I disavow any responsibility for content therein :-) )

U.C. Berkeley   UCB CS Dept.   Titanium Project  
    My school...

Tau Beta Pi   ACM   Mensa   Phi Kappa Phi  
    My Society Memberships...


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Page last updated Monday May 04, 2009