Summary

Computational scientist with extensive experience in all aspects of operational high-performance computing. Formal education in materials science with a specialty in molecular dynamics. Extensive, hands-on experience in system administration, application support, debugging, performance analysis, parallel application development, system and user documentation, and education, outreach, and training. Deep specific expertise in extreme-scale parallel I/O, parallel file system architectures, I/O middleware, and future I/O technologies and architectures.

Fundamentally driven by philosophy that HPC must be usable by users to be useful. Active participant in user engagement, classroom and written training, community outreach, and collaboration with the global HPC user, vendor, and operations communities.

Education

Ph.D., Materials Science,
Rutgers University
January 2008 - November 2012
Probing the chemistry, structure, and dynamics of the water-silica interface
  • Corning Foundation Fellowship (2011)
M.S., Materials Science,
Rutgers University
January 2008 - May 2012
Atomistic study of the self-healing of silica under irradiation in the presence of water
  • US DOE Advanced Fuel Cycle Initiative Fellow (2008-2010)
  • Innovations in Fuel Cycle Research Award (2010)
B.S., Ceramic Engineering,
Rutgers University
September 2003 - May 2007
  • Malcolm G. McLaren Scholarship (2005)
  • Edward J. Bloustein Distinguished Scholar (2003 - 2007)

Experience

Advanced Technologies,
NERSC/LBL
August 2015 - Present
  • Performance analysis of parallel file systems
  • Evaluation and co-design of burst buffer implementations
  • Analysis of future I/O subsystems design and architecture
HPC Operations & Integration,
10X Genomics, Inc.
July 2014 - August 2015
  • Configured, integrated, and managed all R&D cyberinfrastructure (1200-core cluster, 700 TB of NetApp; Illumina HiSeq/NextSeq/MiSeq)
  • Designed, implemented, and managed a custom continuous integration system for software group
  • Designed, implemented, and maintained middleware to integrate R&D CI operations with Amazon EC2 and S3
User Services Consultant,
San Diego Supercomputer Center
December 2012 - July 2014
  • Provided full spectrum support for XSEDE systems (26K cores total, 1,000 unique users anually) including software integration, performance tuning, and troubleshooting node-, cluster-, and grid-level problems
  • Technical consultant for strategic collaborations with industry (Johnson & Johnson, Human Longevity Inc), academia (UC San Diego, Scripps Translational Health Inst, J. Craig Venter Inst), and non-profit (San Diego Zoo)
  • Technical lead for deploying Hadoop 2 and Spark on SDSC's XSEDE resources; author of myHadoop 0.2 which dramatically reduced entry barrier for Hadoop/Spark users; taught various R and Hadoop workshops and seminars
  • Contributing author, editor, and key personnel on several NSF proposals including awards ACI-1341698 (deployment and operation of Comet, a 2 PF HPC; $21.6M) and IIS-1447861 (scalable middleware for integrating Hadoop/Spark on HPCs; $360K)
Graduate Research Fellow,
Interfacial Molecular Science Laboratory
January 2008 - November 2012
  • Implemented a variety of novel force fields in both proprietary and open-source molecular dynamics packages
  • Implemented memory-efficient algorithms to improve cache hit rate, improving performance by 50% to 200%
  • Implemented efficient shared-memory parallelization of MD kernels to improve hardware utilization efficiency and reduce time to solution by up to 8x
  • Procured, configured, and managed three 8- to 12-node lab clusters

Technical Presentations

MarFS and the role of object storage in HPC
July 2016

Presented in the Data Seminar Series at Lawrence Berkeley National Laboratory. Berkeley, CA.

Understanding I/O performance on burst buffers through holistic I/O characterization
May 2016

Presented in the MCS Seminar Series at Argonne National Laboratory. Lemont, IL.

Developing a holistic understanding of I/O workloads on future architectures
April 2016

Presented at the 17th SIAM Conference on Parallel Processing (SIAM PP'16). Paris, FR.

Tools and techniques towards a holistic understanding of I/O demands at NERSC
November 2015

Presented at the Analyzing Parallel I/O BOF at SC'15. Austin, TX.

Data-intensive computing at the San Diego Supercomputer Center
June 2014

Invited presentation at the Joint Facilities User Forum on Data-Intensive Computing, sponsored by US Department of Energy. Oakland, CA.

Hadoop: real-world vs. hype
May 2014

Invited panelist at Leverage BIGDATA'14, sponsored by HPCwire/Tabor Communications. Carlsbad, CA.

Understanding the challenges in large-scale genomic analysis
April 2014

Presented in the SDSC Industrial Partnership Program webinar series, sponsored by SDSC. La Jolla, CA.

Effect of the water-silica interface on enhanced proton transport
January 2012

Presented at the 36th International Conference and Exposition on Advanced Ceramics and Composites (ICACC). Daytona Beach, FL.

Effect of the water-silica interface on enhanced H3O+ formation and H+ transport in mesoporous silica
November 2011

Presented at the 2011 Materials Research Society Fall Meeting & Exhibit. Boston, MA.

Effect of moisture on the self-healing of vitreous silica under irradiation
October 2011

Presented at the Materials Science & Technology 2011 Conference & Exhibition (MS&T'11). Columbus, OH.

Bridging oxygen as a site for proton adsorption on the vitreous silica surface
August 2010

Poster presented at the 2010 Gordon Research Conference on Water & Aqueous Solutions. Plymouth, NH.

Atomistic structure, strength, and kinetic properties of intergranular films in ceramics
October 2009

Poster presented at the Synthesis and Processing Sciences Contractors Meeting, sponsored by US Department of Energy. Warrenton, VA.

Publications

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

Grace X. Y. Zheng, Billy T. Lau, Michael Schnall-Levin, Mirna Jarosz, et al. Nature Biotechnol. 34, 303 (2016).

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

K. A. Standish, T. M. Carland, G. K. Lockwood, Wayne Pfeiffer, et al. BMC Bioinformatics 16, 304 (2015).

Storage utilization in the long tail of science

G. K. Lockwood, R. Wagner, and M. Tatineni. Proceedings of the 2015 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE'15 (2015).

Proton dynamics at the water-silica interface via dissociative molecular dynamics

G. K. Lockwood and S. H. Garofalini. J. Phys. Chem. C 118, 29750 (2014).

SR-IOV: Performance benefits for virtualized interconnects

G. K. Lockwood, M. Tatineni, and R. Wagner. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE'14 (2014).

Performance of applications using dual-rail InfiniBand 3D torus network on the Gordon Supercomputer

D. J. Choi, G. K. Lockwood, R. S. Sinkovits, M. Tatineni. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE'14 (2014).

Efficient 3D movement-based kernel density estimator and application to wildlife ecology

J. A. Tracey, J. K. Sheppard, G. K. Lockwood, A. Chourasia, M. Tatineni, R. N. Fisher, and R. S. Sinkovits. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE'14 (2014).

Reactive simulation of the activation barrier to dissolution of amorphous silica in water

M. Kagan, G. K. Lockwood and S. H. Garofalini. Phys. Chem. Chem. Phys. 16, 9294 (2014).

Lifetimes of excess protons in water using a dissociative water potential

G. K. Lockwood and S. H. Garofalini. J. Phys. Chem. B 117, 4089 (2013).

Reactions between water and vitreous silica during irradiation

G. K. Lockwood and S. H. Garofalini. J. Nucl. Mater. 430, 239 (2012).

Development of a transferable variable charge potential for the study of energy conversion materials

Y. Ma, G. K. Lockwood and S. H. Garofalini. J. Phys. Chem. C 115, 24198 (2011).

Effect of moisture on the self-healing of vitreous silica under irradiation

G. K. Lockwood and S. H. Garofalini. J. Nucl. Mater 400, 73 (2010).

Bridging oxygen as a site for proton adsorption on the vitreous silica surface

G. K. Lockwood and S. H. Garofalini. J. Chem. Phys. 131, 074703 (2009).

Anisotropic dissolution of α-alumina (0001) and (1120) surfaces into adjoining silicates

G. K. Lockwood, S. Zhang, and S. H. Garofalini. J. Am. Ceram. Soc 91, 3536 (2008).

Teaching Experience

Hadoop Essentials,
UC San Diego Extension
November 2013, March 2014

One of three instructors for a two-day, hands-on workshop illustrating the essential concepts of Hadoop provided through UCSD Extension, UCSD's continuing education program. In addition to teaching, coordinated online logistics of course material.

Parallel Computing in R / Introduction to Hadoop,
San Diego R User Group
September 2013

Volunteered to present the 65-minute "Parallel Options for R / Introduction to Hadoop" talk (see below) to the San Diego R User Group as an outreach event on behalf of SDSC. Orchestrated logistics of hosting user group meetings at SDSC facilities.

Parallel Options for R / Introduction to Hadoop,
SDSC 2013 Summer Institute
July 2013

Provided a 45-minute presentation on parallelization libraries (via MPI and Hadoop) for the R language at SDSC's 2013 Summer Institute. Supplemented with a 25-minute conceptual overview of Hadoop based on earlier attendee feedback.

Introduction to Hadoop on the SDSC Gordon data-intensive supercomputer
XSEDE 2013 Conference Tutorials
July 2013

Contributed slides for a half-day tutorial on using Hadoop on traditional supercomputers and provided individual support to attendees.

OpenACC GPU Programming Workshop
XSEDE Training
January 2013

Local facilitator for videconferenced course; provided individual support to attendees.

Mechanical Behavior of Ceramic Materials
Rutgers University
September 2009 - December 2009

Instructed a three-credit, core curriculum graduate course for fifteen students at Picatinny Arsenal (U.S. Army) on behalf of Rutgers University. All Ph.D. students who took this course went on to qualify for candidacy.

Press Recognition

The Mechanism of Short-term Memory,
XSEDE News
April 2014
How HPC is Hacking Hadoop,
HPCwire
February 2014