- Thomas L. Sterling, John Salmon, Don J. Becker, and Daniel F. Savarese,
*How to build a Beowulf*, MIT Press, Spring 1999. (available at Amazon)

- Geoffrey C. Fox, Mark A. Johnson, Gregory A. Lyzenga, Steven W. Otto, John K.
Salmon, and David W. Walker,
*Solving Problems on Concurrent Processors*, Prentice Hall, Englewood Cliffs, NJ, 1988.

- John K. Salmon,
*Parallel Hierarchical N-Body Methods*, PhD thesis, California Institute of Technology, 1990.

- John K. Salmon, Mark A. Moraes,
Ron O. Dror, David E. Shaw,
"Parallel Random Numbers: As Easy as 1,2,3",
*SuperComputing '11 Proceedings*, November, 2011. (available online)

- David E. Shaw, Peter J. Adams, .... John K. Salmon, et al.,
"Anton 3: twenty microseconds of molecular dynamics simulation before lunch",
*Supercomputing '21*, : November 2021.

- Stefano Piana, Kresten Lindorff-Larsen, Robert M. Dirks, John K. Salmon,
Ron O. Dror, David E. Shaw,
"Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein
folding simulations",
*PLoS one*,**7**: June 2012. (available online)

- Ron O. Dror, J.P. Grossman, Kenneth M Mackenzie, Brian Towles, Edmond Chow,
John K. Salmon, Cliff Youg, Joseph A Bank, Brannon Batson, Martin M. Deneroff,
Jeffrey S. Kuskin, Richard H. Larson, Mark A Moraes, David E. Shaw,
"Exploiting 162-nanosecond end-to-end communication latency on Anton",
*Supercomputing '10*, : November 2010. (available online)

- David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana,
Ron O. Dror, Michael P. Eastwood, Joseph A Bank, John M. Jumper, John K. Salmon,
Yibing Shan, Willy Wriggers,
"Atomic-level characterization of the structural dynamics of proteins",
*Science*,**330**:341-346, October 2010. (available online)

- P. Ploumhans, Gregoire S. Winckelmans, John K. Salmon,
Anthony Leonard, and Michael S. Warren,
"Vortex methods for direct numerical simulation of three-dimensional
bluff body flows: Application to the sphere at Re=300, 500, and 1000",
*Journal of Computational Physics*,**178**:427-463, 2002.

- P. Ploumhans, Gregoire S. Winckelmans, and John Salmon,
"Vortex particles and tree codes: I. Flows with arbitrary crossing
between solid boundaries and particle redistribution lattice",
*Electron. Proc. 3rd Int. Workshop on Vortex Flows and Related Numerical Methods*ESAIM 7, 1999.

- P. Ploumhans, Gregoire S. Winckelmans, and John Salmon,
"Vortex particles and tree codes: II. Vortex ring encountering a
plane at an angle",
*Electron. Proc. 3rd Int. Workshop on Vortex Flows and Related Numerical Methods*ESAIM 7, 1999.

- Michael S. Warren, Timothy C. Germann, Peter S. Lomdahl, David M. Beazley,
and John K. Salmon,
"Avalon: An Alpha/Linux cluster achieves 10 Gflops for $150k",
In
*Supercomputing '98*, Los Alamitos, 1998, IEEE Comp. Soc. ( postscript version)

- John K. Salmon, Christopher Stein, and Thomas Sterling,
"Scaling of Beowulf-class distributed systems",
In
*Supercomputing '98*, Los Alamitos, IEEE Comp. Soc., 1998. (available online)

- Thomas Sterling, Tom Cwik, Don Becker, John Salmon, Mike Warren, and
Bill Nitzberg,
"An assessment of Beowulf-class computing for NASA requirements: Initial
findings from the first NASA workshop on Beowulf class clustered computing",
In
*Proceedings, IEEE Aerospace Conference*IEEE, March 21-28, Aspen CO, 1998. (available online)

- David Pfitzner, John Salmon, and Thomas Sterling,
"Halo world: Tools for parallel cluster finding in astrophysical
N-body simulations."
*J. of Data Mining and Knowledge Discovery***418-438**, 1997. (available online)

- Michael S. Warren, John K. Salmon, Donald J. Becker, M. Patrick Goda,
Thomas Sterling, and Gregoire S. Winckelmans,
"PentiumPro inside: I. a treecode at 430 Gflops on ASCI red,
II. Price/performance of $50/Mflop on Loki and Hyglac",
In
*Supercomputing '97*, Los Alamitos, 1997, IEEE Comp. Soc. (1997 Gordon Bell Prize winner)

- John K. Salmon and Michael S. Warren,
"Parallel out-of-core methods for N-body simulation",
Michael Heath, Virginia Torczon, et al., editors, In
*Eighth SIAM Conference on Parallel Processing for Scientific Computing*, SIAM, 1997. (available online)

- Michael S. Warren, Donald J. Becker, M. Patrick Goda, John K. Salmon,
and Thomas Sterling,
"Parallel supercomputing with commodity components",
H. Arabnia, editor, In
*International Conference on Parallel and Distributed Processing Techniques and Applications*(PDPTA '97), pages 1372-1381, CSREA, Las Vegas, NV June 30 - July 3, 1997.

- David W. Pfitzner and John K. Salmon,
"Parallel halo finding in N-body cosmology simulations",
Evangelos Simoudis, Jiawei Han, and Usama Fayyad, editors,
In
*KDD-96 Proceedings: The Second International Conference on Knowledge Discovery & Data Mining*pages 26-31, AAAI Press, 1996. ( available online)

- Gregoire S. Winckelmans, John K. Salmon, Michael S. Warren,
Anthony Leonard, and B. Jodoin,
"Application of fast parallel and sequential tree codes to computing
three dimensional flows with the vortex element and boundary element methods",
In
*Second International Workshop on Vortex Flows*, 1996.

- Gregoire S. Winckelmans, John K. Salmon, Anthony Leonard, and
Michael S. Warren,
"Three-dimensional vortex particle and panel methods: fast tree-code solvers
with active error control for arbitrary distributions/geometries",
In
*Forum on Vortex Methods for Engineering Applications*, pages 23-43, 1995.

- Michael S. Warren and John K. Salmon,
"A portable parallel particle program",
*Computer Physics Communications, 87*pages 266-290, 1995. (available online)

- John Salmon,
"Generation of correlated and constrained Gaussian stochastic
processes for N-body simulations",
*Astrophys. J.*,**460**:59-67, 1996. (available online)

- Michael S. Warren and John K. Salmon,
"A parallel, portable, and versatile tree code",
In
*Seventh SIAM Conference on Parallel Processing for Scientific Computing*, pages 319-324, SIAM, 1995.

- Gregoire S. Winckelmans, John K. Salmon, Michael S. Warren,
and Anthony Leonard,
"The fast solution of three-dimensional fluid dynamical N-body
problems using parallel tree codes: vortex element method and boundary
element method.
In
*Seventh SIAM Conference on Parallel Processing for Scientific Computing*, pages 301-306, SIAM, 1995.

- W. H. Zurek, P. J. Quinn, J. K. Salmon, and M. S. Warren,
"Large scale structure after COBE: Peculiar velocities and
correlations of cold dark matter halos",
*Astrophysical Journal*,**431**:559--568, 1994. (available online)

- John K. Salmon, Gregoire S. Winckelmans, and Michael S. Warren,
"Fast parallel treecodes for gravitational and fluid dynamical
N-body problems",
*J. Supercomputer Appl.*,**8**:129--142, 1994. (available online)

- John K. Salmon and Michael S. Warren,
"Skeletons from the treecode closet",
*Journal of Computational Physics*,**111**(1):136-155, 1994. (available online)

- W.H. Zurek, Michael S. Warren, Peter J. Quinn, and
John K. Salmon,
"The second coming of cold dark matter",
*Proceedings of the 9th IAP Meeting*Paris, France, July 1993.

- Michael S. Warren and John K. Salmon,
"A parallel hashed oct-tree N-body algorithm",
In
*Supercomputing '93*, pages 12-21, Los Alamitos, IEEE Comp. Soc, 1993. (available online)**Supercomputing 2018 test of time award winner.**

- Michael S. Warren, Peter J. Quinn, John K. Salmon, and
Wojciech H. Zurek,
"Dark halos formed via dissipationless collapse: I. shapes and alignment of
angular momentum",
*Astrophysical Journal*,**399**:405-425, 1992.

- Michael S. Warren and John K. Salmon,
"Astrophysical N-body Simulations Using
Hierarchical Tree Data Structures",
*Supercomputing '92*, IEEE Comp. Soc., Los Alamitos, pages 570--576, 1992. (available online (pdf)) // (available as postscript) // (1992 Gordon Bell Prize winner)

- David P. Fullagar, Peter J. Quinn, Carl J. Grillmair,
John K. Salmon and Michael S. Warren,
"N-body Methods on MIMD Supercomputers:
Astrophysics on the Intel Touchstone Delta",
In
*"Fifth Australian Supercomputing Conference*, 7-9 Dec., 1992. (available online)

- John K. Salmon and Paul Messina,
"Touchstone Delta Update",
*"Intel Supercomputer Users' Group Conference*, 4-7 Oct., 1992, Harvey Hotel, Dallas, Texas (available online)

- David P. Fullagar, Peter J. Quinn, and
John K. Salmon,
"N-body simulations of a4 isophote deviations in elliptical galaxies",
I.J. Danziger, editor, In
*Proceedings of ESO/EIPC Workshop on the Structure, Dynamics and Chemical Evolution of Early-Type Galaxies, Elba, 25-30, May 1992*, European Southern Observatory, 1993.

- Peter J. Quinn, Michael S. Warren, John K. Salmon, and
Wojciech H. Zurek,
"The shapes of galaxies formed in dissipationless cosmological models",
I.J. Danziger, editor, In
*Proceedings of ESO/EIPC Workshop on the Structure, Dynamics and Chemical Evolution of Early-Type Galaxies*, European Southern Observatory, Munich, 1992.

- Michaels S. Warren, Wojciech H. Zurek,
Peter J. Quinn, and John K. Salmon,
"The shape of the invisible halo: N-body simulations on parallel
supercomputers",
S. Holt, V. Trimble, and C. Bennett, editors, In
*After the First Three Minutes Workshop Proceedings*, AIP Press, New York, 1991.

- John K. Salmon,
"Parallel
*N*log*N*N-body algorithms and applications to astrophysics", In*Compcon Spring 91*, IEEE Computer Society Press, Los Alamitos, California, pp. 73-78, 1991. (available online)

- John K. Salmon, Peter J. Quinn, and Michael S. Warren,
"Using parallel computers for very large N-body simulations: Shell formation
using 180k particles", R. Wielen, editor, In
*Heidelberg Conference on Dynamics and Interactions of Galaxies*, pages 216-218, Springer-Verlag, New York, 1990.

- Peter J. Quinn, Wojciech H. Zurek, John K. Salmon, and
Michael S. Warren,
"The formation of halos via mergers: the organized and organizing
dynamics of mergers",
R. Wielen, editor, In
*Heidelberg Conference on Dynamics and Interactions of Galaxies*, pages 10-13, Springer-Verlag, New York, 1990.

- Geoffrey C. Fox, Paul Hipes, and John K. Salmon,
"Practical parallel supercomputing: examples from chemistry and physics",
In
*Supercomputing '89*, pages 58-70, ACM Press, 1989.

- Jeffrey Goldsmith and John K. Salmon,
"A hypercube ray-tracer", Geoffrey C. Fox, editor, In
*Third Conference on Hypercube Concurrent Computers and Applications*, pages 1194-1206, ACM Press, New York, 1988. (available online)

- John K. Salmon,
"A mathematical analysis of the scattered decomposition",
Geoffrey C. Fox, editor, In
*Third Conference on Hypercube Concurrent Computers and Applications*, pages 239-240, ACM Press, New York, 1988. (available online)

- John K. Salmon, Sean Callahan, Adam Kolowa, and Jon Flower,
"MOOSE: A multi-tasking operating system for hypercubes",
Geoffrey C. Fox, editor, In
*Third Conference on Hypercube Concurrent Computers and Applications*, pages 391-396, ACM Press, New York, 1988. (available online)

- Michael S. Warren and John K. Salmon,
"An O(N log N) Hypercube N-body integrator",
Geoffrey C. Fox, editor, In
*Third Conference on Hypercube Concurrent Computers and Applications*, pages 971-975, ACM Press, New York, 1988. (available online)

- Wojciech H. Zurek, Peter J. Quinn, and John K. Salmon,
"Rotation of halos in open and closed universes: differentiated merging and
natural selection of galaxy types",
*Astrophysical Journal*,**330**:519-534, 1988.

- Jeffrey Goldsmith and John K. Salmon,
"Automatic creation of object hierarchies for ray tracing",
*Computer Graphics & Applications*,**14**:14-20, 1987. (available online)

- John K. Salmon,
"CUBIX: Programming hypercubes without programming hosts",
M.T. Heath, editor, In
*Hypercube Multi-Processors 1987*, pages 3-9, SIAM, Philadelphia, 1987. (available online)

- Peter J. Quinn, John K. Salmon, and Wojciech H. Zurek,
"Numerical experiments on galactic halo formation",
Piet Hut and S. McMillan, editors, In
*The Use of Supercomputers in Stellar Dynamics*page 130, Springer-Verlag, New York, 1986.

- Peter J. Quinn, John K. Salmon, and Wojciech H. Zurek,
"Primordial density fluctuations and the structure of galactic haloes",
*Nature*,**322**:329, 1986.

- John K. Salmon and Craig Hogan,
"Correlation of QSO absorption lines in universes dominated by cold
dark matter",
*Monthly Notices of the Royal Astronomical Society*,**221**:93, 1986.

- John K. Salmon, Thomas Sterling, Rajesh Bordawekar, and
Christopher Stein,
"Scaling of Beowulf-class distributed systems" (extended abstract)
I. Foster, editor, In
*Seventh IEEE International Symposium on High Performance Distributed Computing*pages 368-369, IEEE, 1998.

- Michael S. Warren and John K. Salmon,
"Abstractions and techniques for parallel N-body simulations",
*Parallel Object Oriented Methods and Applications (POOMA) '96*, Los Alamos National Lab, 1996.

- Michael S. Warren, W.H. Zurek, B.C. Bromley, T. G. Brainerd,
John K. Salmon, and Peter J. Quinn,
"N-body simulation of the cold dark matter cosmology",
J. Cohen, editor, In
*Images of Earth and Space: The Role of Visualization in NASA Science*, 1995.

- Michael S. Warren, and John K. Salmon,
"A Fast Tree Code for Many-body Problems",
*Los Alamos Science*, Number 22, 1994, pp. 88-97. (available online)

- John Salmon, Al Bessey, Heidi Lorenz-Wirzba, Jan Lindheim,
David Payne, and Sharon Brunett,
"Report of the committee to investigate the PFS crash of March 17, 1994",
Caltech report, April 5, 1994.

- John K. Salmon and Michael S. Warren,
"Astrophysical N-body simulations on the Delta", 1992.
(
available online)
(winning entry in the
1992 Intel Grand Challenge Award)

- Michael S. Warren and John K. Salmon,
"A parallel treecode for gravitational N-body simulations with up to
20 million particles",
*Bulletin of the American Astronomical Society***23**:1345, 1991.

- W.H. Zurek, Michael S. Warren, Peter J. Quinn, and John K. Salmon,
"The shape and kinematics of dark halos formed via dissipationless collapse",
*Bulletin of the American Astronomical Society***23**:1345, 1991.

- John Salmon, Sean Callahan, Jon Flower, and Adam Kolowa,
"A MOOSE Status Report",
Technical Report 427, Caltech Concurrent Computation Project, 1986.

- John K. Salmon,
"The many body problem and the FFT",
Technical Report 419.3, Caltech Concurrent Computation Project, 1986. (video)

- Jeffrey Goldsmith and John K. Salmon,
"Static and dynamic database distribution for graphics ray tracing on
the hypercube",
Technical Report 360, Caltech Concurrent Computation Project, 1986.

- John K. Salmon,
"Cubix: an I/O system for the Hypercube",
Technical Report 293, Caltech Concurrent Computation Project, 1986.

- John K. Salmon and Roy D. Williams,
"Fast Fourier transforms in parallel",
Technical Report 283, Caltech Concurrent Computation Project, 1986.

- Jeffrey Goldsmith and John K. Salmon,
"A proposal to develop a ray tracing graphics system for the
Caltech hypercube",
Technical Report 166, Caltech Concurrent Computation Project, 1985.

- Jeffrey Goldsmith and John K. Salmon,
"A ray tracing system for the hypercube",
Technical Report 154, Caltech Concurrent Computation Project, 1985.

- John K. Salmon,
"Hypercube Simulator V2.5",
Technical Report 108, Caltech Concurrent Computation Project, 1984.

- John K. Salmon,
"An astrophysical N-body simulation on the hypercube",
Technical Report 78, Caltech Concurrent Computation Project, 1984.

- John K. Salmon,
"A program to automatically decompose a physical lattice into
a hypercube",
Technical Report 53, Caltech Concurrent Computation Project, 1984.

- John K. Salmon,
"Binary gray codes and the mapping of a physical lattice
into a hypercube",
Technical Report 51, Caltech Concurrent Computation Project, 1984.

- "The Mark III Hypercube", Caltech, 1984?
(available online)

- John K. Salmon, "Asymptotic approximation in quantum mechanics using Feynman path integrals", Undergraduate thesis, Massachusetts Institute of Technology, 1981.

- 1992 Peak performance:
Michael S. Warren, Los Alamos National Laboratory and
John K. Salmon, Caltech;
"Simulation of 9 million gravitation stars by parallelizing a tree code,"
5 Gflops/s on an Intel Touchstone Delta

- 1997 Peak performance:
Michael S. Warren, Los Alamos National Laboratory and
John K. Salmon, Caltech;
"simulating the motion of 322,000,000 self-gravitating particles,"
430 Gflop/s on ASCI Red using 4096 processors.

- 1997 Price/performance:
Michael S. Warren, Los Alamos National Laboratory,
John K. Salmon, Caltech, Donald J. Becker, NASA Goddard,
M. Patrick Goda, Los Alamos, Thomas Sterling, Caltech,
Gregoire S. Winckelmans, Universite Catholique de Louvain;
"Two problems: vortex fluid flow modeled with 360,000 particles;
galaxy formation following 10,000,000 self-gravitating particles,"
18 Gflop/s/US$1 M on a cluster of 16 Intel Pentium Pros (200 MHz).

- 1998 Price/performance:
Michael S. Warren, Timothy C. Germann, Peter S. Lomdahl and
David M. Beazley, Los Alamos National Laboratory,
John K. Salmon, Caltech,
"Simulation of a shock wave propagating through a structure of 61 million atoms,"
64.9 Gflop/s/US$1 M using a 70 PE system of DEC Alpha's (533 MHz).

- 2008 Special category:
David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth
M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon
Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas
J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson,
Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano
Piana, Yibing Shan and Brian Towles, all of D.E. Shaw Research;
"Millisecond-scale molecular dynamics simulations on Anton."

- 2014 Best performance of a high-performance application: David E. Shaw, J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, Ron O. Dror, Amos Even, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Brian Greskamp, C. Richard Ho, Douglas J. Ierardi, Lev Iserovich, Jeffrey S. Kuskin, Richard H. Larson, Timothy Layman, Li-Siang Lee, Adam K. Lerer, Chester Li, Daniel Killebrew, Ken- neth M. Mackenzie, Shark Yeuk-Hai Mok, Mark A. Mor- aes, Rolf Mueller, Lawrence J. Nociolo, Jon L. Peticolas, Terry Quan, Daniel Ramot, John K. Salmon, Daniele P. Scarpazza, U. Ben Schafer, Naseer Siddique, Christopher W. Snyder, Jochen Spengler, Ping Tak Peter Tang, Michael Theobald, Horia Toma, Brian Towles, Benjamin Vitale, Stanley C. Wang and Cliff Young: all of D.E. Shaw Research; "Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer." Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 us/day -- 180 times faster than any commodity hardware platform or general-purpose supercomputer.

John Salmon