Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

We demonstrate that a monolayer graphene membrane is impermeable to standard gases including helium. By applying a pressure difference across the membrane, we measure both the elastic constants and the mass of a single layer of graphene. This pressurized graphene membrane is the world's thinnest balloon and provides a unique separation barrier between 2 distinct regions that is only one atom thick.

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Impermeable atomic membranes from graphene sheets.

SINCE the invention of the scanning tunnelling microscope1, the value of establishing a physical connection between the macroscopic world and individual nanometre-scale objects has become increasingly evident, both for probing these objects2–4 and for direct manipulation5–7 and fabrication8–10 at the nanometre scale. While good progress has been made in controlling the position of the macroscopic probe of such devices to sub-angstrom accuracy, and in designing sensitive detection schemes, less has been done to improve the probe tip itself4. Ideally the tip should be as precisely defined as the object under investigation, and should maintain its integrity after repeated use not only in high vacuum but also in air and water. The best tips currently used for scanning probe microscopy do sometimes achieve sub-nanometre resolution, but they seldom survive a 'tip crash' with the surface, and it is rarely clear what the atomic configuration of the tip is during imaging. Here we show that carbon nanotubes11,12 might constitute well defined tips for scanning probe microscopy. We have attached individual nanotubes several micrometres in length to the silicon cantilevers of conventional atomic force microscopes. Because of their flexibility, the tips are resistant to damage from tip crashes, while their slenderness permits imaging of sharp recesses in surface topography. We have also been able to exploit the electrical conductivity of nanotubes by using them for scanning tunnelling microscopy.

Nanotubes as nanoprobes in scanning probe microscopy

The Interaction of Water with Solid Surfaces: Fundamental Aspects Revisited

A concept for molecular electronics exploiting carbon nanotubes as both molecular device elements and molecular wires for reading and writing information was developed. Each device element is based on a suspended, crossed nanotube geometry that leads to bistable, electrostatically switchable ON/OFF states. The device elements are naturally addressable in large arrays by the carbon nanotube molecular wires making up the devices. These reversible, bistable device elements could be used to construct nonvolatile random access memory and logic function tables at an integration level approaching 10 12 elements per square centimeter and an element operation frequency in excess of 100 gigahertz. The viability of this concept is demonstrated by detailed calculations and by the experimental realization of a reversible, bistable nanotube-based bit.

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Carbon nanotube-based nonvolatile random access memory for molecular computing

Laser Optogalvanic Detection of Molecular Ions

Applications on today?s massively parallel supercomputers are often guided with performance analysis tools toward scalable performance on thousands of processors. However, conventional tools for parallel performance analysis have serious problems due to the large data volume that needs to be handled. In this paper, we discuss the scalability issue for MPI performance analysis on Blue Gene/L, the world?s fastest supercomputing platform. First we present an experimental study of existing MPI performance tools that were ported to BG/L from other platforms. These tools can be classified into two categories: profiling tools that collect timing summaries, and tracing tools that collect a sequence of time-stamped events. Profiling tools produce small data volumes and can scale well, but tracing tools tend to scale poorly. We then describe a configurable MPI tracing tool developed for BG/L. By providing a configurable method for trace generation, the volume of trace data can be controlled, and scalability is significantly improved.

MPI performance analysis tools on Blue Gene/L

Vibrational Heating and Atom Transfer with the STM

We present a novel performance monitor architecture, implemented in the Blue Gene/PTM supercomputer. This performance monitor supports the tracking of a large number of concurrent events by using a hybrid counter architecture. The counters have their low order data implemented in registers which are concurrently updated, while the high order counter data is maintained in a dense SRAM array that is updated from the registers on a regular basis. The per formance monitoring architecture includes support for per- event thresholding and fast event notification, using a two- phase interrupt-arming and triggering protocol. A first implementation provides 256 concurrent 64b counters which offers an up to 64x increase in counter number compared to performance monitors typically found in microprocessors today, and thereby dramatically expands the capabilities of counter-based performance tuning.

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Next-Generation Performance Counters: Towards Monitoring Over Thousand Concurrent Events

As the global energy economy makes the transition from fossil fuels toward cleaner alternatives, nuclear fusion becomes an attractive potential solution for satisfying growing needs. Fusion, the power source of the stars, has been the focus of active research since the early, 1950s. While progress has been impressive--especially for magnetically confined plasma devices called tokamaks--the design of a practical power plant remains an outstanding challenge. A key topic of current interest is microturbulence, which is believed to be responsible for the unacceptably large leakage of energy and particles out of the hot plasma core. Understanding and controlling this process is of utmost importance for operating current devices and designing future ones. In addressing such issues, the Gyrokinetic Toroidal Code (GTC) was developed to study the global influence of microturbulence on particle and energy confinement. It has been optimized on the IBM Blue Gene/L™ (BG/L) computer, achieving essentially linear scaling on more than 30,000 processors. A full simulation of unprecedented phase-space resolution was carried out with 32,768 processors on the BG/L supercomputer located at the IBM T. J. Watson Research Center, providing new insights on the influence of collisions on microturbulence.

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Robert E. Walkup

Papers

Laser Optogalvanic Detection of Molecular Ions

MPI performance analysis tools on Blue Gene/L

Vibrational Heating and Atom Transfer with the STM

Next-Generation Performance Counters: Towards Monitoring Over Thousand Concurrent Events

Large-scale gyrokinetic particle simulation of microturbulence in magnetically confined fusion plasmas