OpenAtom
Encyclopedia
OpenAtom is a massively parallel quantum chemistry
application written in Charm++
for simulations on supercomputers. Its developmental version was called LeanCP. Many important problems in material science, chemistry
, solid-state physics
, and biophysics
require a modeling approach based on fundamental quantum mechanical
principles. A particular approach that has proved to be relatively efficient and useful is Car-Parrinello ab initio molecular dynamics (CPAIMD). It is widely used to study systems consisting of hundreds to thousands of atoms. CPAIMD computations involve a large number of interdependent phases with high communication overhead including multiple concurrent sparse 3D Fast Fourier Transforms (3D-FFTs), non-square matrix multiplies and few concurrent dense 3D-FFTs.
Parallelization of this approach beyond a few hundred processors is challenging, due to the complex dependencies among various subcomputations, which lead to complex communication optimization and load balancing problems. Using Charm++ and its concept of processor virtualization, the phases are discretized into a large number of virtual processors which are, in turn, mapped flexibly onto physical processors, thereby allowing significant interleaving of work. Interleaving is enhanced through both architecturally independent methods and network topology aware mapping techniques. OpenAtom has shown good scaling up to 20,480 processors of IBM's Blue Gene/L and 4,096 processors of Cray XT3
.
OpenAtom is freely available for download at the OpenAtom webpage. Published papers can also be found at the website.
Quantum chemistry
Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems...
application written in Charm++
Charm++
Charm++ is a parallel object-oriented programming language based on C++ and developed in the Parallel Programming Laboratory at the University of Illinois. Charm++ is designed with the goal of enhancing programmer productivity by providing a high-level abstraction of a parallel program while at the...
for simulations on supercomputers. Its developmental version was called LeanCP. Many important problems in material science, chemistry
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
, solid-state physics
Solid-state physics
Solid-state physics is the study of rigid matter, or solids, through methods such as quantum mechanics, crystallography, electromagnetism, and metallurgy. It is the largest branch of condensed matter physics. Solid-state physics studies how the large-scale properties of solid materials result from...
, and biophysics
Biophysics
Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems. Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems...
require a modeling approach based on fundamental quantum mechanical
Quantum mechanics
Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...
principles. A particular approach that has proved to be relatively efficient and useful is Car-Parrinello ab initio molecular dynamics (CPAIMD). It is widely used to study systems consisting of hundreds to thousands of atoms. CPAIMD computations involve a large number of interdependent phases with high communication overhead including multiple concurrent sparse 3D Fast Fourier Transforms (3D-FFTs), non-square matrix multiplies and few concurrent dense 3D-FFTs.
Parallelization of this approach beyond a few hundred processors is challenging, due to the complex dependencies among various subcomputations, which lead to complex communication optimization and load balancing problems. Using Charm++ and its concept of processor virtualization, the phases are discretized into a large number of virtual processors which are, in turn, mapped flexibly onto physical processors, thereby allowing significant interleaving of work. Interleaving is enhanced through both architecturally independent methods and network topology aware mapping techniques. OpenAtom has shown good scaling up to 20,480 processors of IBM's Blue Gene/L and 4,096 processors of Cray XT3
Cray XT3
The Cray XT3 is a distributed memory massively parallel MIMD supercomputer designed by Cray Inc. with Sandia National Laboratories under the codename Red Storm. Cray turned the design into a commercial product in 2004...
.
OpenAtom is freely available for download at the OpenAtom webpage. Published papers can also be found at the website.
See also
- Charm++Charm++Charm++ is a parallel object-oriented programming language based on C++ and developed in the Parallel Programming Laboratory at the University of Illinois. Charm++ is designed with the goal of enhancing programmer productivity by providing a high-level abstraction of a parallel program while at the...
- NAMDNAMDNAMD is a free-of-charge molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems...
- List of quantum chemistry and solid state physics software