Related papers: CUBE: An Information-optimized parallel Cosmologic…
We present a novel multi-scale embedding scheme that links conventional QM/MM embedding and bootstrap embedding (BE) to allow simulations of large chemical systems on limited quantum devices. We also propose a mixed-basis BE scheme that…
Understanding the universe is hampered by the elusiveness of its most common constituent, cold dark matter. Almost impossible to observe, dark matter can be studied effectively by means of simulation and there is probably no other research…
Recently, we have shown how current cosmological N-body codes already follow the fine grained phase-space information of the dark matter fluid. Using a tetrahedral tesselation of the three-dimensional manifold that describes perfectly cold…
We present a novel, highly efficient algorithm to parallelize O(N^2) direct summation method for N-body problems with individual timesteps on distributed-memory parallel machines such as Beowulf clusters. Previously known algorithms, in…
Modern dense Flash memory devices operate at very low error rates, which require powerful error correcting coding (ECC) techniques. An emerging class of graph-based ECC techniques that has broad applications is the class of…
Cosmological N-Body simulations are used for a variety of applications. Indeed progress in the study of large scale structures and galaxy formation would have been very limited without this tool. For nearly twenty years the limitations…
A simple method for improving cache efficiency of serial and parallel explicit finite procedure with application to casting solidification simulation over three-dimensional complex geometries is presented. The method is based on division of…
As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring…
Nested parallelism exists in scientific codes that are searching multi-dimensional spaces. However, implementations of nested parallelism often have overhead and load balance issues. The Orbital Analysis code we present exhibits a sparse…
Real-time data processing is one of the central processes of particle physics experiments which require large computing resources. The LHCb (Large Hadron Collider beauty) experiment will be upgraded to cope with a particle bunch collision…
We present Particle-Particle-Particle-Mesh (PPPM) and Tree Particle-Mesh (TreePM) implementations on GRAPE-5 and GRAPE-6A systems, special-purpose hardware accelerators for gravitational many-body simulations. In our PPPM and TreePM…
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical…
CO$N$CEPT (COsmological $N$-body CodE in PyThon) is a free and open-source code for cosmological $N$-body simulations on massively parallel computers with distributed memory. Collisionless dark matter is the only implemented particle…
The ability to extract relevant information is critical to learning. An ingenious approach as such is the information bottleneck, an optimisation problem whose solution corresponds to a faithful and memory-efficient representation of…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
The integration of the equations of motion of N interacting particles, represents a classical problem in many branches of physics and chemistry. The direct N-body problem is at the heart of simulations studying Coulomb Crystals. We present…
Although poor for small dynamic scales, the Particle-Mesh (PM) model allows in astrophysics good insight for large dynamic scales at low computational cost. Furthermore, it is possible to employ a very high number of particles to get high…
We present the results of gravitational direct $N$-body simulations using the commercial graphics processing units (GPU) NVIDIA Quadro FX1400 and GeForce 8800GTX, and compare the results with GRAPE-6Af special purpose hardware. The force…
Unstructured meshes present challenges in scientific data analysis due to irregular distribution and complex connectivity. Computing and storing connectivity information is a major bottleneck for visualization algorithms, affecting both…
Our computers today, from sophisticated servers to small smartphones, operate based on the same computing model, which requires running a sequence of discrete instructions, specified as an algorithm. This sequential computing paradigm has…