scholarly journals Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

2006 ◽  
pp. 846-854 ◽  
Author(s):  
Blake G. Fitch ◽  
Aleksandr Rayshubskiy ◽  
Maria Eleftheriou ◽  
T. J. Christopher Ward ◽  
Mark Giampapa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strong Scaling ◽  
Blue Gene

Reactive Molecular Dynamics Simulations, Data Analytics and Visualization

2015 ◽  
Vol 1756 ◽  
Author(s):  
Priya Vashishta ◽  
Rajiv K. Kalia ◽  
Aiichiro Nakano ◽  
Ying Li ◽  
Ken-ichi Nomura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Production ◽  
Density Functional ◽  
Silica Surface ◽  
Hydrogen Gas ◽  
Divide And Conquer ◽  
List Type ◽  
Reactive Molecular Dynamics ◽  
Production Of Hydrogen ◽  
Blue Gene

ABSTRACTMultimillion-atom reactive molecular dynamics (RMD) and large quantum molecular dynamics (QMD) simulations are used to investigate structural and dynamical correlations under highly nonequilibrium conditions and reactive processes in nanostructured materials under extreme conditions. This paper discusses four simulations:1.RMD simulations of heated aluminum nanoparticles have been performed to study the fast oxidation reaction processes of the core (aluminum)-shell (alumina) nanoparticles and small complexes.2.Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We have used billion-atom RMD simulations on a 163,840-processor Blue Gene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated.3.Our QMD simulation reveals rapid hydrogen production from water by an Al superatom. We have found a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production.4.We have introduced an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large QMD simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786,432 cores for a 50.3 million-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16,661 atoms was performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles.

scholarly journals TweTriS: Twenty trillion-atom simulation

2019 ◽  
Vol 33 (5) ◽  
pp. 838-854 ◽  
Author(s):  
Nikola Tchipev ◽  
Steffen Seckler ◽  
Matthias Heinen ◽  
Jadran Vrabec ◽  
Fabio Gratl ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Chemical Engineering ◽  
Phase 1 ◽  
Fivefold Increase ◽  
Strong Scaling ◽  
Third Law ◽  
Force Calculation ◽  
Memory Efficient ◽  
Efficient Execution

Significant improvements are presented for the molecular dynamics code ls1 mardyn — a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell-based force calculation are presented, which are able to retain Newton’s third law optimization. Comparisons to well-optimized Verlet list-based codes, such as LAMMPS and GROMACS, demonstrate the viability of the linked cell-based approach. The present version of ls1 mardyn is used to run simulations on entire supercomputers, maximizing the number of sampled atoms. Compared to the preceding version of ls1 mardyn on the entire set of 9216 nodes of SuperMUC, Phase 1, 27% more atoms are simulated. Weak scaling performance is increased by up to 40% and strong scaling performance by up to more than 220%. On Hazel Hen, strong scaling efficiency of up to 81% and 189 billion molecule updates per second is attained, when scaling from 8 to 7168 nodes. Moreover, a total of 20 trillion atoms is simulated at up to 88% weak scaling efficiency running at up to 1.33 PFLOPS. This represents a fivefold increase in terms of the number of atoms simulated to date.

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

2008 ◽  
Vol 52 (1.2) ◽  
pp. 177-188 ◽  
Author(s):  
S. Kumar ◽  
C. Huang ◽  
G. Zheng ◽  
E. Bohm ◽  
A. Bhatele ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
L System ◽  
Blue Gene

Fine-grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer

2008 ◽  
Vol 52 (1.2) ◽  
pp. 159-175 ◽  
Author(s):  
E. Bohm ◽  
A. Bhatele ◽  
L. V. Kale ◽  
M. E. Tuckerman ◽  
S. Kumar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Method ◽  
Ab Initio Molecular Dynamics ◽  
Fine Grained ◽  
Blue Gene ◽  
Dynamics Method

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

2005 ◽  
Vol 49 (2.3) ◽  
pp. 475-487 ◽  
Author(s):  
F. Suits ◽  
M. C. Pitman ◽  
J. W. Pitera ◽  
W. C. Swope ◽  
R. S. Germain
Keyword(s):  
Molecular Dynamics ◽  
Scientific Results ◽  
Blue Gene

MOLECULAR DYNAMICS COMES OF AGE: 320 BILLION ATOM SIMULATION ON BlueGene/L

2006 ◽  
Vol 17 (12) ◽  
pp. 1755-1761 ◽  
Author(s):  
KAI KADAU ◽  
TIMOTHY C. GERMANN ◽  
PETER S. LOMDAHL
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Materials Science ◽  
Edge Length ◽  
Double Precision ◽  
Computational Power ◽  
Classical Molecular Dynamics ◽  
Strong Scaling ◽  
Dynamics Simulations ◽  
Solid Copper

As computational power is increasing, molecular dynamics simulations are becoming more important in materials science, chemistry, physics, and other fields of science. We demonstrate weak and strong scaling of our classical molecular dynamics code SPaSM on Livermore's BlueGene/L architecture containing 131 072 IBM PowerPC440 processors. A maximum of 320 billion atoms have been simulated in double precision, corresponding to a cubic piece of solid copper with an edge length of 1.56 μm.

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