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Load balancing of molecular dynamics simulation with NWChem
2001
IBM Systems Journal
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This contribution provides details of the classical molecular dynamics module and focuses on issues related to load balancing on massively parallel computers, in particular the IBM SP TM and the Cray T3E ...
This software integrates a range of modules for computational chemistry applications, including classical molecular dynamics simulations and quantum mechanical calculations. ...
To make molecular simulations of such systems efficient, dynamic load-balancing techniques are needed. ...
doi:10.1147/sj.402.0328
fatcat:45of457fjvhmzpnsiftdliabia
Inspector-Executor Load Balancing Algorithms for Block-Sparse Tensor Contractions
2013
2013 42nd International Conference on Parallel Processing
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Developing effective yet scalable load-balancing methods for irregular computations is critical to the successful application of simulations in a variety of disciplines at petascale and beyond. ...
These two schemes, which have not been previously implemented in NWChem or its proxies (i.e. quantum chemistry mini-apps) are compared to the original centralized dynamic load-balancing algorithm as well ...
NWChem NWChem [9] is the DOE flagship computational chemistry package, which supports most of the widely used methods across a range of accuracy scales (classical molecular dynamics, ab initio molecular ...
doi:10.1109/icpp.2013.12
dblp:conf/icpp/OzogHDBSM13
fatcat:an2u6ksugzgphdrhu6fcdgpooq
Inspector/executor load balancing algorithms for block-sparse tensor contractions
2013
Proceedings of the 27th international ACM conference on International conference on supercomputing - ICS '13
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to centralized dynamic load balancing. ...
Good load-balancing methods are required in order to obtain scalability from the NWChem coupled-cluster module, which allows the detailed study of chemical problems by iteratively solving the Schrödinger ...
Scalability of centralized load-balancing The scalability of centralized dynamic load balancing with NXTVAL in the context of CC tensor contractions in NWChem CCSD simulation (15 iterations) with the aug-cc-pVDZ ...
doi:10.1145/2464996.2467282
dblp:conf/ics/OzogSMHDB13
fatcat:3jk6oyhbqngnzntnwescslxrb4
NWChem: New Functionality
[chapter]
2003
Lecture Notes in Computer Science
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Through effective use of the aggregate resources of such computers, NWChem enables much larger and more accurate production simulations than previously feasible. ...
In this paper we briefly describe the NWChem architecture and highlight some of the new capabilities in NWChem. ...
Molecular Dynamics Simulations of Biological Membranes The molecular dynamics (MD) simulation of biological membranes is generally more difficult to setup compared to simulations of other biological systems ...
doi:10.1007/3-540-44864-0_18
fatcat:ek3rogatfndahbinnfdhtqn2wq
NWChem: Past, Present, and Future
[article]
2020
Journal of Chemical Physics
accepted
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and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. ...
In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. ...
ACKNOWLEDGMENTS The authors acknowledge the important contributions to the NWChem project of the following deceased researchers: Ricky A. Kendall, Jarek Nieplocha, and Daniel W. Silverstein. ...
doi:10.1063/5.0004997
pmid:32414274
arXiv:2004.12023v2
fatcat:zzz2vczvkjbnjmqz2ssvd6ouku
NAMD: Biomolecular Simulation on Thousands of Processors
2002
ACM/IEEE SC 2002 Conference (SC'02)
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NAMD is a parallel, object-oriented molecular dynamics program designed for high performance simulation of large biomolecular systems. ...
This paper discusses the techniques which have allowed NAMD to effectively employ over one thousand processors in production simulations of biomedical relevance. ...
Importance of molecular dynamics simulation software. ...
doi:10.1109/sc.2002.10019
dblp:conf/sc/PhillipsZKK02
fatcat:slik5zdeqvbzpm6h4722seroku
A New Scalable Parallel Algorithm for Fock Matrix Construction
2014
2014 IEEE 28th International Parallel and Distributed Processing Symposium
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Fine-grained tasks are better for load balance, but coarse-grained tasks require less communication. ...
Existing algorithms and software, however, may fail to scale for large numbers of cores of a distributed machine, particularly in the simulation of moderately-sized molecules. ...
A value of 1.000 indicates perfect load balance. ...
doi:10.1109/ipdps.2014.97
dblp:conf/ipps/LiuPC14
fatcat:zwhkhcj7hnbohmc3evmcjvneem
Performance Analysis of the NWChem TCE for Different Communication Patterns
[chapter]
2014
Lecture Notes in Computer Science
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We show that apart from the classical approach involving dynamic scheduling of data-blocks for load-balancing, reordering one-sided Get and Accumulate calls affects the performance of tensor contractions ...
GA is used in a number of application codes, especially NWChem, and provides a superset of SHMEM functionality that includes remote accumulate, among other features. ...
This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. ...
doi:10.1007/978-3-319-10214-6_14
fatcat:b2cknz7vv5ednlta6a3pm2tbnm
WorkQ: A many-core producer/consumer execution model applied to PGAS computations
2014
2014 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS)
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Load balance, synchronization, and overlap of communication and computation are facilitated by a tunable nodewise FIFO message queue protocol. ...
(step 3); but processes can switch roles dynamically for the sake of performance. ...
NWChem is known for its strong capabilities in ab initio quantum chemistry methods invoking molecular electron structure theory, yet it also provides modules for simulating classical molecular dynamics ...
doi:10.1109/padsw.2014.7097863
dblp:conf/icpads/OzogMHB14
fatcat:dhtsfj4ozbb7nm62adnctznxly
Hard scaling challenges forab initiomolecular dynamics capabilities in NWChem: Using 100,000 CPUs per second
2009
Journal of Physics, Conference Series
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An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. ...
Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second To cite this article: Eric J Bylaska et al 2009 J. Phys.: Conf. ...
The results shown are from NWChem ab initio molecular dynamics simulation of UO 2 2+ and 122 H 2 O molecules [2] . ...
doi:10.1088/1742-6596/180/1/012028
fatcat:xvts22vttjck3izu5uxocgnaue
Exploiting variability for energy optimization of parallel programs
2016
Proceedings of the Eleventh European Conference on Computer Systems - EuroSys '16
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By recognizing the "shape of variability" we can optimize codes with highly dynamic behavior, which pose challenges to all existing DVFS techniques. ...
With NWChem on MPI two-sided and offline analysis, capturing the initialization, we find energy savings of up to 20%, with less than 1% performance cost. Publication rights licensed to ACM. ...
Dynamic Behavior of NWChem: Slack is virtually nonexistent, as a result of dynamic load balancing in NWChem. ...
doi:10.1145/2901318.2901329
dblp:conf/eurosys/LavrijsenIJCS16
fatcat:kh3p5fzmqff3pkqelrjisuw724
High performance computations using dynamical nucleation theory
2008
Journal of Physics, Conference Series
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Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. ...
Disciplines Chemistry Comments This article is from Abstract: Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical ...
It tolerates or hides latency by virtualizing the threads, facilitating the migration of the threads and provides dynamic load balancing to distribute work across the algorithm. ...
doi:10.1088/1742-6596/125/1/012017
fatcat:akhhbjl2qfccjjppu5sbfqoxci
Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms
[chapter]
2014
Lecture Notes in Computer Science
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Our optimization schemes leverage key architectural features including vectorization and simultaneous multithreading, and results in speedups of up to 2.5x compared with the original implementation. ...
Attaining performance in the evaluation of twoelectron repulsion integrals and constructing the Fock matrix is of considerable importance to the computational chemistry community. ...
Task Granularity for Dynamic Load Balancing Profiling results indicate that the non-perfect linear scaling behavior is related with the dynamic load balancing approach. ...
doi:10.1007/978-3-319-10214-6_13
fatcat:wkirbsbqlbel5fylapjbbxiowy
A Hartree-Fock Application Using UPC++ and the New DArray Library
2016
2016 IEEE International Parallel and Distributed Processing Symposium (IPDPS)
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The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front ...
We analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. ...
NWChem balances load with a centralized dynamic scheduler, which is controlled by a single global counter control referred to as nxtval (for "next value"). ...
doi:10.1109/ipdps.2016.108
dblp:conf/ipps/OzogKZHHMJY16
fatcat:2kj32jz7grextjtzctsrbcoe6m
Barrier elision for production parallel programs
2015
SIGPLAN notices
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Overall, we demonstrate the value of holistic context-sensitive analyses that consider the domain science in conjunction with the associated runtime software stack. ...
In this paper, we present context-sensitive dynamic optimizations that elide barriers redundant during the program execution. ...
Department of Energy, Office of Science, Advanced Scientific Computing Research under collaborative agreement numbers DE-SC0008699 and DE-SC0010473. ...
doi:10.1145/2858788.2688502
fatcat:ijdxemwqcvfefihilzvif3hyn4
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