Efficient HPC implementations for large-scale molecular simulation in process engineering:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
München
Verl. Dr. Hut
2014
|
| Ausgabe: | 1. Aufl. |
| Schriftenreihe: | Informatik
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | X, 186 S. Ill., graph. Darst. 210 mm x 148 mm, 330 g |
| ISBN: | 9783843917469 3843917469 |
Internformat
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Datensatz im Suchindex
| _version_ | 1806329461287682048 |
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| adam_text |
VII
CONTENTS
1 INTRODUCTION 1
1 PARALLEL LARGE-SCALE MOLECULAR DYNAMICS SIMULATION OF FLUIDS 5
2 MOLECULAR DYNAMICS SIMULATIONS 9
2.1 MODELLING ASPECTS AND EXAMPLE APPLICATIONS 9
2.2 MOLECULAR MODELS AND POTENTIALS 11
2.2.1 MOLECULAR MODELS 11
2.2.2 ALGORITHMS FOR TIME INTEGRATION 14
2.2.3 CONSTRAINT-MOTION MOLECULAR DYNAMICS 15
2.2.4 RIGID-BODY MOLECULAR DYNAMICS 16
2.2.5 INTERINOLECULAR POTENTIALS 17
2.3 STATISTICAL ENSEMBLES 20
2.4 ALGORITHMS FOR NEAREST-NEIGHBOUR SEARCH 21
2.5 ALGORITHMS FOR LONG-RANGE INTERACTIONS 23
2.6 CHARACTERISTICS OF LARGE-SCALE MOLECULAR DYNAMICS SIMULATION OF
FLUIDS . 28
3 PARAILELISATION CONSIDERATIONS 31
3.1 TARGET PLATFORMS 31
3.2 VECTORISATION-BASCD PARAILELISATION 33
3.3 SHARED-MEMORY PARAILELISATION 38
3.4 DISTRIBUTED-MEMORY PARAILELISATION 39
3.5 PARAILELISATION OF MD-ALGORITHMS AND LOAD BALANCING 41
3.5.1 SPATIAL DOMAIN DECOMPOSITION 41
3.5.2 LOAD BALANCING BASED ON KD-TREES 42
4 SIMULATION CODE
ISL MARDYN
45
4.1 DEVELOPMENT OF ISL MARDYN 45
4.1.1 HISTORY OF DEVELOPMENT 45
4.1.2 SOFTWARE STRUCTURE 46
4.2 TESTS AND CONTINUOUS INTEGRATION 49
4.2.1 UNIT TESTING WITH CPPUNIT 50
4.2.2 CONTINUOUS INTEGRATION WITH JENKINS 52
4.3 GENERATION OF LARGE INPUT SETS 53
4.3.1 GENERATOR FRAMEWORK 53
4.3.2 PARTICLE GENERATION WITH A GRAPHICAL USER INTERFACE 54
4.3.3 LARGE-SCALE PARALLEL GENERATION OF INPUT DATA 56
4.4 REFINED LOAD BALANCING 57
HTTP://D-NB.INFO/105909651X
VIII CONTENTS
II IMPLEMENTATIONS OF THE LINKED-CETLS ALGORITHM 61
5 PARALLEL LINKED-CELLS ALGORITHM ON CPUS 65
5.1 SLIDING WINDOW TRAVERSAL OF THE LINKED-CELLS DATA STRUCTURE 65
5.2 MEMORY-EFFICIENT IMPLEMENTATION 67
5.2.1 SCHEME A: LIGHT-WEIGHT REPRESENTATION 68
5.2.2 SCHEME B: FAT REPRESENTATION 68
5.2.3 COMPARISON 69
5.2.4 HYBRID SCHEME 69
5.2.5 MEMORY-EFFICIENCY OF THE LINKED-CELLS DATA STRUCTURE 71
5.3 RUNTIME-EFFICIENT IMPLEMENTATION WITH SSE / AVX 73
5.3.1 RELATED WORK 73
5.3.2 SINGLE-SITE MOLECULES 74
5.3.3 EXTENSION TO MOLECULES WITH MULTIPLE SITES 75
5.3.4 FURTHER OPTIMISATIONS OF THE COMPUTE KERNEL 76
5.4 OPTIMISATION FOR LARGE-SCALE SIMULATION OF INERT FLUIDS 80
5.4.1 RELATED WORK 81
5.4.2 HOMOGENEOUS PARTICLE DISTRIBUTIONS 81
5.4.3 HETEROGENEOUS PARTICLE DISTRIBUTIONS 83
5.5 SUMMARY 84
6 PARALLEL LINKED-CELLS ALGORITHM ON GPUS 85
6-1 RELATED WORK 85
6.2 IMPLEMENTATION OF THE LINKED-CELLS ALGORITHM FOR GPGPUS 88
6.2.1 IMPLEMENTATION ON GPU 89
6.2.2 SOFTWARE-TECHNICAL INTEGRATION 92
6.2.3 EXTENSION TO MULTI-GPU 92
6.2.4 LIMITATIONS OF THE IMPLEMENTATION AND FUTURE IMPROVEMENTS 93
6.3 SUMMARY 95
7 NUMERICAL EXPERIMENTS 97
7.1 EVALUATION SCENARIOS 97
7.2 PERFORMANCE EVALUATION OF THE CPU IMPLEMENTATION 98
7.2.1 MEMORY-EFFICIENCY 98
7.2.2 RUNTIME-EFFICIENCY 100
7.3 PERFORMANCE EVALUATION OF THE GPU IMPLEMENTATION 106
7.4 MULTI-TRILLION PARTICLES SIMULATIONS ON SUPCRMUC 108
7.5 SUMMARY ILL
III METHODS FOR LONG-RANGE INTERACTIONS 113
8 EWALD SUMMATION FOR LONG-RANGE POTENTIALS 117
8.1 EWALD SUMMATION METHOD 117
8.1.1 DERIVATION OF THE EWALD SUMMATION 118
8.1.2 FORMULATION WITH STRUCTURE FACTORS 121
8.1.3 FURTHER OPTIMISATIONS 123
8.1.4 CHOICE OF PARAMETERS AND ERROR ESTIMATES 123
8.2 SEQUENTIAL IMPLEMENTATION 125
CONTENTS IX
8.3 PARALLELISED IMPLEMENTATION 126
8.3.1 SHARED-MEMORY PARALLELISATION WITH OPENMP 127
8.3.2 DLSTRIBUTED-MEMORY PARALLELISATION WITH MPI 128
8.3.3 HYBRID PARALLELISATION 128
8.4 IMPLEMENTATION AS A LIBRARY 129
8.5 INTEGRATION WITH ISL MARDYN 130
8.6 SUMMARY 132
9 PARALLEL TREE-BASED METHODS FOR LONG-RANGE INTERACTIONS 133
9.1 BARNES-HUT ALGORITHM 134
9.2 FAST MULTIPOLC METHOD 138
9.3 EXAFMM LIBRARY FOR THE FAST MULTIPOLE METHOD 142
9.4 INTEGRATION OF EXAFMM WITH ISL MARDYN 142
9.5 SUMMARY 144
10 NUMERICAL EXPERIMENTS 145
10.1 VALIDATION SCENARIOS 145
10.1.1 COMPUTATION OF THE MADELUNG CONSTANT 146
10.1.2 COMPARISON WITH DIRECT COMPUTATION 146
10.1.3 SIMULATION OF WATER AND AQUEOUS NACL SOLUTION 147
10.2 EVALUATION OF THE EWALD SUMMATION 149
10.2.1 SINGLE-CORE PERFORMANCE 150
10.2.2 SCALABILITY 151
10.3 EVALUATION OF THE EXAFMM LIBRARY 155
10.3.1 SINGLE-CORE PERFORMANCE 155
10.3.2 SCALABILITY 156
10.3.3 LARGE-SCALE SIMULATION OF TIP4P WATER 157
10.4 SUMMARY 160
11 CONCLUSION 161
A CODE LISTING OF THE TEST KERNEL 163
B EWALD SUMMATION 167
B.L VALIDATION OF THE EWALD SUMMATION AGAINST DIRECT SUMMATION 167
B.2 SINGLE-CORE RUNTIME EXPERIMENTS 169
BIBLIOGRAPHY 171 |
| any_adam_object | 1 |
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| author_facet | Eckhardt, Wolfgang |
| author_role | aut |
| author_sort | Eckhardt, Wolfgang |
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| dewey-search | 004.35 |
| dewey-sort | 14.35 |
| dewey-tens | 000 - Computer science, information, general works |
| discipline | Informatik |
| edition | 1. Aufl. |
| format | Thesis Book |
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| physical | X, 186 S. Ill., graph. Darst. 210 mm x 148 mm, 330 g |
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| spelling | Eckhardt, Wolfgang Verfasser aut Efficient HPC implementations for large-scale molecular simulation in process engineering Wolfgang Eckhardt 1. Aufl. 201409 München Verl. Dr. Hut 2014 X, 186 S. Ill., graph. Darst. 210 mm x 148 mm, 330 g txt rdacontent n rdamedia nc rdacarrier Informatik Zugl.: München, Technische Universität, Diss., 2014 Hardware (DE-588)4023422-8 gnd rswk-swf Parallelverarbeitung (DE-588)4075860-6 gnd rswk-swf Molekulardynamik (DE-588)4170370-4 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Molekulardynamik (DE-588)4170370-4 s Hardware (DE-588)4023422-8 s Parallelverarbeitung (DE-588)4075860-6 s DE-604 Erscheint auch als Online-Ausgabe Eckhardt, Wolfgang Efficient HPC Implementations for Large-Scale Molecular Simulation in Process Engineering X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=4788884&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027583446&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Eckhardt, Wolfgang Efficient HPC implementations for large-scale molecular simulation in process engineering Hardware (DE-588)4023422-8 gnd Parallelverarbeitung (DE-588)4075860-6 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| subject_GND | (DE-588)4023422-8 (DE-588)4075860-6 (DE-588)4170370-4 (DE-588)4113937-9 |
| title | Efficient HPC implementations for large-scale molecular simulation in process engineering |
| title_auth | Efficient HPC implementations for large-scale molecular simulation in process engineering |
| title_exact_search | Efficient HPC implementations for large-scale molecular simulation in process engineering |
| title_full | Efficient HPC implementations for large-scale molecular simulation in process engineering Wolfgang Eckhardt |
| title_fullStr | Efficient HPC implementations for large-scale molecular simulation in process engineering Wolfgang Eckhardt |
| title_full_unstemmed | Efficient HPC implementations for large-scale molecular simulation in process engineering Wolfgang Eckhardt |
| title_short | Efficient HPC implementations for large-scale molecular simulation in process engineering |
| title_sort | efficient hpc implementations for large scale molecular simulation in process engineering |
| topic | Hardware (DE-588)4023422-8 gnd Parallelverarbeitung (DE-588)4075860-6 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| topic_facet | Hardware Parallelverarbeitung Molekulardynamik Hochschulschrift |
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