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Nordén, Markus

Open this publication in new window or tab >>Dynamic data migration for structured AMR solvers### Nordén, Markus

### Löf, Henrik

### Rantakokko, Jarmo

### Holmgren, Sverker

PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_0_j_idt188_some",{id:"formSmash:j_idt184:0:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_0_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_0_j_idt188_otherAuthors",{id:"formSmash:j_idt184:0:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_0_j_idt188_otherAuthors",multiple:true}); 2007 (English)In: International journal of parallel programming, ISSN 0885-7458, E-ISSN 1573-7640, Vol. 35, p. 477-491Article in journal (Refereed) Published
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-11396 (URN)10.1007/s10766-007-0056-z (DOI)000249405600004 ()
#####

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Available from: 2007-09-11 Created: 2007-09-11 Last updated: 2018-01-12Bibliographically approved

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.

Open this publication in new window or tab >>Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Löf, Henrik

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Rantakokko, Jarmo

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_1_j_idt188_some",{id:"formSmash:j_idt184:1:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_1_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_1_j_idt188_otherAuthors",{id:"formSmash:j_idt184:1:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_1_j_idt188_otherAuthors",multiple:true}); 2006 (English)Report (Other academic)
##### Series

Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2006-038
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-81928 (URN)
#####

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Available from: 2008-02-15 Created: 2008-02-15 Last updated: 2018-01-13Bibliographically approved

Open this publication in new window or tab >>Multithreaded PDE Solvers on Non-Uniform Memory Architectures### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_2_j_idt188_some",{id:"formSmash:j_idt184:2:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_2_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_2_j_idt188_otherAuthors",{id:"formSmash:j_idt184:2:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_2_j_idt188_otherAuthors",multiple:true}); 2006 (English)Doctoral thesis, comprehensive summary (Other academic)
##### Abstract [en]

##### Place, publisher, year, edition, pages

Uppsala: Acta Universitatis Upsaliensis, 2006. p. 33
##### Series

Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 224
##### Keywords

PDE solver, high-performance, NUMA, UMA, OpenMP, MPI, data migration, data replication, thread scheduling, data affinity
##### National Category

Software Engineering
##### Research subject

Scientific Computing
##### Identifiers

urn:nbn:se:uu:diva-7149 (URN)91-554-6656-7 (ISBN)
##### Public defence

2006-10-20, Room 2446, Polacksbacken, Lägerhyddsvägen 2D, Uppsala, 10:15 (English)
##### Opponent

### Cai, Xing

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##### Supervisors

### Thuné, Michael

### Holmgren, Sverker

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#####

Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2018-01-13Bibliographically approved

A trend in parallel computer architecture is that systems with a large shared memory are becoming more and more popular. A shared memory system can be either a uniform memory architecture (UMA) or a cache coherent non-uniform memory architecture (cc-NUMA).

In the present thesis, the performance of parallel PDE solvers on cc-NUMA computers is studied. In particular, we consider the shared namespace programming model, represented by OpenMP. Since the main memory is physically, or *geographically* distributed over several multi-processor nodes, the latency for local memory accesses is smaller than for remote accesses. Therefore, the *geographical locality* of the data becomes important.

The focus of the present thesis is to study *multithreaded* PDE solvers on cc-NUMA systems, in particular their memory access pattern with respect to geographical locality. The questions posed are: (1) How large is the influence on performance of the non-uniformity of the memory system? (2) How should a program be written in order to reduce this influence? (3) Is it possible to introduce optimizations in the computer system for this purpose?

The main conclusion is that geographical locality is important for performance on cc-NUMA systems. This is shown experimentally for a broad range of PDE solvers as well as theoretically using a model involving characteristics of computer systems and applications.

Geographical locality can be achieved through migration directives that are inserted by the programmer or — possibly in the future — automatically by the compiler. On some systems, it can also be accomplished by means of transparent, hardware initiated migration and replication. However, a necessary condition that must be fulfilled if migration is to be effective is that the memory access pattern must not be "speckled", i.e. as few threads as possible shall make accesses to each memory page.

We also conclude that OpenMP is competitive with MPI on cc-NUMA systems if care is taken to get a favourable data distribution.

University of Oslo, Department of Informatics.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.

Open this publication in new window or tab >>OpenMP versus MPI for PDE solvers based on regular sparse numerical operators### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Thuné, Michael

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_3_j_idt188_some",{id:"formSmash:j_idt184:3:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_3_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_3_j_idt188_otherAuthors",{id:"formSmash:j_idt184:3:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_3_j_idt188_otherAuthors",multiple:true}); 2006 (English)In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 22, p. 194-203Article in journal (Refereed) Published
##### National Category

Software Engineering Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-47210 (URN)10.1016/j.future.2003.09.004 (DOI)000234408800016 ()
#####

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Available from: 2006-05-23 Created: 2006-05-23 Last updated: 2018-01-11Bibliographically approved

Open this publication in new window or tab >>Performance modelling for parallel PDE solvers on NUMA-systems### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_4_j_idt188_some",{id:"formSmash:j_idt184:4:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_4_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_4_j_idt188_otherAuthors",{id:"formSmash:j_idt184:4:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_4_j_idt188_otherAuthors",multiple:true}); 2006 (English)Report (Other academic)
##### Series

Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2006-041
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-81930 (URN)
#####

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Available from: 2008-02-19 Created: 2008-02-19 Last updated: 2018-01-13Bibliographically approved

Open this publication in new window or tab >>Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers### Löf, Henrik

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_5_j_idt188_some",{id:"formSmash:j_idt184:5:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_5_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_5_j_idt188_otherAuthors",{id:"formSmash:j_idt184:5:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_5_j_idt188_otherAuthors",multiple:true}); 2004 (English)In: Computational Science – ICCS 2004, Berlin: Springer-Verlag , 2004, p. 9-16Conference paper, Published paper (Refereed)
##### Place, publisher, year, edition, pages

Berlin: Springer-Verlag, 2004
##### Series

Lecture Notes in Computer Science ; 3037
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-71098 (URN)10.1007/b97988 (DOI)
#####

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Available from: 2007-03-11 Created: 2007-03-11 Last updated: 2018-01-10Bibliographically approved

Open this publication in new window or tab >>Improving geographical locality of data for shared memory implementations of PDE solvers### Löf, Henrik

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_6_j_idt188_some",{id:"formSmash:j_idt184:6:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_6_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_6_j_idt188_otherAuthors",{id:"formSmash:j_idt184:6:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_6_j_idt188_otherAuthors",multiple:true}); 2004 (English)Report (Other academic)
##### Series

Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2004-006
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-66907 (URN)
#####

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Available from: 2006-12-05 Created: 2006-12-05 Last updated: 2018-01-10Bibliographically approved

Open this publication in new window or tab >>Parallel PDE Solvers on cc-NUMA Systems### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_7_j_idt188_some",{id:"formSmash:j_idt184:7:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_7_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_7_j_idt188_otherAuthors",{id:"formSmash:j_idt184:7:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_7_j_idt188_otherAuthors",multiple:true}); 2004 (English)Licentiate thesis, comprehensive summary (Other academic)
##### Abstract [en]

##### Place, publisher, year, edition, pages

Uppsala University, 2004
##### Series

Information technology licentiate theses: Licentiate theses from the Department of Information Technology, ISSN 1404-5117 ; 2004-002
##### National Category

Software Engineering
##### Research subject

Scientific Computing
##### Identifiers

urn:nbn:se:uu:diva-86307 (URN)
#####

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##### Supervisors

### Thuné, Michael

### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_7_j_idt188_j_idt365",{id:"formSmash:j_idt184:7:j_idt188:j_idt365",widgetVar:"widget_formSmash_j_idt184_7_j_idt188_j_idt365",multiple:true});
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Available from: 2004-03-26 Created: 2006-05-14 Last updated: 2018-01-13Bibliographically approved

The current trend in parallel computers is that systems with a large shared memory are becoming more and more popular. A shared memory system can be either a uniform memory architecture (UMA) or a cache coherent non-uniform memory architecture (cc-NUMA).

In the present thesis, the performance of parallel PDE solvers on cc-NUMA computers is studied. In particular, we consider the shared namespace programming model, represented by OpenMP. Since the main memory is physically, or *geographically* distributed over several multi-processor nodes, the latency for local memory accesses is smaller than for remote accesses. Therefore, the *geographical locality* of the data becomes important.

The questions posed in this thesis are: (1) How large is the influence on performance of the non-uniformity of the memory system? (2) How should a program be written in order to reduce this influence? (3) Is it possible to introduce optimizations in the computer system for this purpose?

Most of the application codes studied address the Euler equations using a finite difference method and a finite volume method respectively and are parallelized with OpenMP. Comparisons are made with an alternative implementation using MPI and with PDE solvers implemented with OpenMP that solve other equations using different numerical methods.

The main conclusion is that geographical locality is important for performance on cc-NUMA systems. This can be achieved through self optimization provided in the system or through migrate-on-next-touch directives that could be inserted automatically by the compiler.

We also conclude that OpenMP is competitive with MPI on cc-NUMA systems if care is taken to get a favourable data distribution.

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.

Open this publication in new window or tab >>OpenMP versus MPI for PDE solvers based on regular sparse numerical operators### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Thuné, Michael

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_8_j_idt188_some",{id:"formSmash:j_idt184:8:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_8_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_8_j_idt188_otherAuthors",{id:"formSmash:j_idt184:8:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_8_j_idt188_otherAuthors",multiple:true}); 2002 (English)In: Computational Science – ICCS 2002, Berlin: Springer-Verlag , 2002, p. 681-690Conference paper, Published paper (Other academic)
##### Place, publisher, year, edition, pages

Berlin: Springer-Verlag, 2002
##### Series

Lecture Notes in Computer Science ; 2331
##### National Category

Software Engineering Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-44296 (URN)
#####

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Available from: 2006-05-17 Created: 2006-05-17 Last updated: 2018-01-11Bibliographically approved

Open this publication in new window or tab >>Performance of PDE solvers on a self-optimizing NUMA architecture### Holmgren, Sverker

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Nordén, Markus

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Rantakokko, Jarmo

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.### Wallin, Dan

PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_9_j_idt188_some",{id:"formSmash:j_idt184:9:j_idt188:some",widgetVar:"widget_formSmash_j_idt184_9_j_idt188_some",multiple:true}); PrimeFaces.cw("AccordionPanel","widget_formSmash_j_idt184_9_j_idt188_otherAuthors",{id:"formSmash:j_idt184:9:j_idt188:otherAuthors",widgetVar:"widget_formSmash_j_idt184_9_j_idt188_otherAuthors",multiple:true}); 2002 (English)In: Parallel Algorithms and Applications, ISSN 1063-7192, E-ISSN 1029-032X, Vol. 17, p. 285-299Article in journal (Refereed) Published
##### National Category

Computer Sciences Computational Mathematics
##### Identifiers

urn:nbn:se:uu:diva-66909 (URN)10.1080/01495730208941445 (DOI)
#####

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Available from: 2006-05-22 Created: 2006-05-22 Last updated: 2018-01-10Bibliographically approved

Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.