Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
Link to record
Permanent link

Direct link
Nordén, Markus
Publications (10 of 11) Show all publications
Nordén, M., Löf, H., Rantakokko, J. & Holmgren, S. (2007). Dynamic data migration for structured AMR solvers. International journal of parallel programming, 35, 477-491
Open this publication in new window or tab >>Dynamic data migration for structured AMR solvers
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 ()
Available from: 2007-09-11 Created: 2007-09-11 Last updated: 2018-01-12Bibliographically approved
Nordén, M., Löf, H., Rantakokko, J. & Holmgren, S. (2006). Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers.
Open this publication in new window or tab >>Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers
2006 (English)Report (Other academic)
Abstract [en]

On cc-NUMA multi-processors, the non-uniformity of main memory latencies motivates the need for co-location of threads and data. We call this special form of data locality, geographical locality. In this article, we study the performance of a parallel PDE solver with adaptive mesh refinement. The solver is parallelized using OpenMP and the adaptive mesh refinement makes dynamic load balancing necessary. Due to the dynamically changing memory access pattern caused by the runtime adaption, it is a challenging task to achieve a high degree of geographical locality.

The main conclusions of the study are: (1) that geographical locality is very important for the performance of the solver, (2) that the performance can be improved significantly using dynamic page migration of misplaced data, (3) that a migrate-on-next-touch directive works well whereas the first-touch strategy is less advantageous for programs exhibiting a dynamically changing memory access patterns, and (4) that the overhead for such migration is low compared to the total execution time.

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)
Note

Note: To appear in Proceedings of the 2:nd International Workshop on OpenMP (IWOMP)

Available from: 2008-02-15 Created: 2008-02-15 Last updated: 2024-05-31Bibliographically approved
Nordén, M. (2006). Multithreaded PDE Solvers on Non-Uniform Memory Architectures. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Multithreaded PDE Solvers on Non-Uniform Memory Architectures
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

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
Supervisors
Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2022-03-11Bibliographically approved
Nordén, M., Holmgren, S. & Thuné, M. (2006). OpenMP versus MPI for PDE solvers based on regular sparse numerical operators. Future generations computer systems, 22, 194-203
Open this publication in new window or tab >>OpenMP versus MPI for PDE solvers based on regular sparse numerical operators
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 ()
Available from: 2006-05-23 Created: 2006-05-23 Last updated: 2018-01-11Bibliographically approved
Nordén, M. (2006). Performance modelling for parallel PDE solvers on NUMA-systems.
Open this publication in new window or tab >>Performance modelling for parallel PDE solvers on NUMA-systems
2006 (English)Report (Other academic)
Abstract [en]

A detailed model of the memory performance of a PDE solver running on a NUMA-system is set up. Due to the complexity of modern computers, such a detailed model inevitably is very complicated. Therefore, approximations are introduced that simplify the model and allows NUMA-systems and PDE solvers to be described conveniently.

Using the simplified model, it is shown that PDE solvers using ordered local methods can be made very unsensitive to high NUMA-ratios, allowing them to scale well on virtually any NUMA-system.

PDE solvers using unordered local methods, semiglobal methods or global methods are more sensitive to high NUMA-ratios and require special techniques in order to scale well beyond a single locality group.

Nevertheless, the potential performance gain of improving the data distribution on a NUMA-system can be considerable for all kinds of PDE solvers studied.

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)
Available from: 2008-02-19 Created: 2008-02-19 Last updated: 2024-05-31Bibliographically approved
Löf, H., Nordén, M. & Holmgren, S. (2004). Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers. In: Computational Science – ICCS 2004 (pp. 9-16). Berlin: Springer-Verlag
Open this publication in new window or tab >>Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers
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)
Available from: 2007-03-11 Created: 2007-03-11 Last updated: 2018-01-10Bibliographically approved
Löf, H., Nordén, M. & Holmgren, S. (2004). Improving geographical locality of data for shared memory implementations of PDE solvers.
Open this publication in new window or tab >>Improving geographical locality of data for shared memory implementations of PDE solvers
2004 (English)Report (Other academic)
Abstract [en]

On cc-NUMA multi-processors, the non-uniformity of main memory latencies motivates the need for co-location of threads and data. We call this special form of data locality, geographical locality, as the non-uniformity is a consequence of the physical distance between the cc-NUMA nodes. In this article, we compare the well established method of exploiting the first-touch strategy using parallel initialization of data to an application-initiated page migration strategy as means of increasing the geographical locality for a set of important scientific applications.

Four PDE solvers parallelized using OpenMP are studied; two standard NAS NPB3.0-OMP benchmarks and two kernels from industrial applications. The solvers employ both structured and unstructured computational grids. The main conclusions of the study are: (1) that geographical locality is important for the performance of the applications, (2) that application-initiated migration outperforms the first-touch scheme in almost all cases, and in some cases even results in performance which is close to what is obtained if all threads and data are allocated on a single node. We also suggest that such an application-initiated migration could be made fully transparent by letting the OpenMP compiler invoke it automatically.

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)
Available from: 2006-12-05 Created: 2006-12-05 Last updated: 2024-05-31Bibliographically approved
Nordén, M. (2004). Parallel PDE Solvers on cc-NUMA Systems. (Licentiate dissertation). Uppsala University
Open this publication in new window or tab >>Parallel PDE Solvers on cc-NUMA Systems
2004 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

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.

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)
Supervisors
Available from: 2004-03-26 Created: 2006-05-14 Last updated: 2018-01-13Bibliographically approved
Nordén, M., Holmgren, S. & Thuné, M. (2002). OpenMP versus MPI for PDE solvers based on regular sparse numerical operators. In: Computational Science – ICCS 2002 (pp. 681-690). Berlin: Springer-Verlag
Open this publication in new window or tab >>OpenMP versus MPI for PDE solvers based on regular sparse numerical operators
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)
Available from: 2006-05-17 Created: 2006-05-17 Last updated: 2018-01-11Bibliographically approved
Holmgren, S., Nordén, M., Rantakokko, J. & Wallin, D. (2002). Performance of PDE solvers on a self-optimizing NUMA architecture. Parallel Algorithms and Applications, 17, 285-299
Open this publication in new window or tab >>Performance of PDE solvers on a self-optimizing NUMA architecture
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)
Available from: 2006-05-22 Created: 2006-05-22 Last updated: 2018-01-10Bibliographically approved
Organisations

Search in DiVA

Show all publications