Performance analysis of a cardiac simulation code using IPM

Peter Strazdins; Markus Hegland

doi:10.1145/2133173.2133186

Performance analysis of a cardiac simulation code using IPM

Peter Strazdins^*, Markus Hegland

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Citations (Scopus)

Abstract

This paper details our experiences in performing a detailed performance analysis on a large-scale parallel cardiac simulation by the Chaste software on an Nehalem and Infiniband-based cluster. Our methodology achieves good accuracy for relatively modest amounts of cluster time. The use of sections in the Chaste internal profiler, coupled with the IPM tool, enabled some detailed insights into the performance and scalability of the application. For large core counts, our analysis showed that performance was no longer dominated by the linear systems solver. The computationally-intensive components scaled well up to 2048 cores, and poorly scaling and highly imbalanced components associated with program output and miscellaneous functions were limiting scalability.

Original language	English
Title of host publication	ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11
Pages	29-32
Number of pages	4
DOIs	https://doi.org/10.1145/2133173.2133186
Publication status	Published - 2011
Event	2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, ScalA'11, Co-located with SC'11 - Seattle, WA, United States Duration: 14 Nov 2011 → 14 Nov 2011

Publication series

Name	ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11

Conference

Conference	2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, ScalA'11, Co-located with SC'11
Country/Territory	United States
City	Seattle, WA
Period	14/11/11 → 14/11/11

Access to Document

10.1145/2133173.2133186

Cite this

Strazdins, P., & Hegland, M. (2011). Performance analysis of a cardiac simulation code using IPM. In ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11 (pp. 29-32). (ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11). https://doi.org/10.1145/2133173.2133186

@inproceedings{3228e82a3cf74419aef0832663c84628,

title = "Performance analysis of a cardiac simulation code using IPM",

abstract = "This paper details our experiences in performing a detailed performance analysis on a large-scale parallel cardiac simulation by the Chaste software on an Nehalem and Infiniband-based cluster. Our methodology achieves good accuracy for relatively modest amounts of cluster time. The use of sections in the Chaste internal profiler, coupled with the IPM tool, enabled some detailed insights into the performance and scalability of the application. For large core counts, our analysis showed that performance was no longer dominated by the linear systems solver. The computationally-intensive components scaled well up to 2048 cores, and poorly scaling and highly imbalanced components associated with program output and miscellaneous functions were limiting scalability.",

keywords = "cardiac modelling, high performance computing, performance evaluation",

author = "Peter Strazdins and Markus Hegland",

year = "2011",

doi = "10.1145/2133173.2133186",

language = "English",

isbn = "9781450311809",

series = "ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11",

pages = "29--32",

booktitle = "ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11",

note = "2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, ScalA'11, Co-located with SC'11 ; Conference date: 14-11-2011 Through 14-11-2011",

}

Strazdins, P & Hegland, M 2011, Performance analysis of a cardiac simulation code using IPM. in ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11. ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11, pp. 29-32, 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, ScalA'11, Co-located with SC'11, Seattle, WA, United States, 14/11/11. https://doi.org/10.1145/2133173.2133186

Performance analysis of a cardiac simulation code using IPM. / Strazdins, Peter; Hegland, Markus.
ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11. 2011. p. 29-32 (ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Performance analysis of a cardiac simulation code using IPM

AU - Strazdins, Peter

AU - Hegland, Markus

PY - 2011

Y1 - 2011

N2 - This paper details our experiences in performing a detailed performance analysis on a large-scale parallel cardiac simulation by the Chaste software on an Nehalem and Infiniband-based cluster. Our methodology achieves good accuracy for relatively modest amounts of cluster time. The use of sections in the Chaste internal profiler, coupled with the IPM tool, enabled some detailed insights into the performance and scalability of the application. For large core counts, our analysis showed that performance was no longer dominated by the linear systems solver. The computationally-intensive components scaled well up to 2048 cores, and poorly scaling and highly imbalanced components associated with program output and miscellaneous functions were limiting scalability.

AB - This paper details our experiences in performing a detailed performance analysis on a large-scale parallel cardiac simulation by the Chaste software on an Nehalem and Infiniband-based cluster. Our methodology achieves good accuracy for relatively modest amounts of cluster time. The use of sections in the Chaste internal profiler, coupled with the IPM tool, enabled some detailed insights into the performance and scalability of the application. For large core counts, our analysis showed that performance was no longer dominated by the linear systems solver. The computationally-intensive components scaled well up to 2048 cores, and poorly scaling and highly imbalanced components associated with program output and miscellaneous functions were limiting scalability.

KW - cardiac modelling

KW - high performance computing

KW - performance evaluation

UR - http://www.scopus.com/inward/record.url?scp=84857570231&partnerID=8YFLogxK

U2 - 10.1145/2133173.2133186

DO - 10.1145/2133173.2133186

M3 - Conference contribution

SN - 9781450311809

T3 - ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11

SP - 29

EP - 32

BT - ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11

T2 - 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, ScalA'11, Co-located with SC'11

Y2 - 14 November 2011 through 14 November 2011

ER -

Strazdins P, Hegland M. Performance analysis of a cardiac simulation code using IPM. In ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11. 2011. p. 29-32. (ScalA'11 - Proceedings of the 2011 ACM Workshop on Scalable Algorithms for Large-Scale Systems, Co-located with SC'11). doi: 10.1145/2133173.2133186

Performance analysis of a cardiac simulation code using IPM

Abstract

Publication series

Conference

Access to Document

Other files and links

Fingerprint

Cite this