The Library

RIOT : a parallel input/output tracer

Tools

Wright, Steven A., Pennycook, Simon J., Hammond, Simon D. and Jarvis, Stephen A. (2011) RIOT : a parallel input/output tracer. In: Proceedings of the UK Performance Engineering Workshop (UKPEW'11), Bradford, United Kingdom, 7-8 July, 2011 (Unpublished)

Preview

PDF
WRAP_Wright_ukpew2011_submission_24-1.pdf - Published Version - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Download (451Kb) | Preview

Official URL: http://www.inf.brad.ac.uk/ukpew11/

Abstract

Input/output (I/O) operations can represent a significant proportion of the run-time when large scientific applications are run in parallel. Although there have been advances in the form of file-format libraries, file-system design and I/O hardware, a growing divergence exists between the performance of parallel file-systems and compute processing rates. The effect is often a bottleneck when any form of file-system interaction is required. In this paper we present RIOT – an input/output tracing toolkit being developed at the University of Warwick for dynamic attachment to parallel applications. The two-stage tracing process includes a lightweight library to record I/O events and an in-depth post-execution analysis tool to extract performance metrics such as MPI-IO bandwidth, effective POSIX/file-system bandwidth, duration of individual or aggregated time spent in obtaining or releasing file locks and temporal information relating to parallel file activity. We present a case study on the use of RIOT for three standard industry I/O benchmarks: the BT-IO micro-application from NASA’s Parallel Benchmark suite, FLASH-IO, a benchmark which replicates the check-pointing operations of the FLASH thermonuclear star modelling code and IOR, an industry standard I/O benchmark using HDF-5 and MPI-IO. Furthermore, we utilise RIOT to assess these codes when running with the Parallel Log-structured File System (PLFS) middleware developed by the Los Alamos National Laboratory.

Item Type:

Conference Item (Paper)

Subjects:

Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software

Divisions:

Faculty of Science > Computer Science

Library of Congress Subject Headings (LCSH):

Parallel processing (Electronic computers), File processing (Computer science)

Official Date:

8 July 2011

Dates:

Date	Event
8 July 2011	Available

Status:

Peer Reviewed

Publication Status:

Unpublished

Conference Paper Type:

Paper

Title of Event:

Proceedings of the UK Performance Engineering Workshop (UKPEW'11)

Type of Event:

Workshop

Location of Event:

Bradford, United Kingdom

Date(s) of Event:

7-8 July, 2011

References:

1. Bailey, D., et al.: The NAS Parallel Benchmarks. Tech. Rep. RNR-94-007, NASA
Ames Research Center (March 1994)
2. Bailey, D.H., Barszcz, E., Barton, J.T., Browning, D.S., Carter, R.L., Dagum, L.,
Fatoohi, R.A., Frederickson, P.O., Lasinski, T.A., Schreiber, R.S., Simon, H.D.,
Venkatakrishnan, V., Weeratunga, S.K.: The NAS Parallel Benchmarks. International
Journal of High Performance Computing Applications 5(3), 63{73 (1991)
3. Bent, J., Gibson, G.A., Grider, G., Mcclelland, B., Nowoczynski, P., Nunez, J.,
Polte, M., Wingate, M.: PLFS: A Checkpoint Filesystem for Parallel Applications.
In: Proceedings of the ACM/IEEE International Conference on Supercomputing
Conference (SC'09) (November 2009)
4. Carns, P., Latham, R., Ross, R., Iskra, K., Lang, S., Riley, K.: 24/7 Characterization
of Petascale I/O Workloads. In: Proceedings of the IEEE International Conference
on Cluster Computing and Workshops (CLUSTER'09). pp. 1{10 (September
2009)
5. Eckart, B., He, X., Ong, H., Scott, S.L.: An Extensible I/O Performance Analysis
Framework for Distributed Environments. In: Proceedings of the 15th International
European Conference on Parallel and Distributed Computing (Euro-Par'09). pp.
57{68 (August 2009)
6. Fryxell, B., Olson, K., Ricker, P., Timmes, F.X., Zingale, M., Lamb, D.Q., MacNeice,
P., Rosner, R., Truran, J.W., Tufo, H.: FLASH: An Adaptive Mesh Hydrodynamics
Code for Modeling Astrophysical Thermonuclear Flashes. The Astrophysical
Journal Supplement Series 131(1), 273 (2000)
7. Fuerlinger, K., Wright, N., Skinner, D.: E ective Performance Measurement at
Petascale Using IPM. In: Proceedings of the IEEE 16th International Conference
on Parallel and Distributed Systems (ICPADS'10). pp. 373{380 (December 2010)
8. Koziol, Q., Matzke, R.: HDF5 { A New Generation of HDF: Reference Manual
and User Guide. Tech. rep., National Center for Supercomputing Applications,
Champaign, Illinois, USA (1998)
9. Nowoczynski, P., Stone, N., Yanovich, J., Sommer eld, J.: Zest Checkpoint Storage
System for Large Supercomputers. In: Proceedings of the 3rd Annual Workshop
on Petascale Data Storage (PDSW'08). pp. 1{5 (November 2008)
10. Polte, M., Simsa, J., Tantisiriroj, W., Gibson, G., Dayal, S., Chainani, M., Uppugandla,
D.: Fast Log-based Concurrent Writing of Checkpoints. In: Proceedings of
the 3rd Annual Workshop on Petascale Data Storage (PDSW'08). pp. 1{4 (November
2008)
11. Polte, M., Lofstead, J., Bent, J., Gibson, G., Klasky, S.A., Liu, Q., Parashar, M.,
Podhorszki, N., Schwan, K., Wingate, M., Wolf, M.: ... And Eat It Too: High
Read Performance in Write-Optimized HPC I/O Middleware File Formats. In:
Proceedings of the 4th Annual Workshop on Petascale Data Storage (PDSW'09).
pp. 21{25 (November 2009)
12. Rosner, R., Calder, A., Dursi, J., Fryxell, B., Lamb, D., Niemeyer, J., Olson, K.,
Ricker, P., Timmes, F., Truran, J., et al.: Flash Code: Studying Astrophysical
Thermonuclear Flashes. Computing in Science & Engineering 2(2), 33{41 (2000)
13. Schmuck, F., Haskin, R.: GPFS: A Shared-Disk File System for Large Computing
Clusters. In: Proceedings of the First USENIX Conference on File and Storage
Technologies (FAST'02). pp. 231{244 (January 2002)
14. Shan, H., Antypas, K., Shalf, J.: Characterizing and Predicting the I/O Performance
of HPC Applications using a Parameterized Synthetic Benchmark. In: Proceedings
of the ACM/IEEE International Conference on Supercomputing (SC'08)
(November 2008)
15. Shan, H., Shalf, J.: Using IOR to Analyze the I/O Performance for HPC Platforms.
In: Cray User Group Conference (CUG'07). Seattle, WA, USA (May 2007)
16. Thakur, R., Lusk, E., Gropp, W.: ROMIO: A High-Performance, Portable MPIIO
Implementation. Tech. Rep. ANL/MCS-TM-234, Mathematics and Computer
Science Division, Argonne National Laboratory (1997)
17. Uselton, A., Howison, M., Wright, N., Skinner, D., Keen, N., Shalf, J., Karavanic,
K., Oliker, L.: Parallel I/O Performance: From Events to Ensembles. In: Proceedings
of the IEEE International Symposium on Parallel Distributed Processing
(IPDPS'10). pp. 1{11 (April 2010)
18. Wang, Y., , Wang, Y., Kaeli, D.: Source Level Transformations to Improve I/O
Data Partitioning. In: Proceedings of the 1st International Workshop on Storage
Network Architecture and Parallel I/Os (SNAPI'03) (September{October 2003)
19. Wang, Y., Kaeli, D.: Pro le-guided I/O Partitioning. In: Proceedings of the 17th
Annual International Conference on Supercomputing (ICS'03). pp. 252{260 (June
2003)
20. Wolman, B., Olson, T.: IOBENCH: A System Independent IO Benchmark. ACM
SIGARCH Computer Architecture News 17(5), 55{70 (1989)