Abstract
While many ideas and proofs of concept for parallel-in-time integration methods exists, the number of large-scale, accessible time-parallel codes is rather small. This is often due to the apparent or subtle complexity of the algorithms and the many pitfalls awaiting developers of parallel numerical software. One example of such a time-parallel code is pySDC, which implements, among others, the parallel full approximation scheme in space and time (PFASST). Inspired by nonlinear multigrid ideas, PFASST allows to integrate multiple time steps simultaneously using a space-time hierarchy of spectral deferred corrections. In this paper, we demonstrate the application of performance analysis tools to the PFASST implementation pySDC. We trace the path we took for this work, show examples of how the tools can be applied, and explain the sometimes surprising findings we encountered. Although focusing only on a single implementation of a particular parallel-in-time integrator, we hope that our results and in particular the way we obtained them are a blueprint for other time-parallel codes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adhianto, L., Banerjee, S., Fagan, M., Krentel, M., Marin, G., Mellor-Crummey, J., Tallent, N.R.: HPCToolkit: Tools for performance analysis of optimized parallel programs. Concurrency and Computation: Practice and Experience 22(6), 685–701 (2010)
Böhme, D., Wolf, F., de Supinski, B.R., Schulz, M., Geimer, M.: Scalable critical-path based performance analysis. In: 2012 IEEE 26th International Parallel and Distributed Processing Symposium, pp. 1330–1340. IEEE (2012)
Bolten, M., Moser, D., Speck, R.: A multigrid perspective on the parallel full approximation scheme in space and time. Numerical Linear Algebra with Applications 24(6), e2110–n/a (2017). DOI https://doi.org/10.1002/nla.2110. E2110 nla.2110
Bolten, M., Moser, D., Speck, R.: Asymptotic convergence of the parallel full approximation scheme in space and time for linear problems. Numerical linear algebra with applications 25(6), e2208 – (2018). DOI https://doi.org/10.1002/nla.2208. URL https://juser.fz-juelich.de/record/857114
Bradley, T.: GPU Performance Analysis and Optimisation. NVIDIA Corporation (2012)
Center, B.S.: Website for POP CoE (2019). URL https://pop-coe.eu/. [Online; accessed August 13, 2019]
Dalcin, L.D., Paz, R.R., Kler, P.A., Cosimo, A.: Parallel distributed computing using python. Advances in Water Resources 34(9), 1124–1139 (2011). DOI https://doi.org/10.1016/j.advwatres.2011.04.013. URL http://www.sciencedirect.com/science/article/pii/S0309170811000777. New Computational Methods and Software Tools
Dalcin, Lisandro and Mortensen, Mikael and Keyes, David E: Fast parallel multidimensional FFT using advanced MPI. Journal of Parallel and Distributed Computing (2019). DOI https://doi.org/10.1016/j.jpdc.2019.02.006
Dutt, A., Greengard, L., Rokhlin, V.: Spectral deferred correction methods for ordinary differential equations. BIT Numerical Mathematics 40(2), 241–266 (2000). DOI https://doi.org/10.1023/A:1022338906936
Emmett, M., Minion, M.L.: Toward an efficient parallel in time method for partial differential equations. Communications in Applied Mathematics and Computational Science 7, 105–132 (2012). DOI https://doi.org/10.2140/camcos.2012.7.105
Emmett, M., Minion, M.L.: Efficient implementation of a multi-level parallel in time algorithm. In: Domain Decomposition Methods in Science and Engineering XXI, Lecture Notes in Computational Science and Engineering, vol. 98, pp. 359–366. Springer International Publishing (2014). DOI https://doi.org/10.1007/978-3-319-05789-7_33
Eschweiler, D., Wagner, M., Geimer, M., Knüpfer, A., Nagel, W.E., Wolf, F.: Open Trace Format 2 - The next generation of scalable trace formats and support libraries. In: Proc. of the Intl. Conference on Parallel Computing (ParCo), Ghent, Belgium, August 30–September 2 2011, Advances in Parallel Computing, vol. 22, pp. 481–490. IOS Press (2012). DOI https://doi.org/10.3233/978-1-61499-041-3-481
Feld, C., Convent, S., Hermanns, M.A., Protze, J., Geimer, M., Mohr, B.: Score-p and ompt: Navigating the perils of callback-driven parallel runtime introspection. In: X. Fan, B.R. de Supinski, O. Sinnen, N. Giacaman (eds.) OpenMP: Conquering the Full Hardware Spectrum, pp. 21–35. Springer International Publishing, Cham (2019)
Gander, M.J.: 50 years of Time Parallel Time Integration. In: Multiple Shooting and Time Domain Decomposition. Springer (2015). DOI https://doi.org/10.1007/978-3-319-23321-5_3
Geimer, M., Wolf, F., Wylie, B.J.N., Ábrahám, E., Becker, D., Mohr, B.: The SCALASCA performance toolset architecture. In: International Workshop on Scalable Tools for High-End Computing (STHEC), Kos, Greece, pp. 51–65 (2008)
Geimer, M., Saviankou, P., Strube, A., Szebenyi, Z., Wolf, F., Wylie, B.J.N.: Further improving the scalability of the scalasca toolset. In: K. Jónasson (ed.) Applied Parallel and Scientific Computing, pp. 463–473. Springer Berlin Heidelberg, Berlin, Heidelberg (2012)
Gocht, A., Schöne, R., Frenzel, J.: Advanced Python Performance Monitoring with Score-P. In: Tools for High Performance Computing 2019, p. to appear. Springer International Publishing (2019)
Harlacher, M., Calotoiu, A., Dennis, J., Wolf, F.: Analysing the Scalability of Climate Codes Using New Features of Scalasca. In: K. Binder, M. Müller, M. Kremer, A. Schnurpfeil (eds.) Proc. of the John von Neumann Institute for Computing (NIC) Symposium 2016, Juelich, Germany, NIC Series, vol. 48, pp. 343–352. Forschungszentrum Jülich, John von Neumann-Institut for Computing (2016)
Hermanns, M.A., Geimer, M., Mohr, B., Wolf, F.: Trace-based detection of lock contention in MPI one-sided communication. In: C. Niethammer, J. Gracia, T. Hilbrich, A. Knüpfer, M.M. Resch, W.E. Nagel (eds.) Tools for High Performance Computing 2016, Proc. of the 10th Parallel Tools Workshop, Stuttgart, Germany, October 2016, pp. 97–114. Springer (2017). DOI https://doi.org/10.1007/978-3-319-56702-0_6. URL http://juser.fz-juelich.de/record/830159
Huang, J., Jia, J., Minion, M.: Accelerating the convergence of spectral deferred correction methods. Journal of Computational Physics 214(2), 633–656 (2006)
Jülich Supercomputing Centre: JURECA: General-purpose supercomputer at Jülich Supercomputing Centre. Journal of large-scale research facilities 2(A62) (2016). DOI https://doi.org/10.17815/jlsrf-2-121
Knobloch, M., Mohr, B.: Tools for GPU Computing – Debugging and Performance Analysis of Heterogenous HPC Applications. Supercomputing Frontiers and Innovations 7(1) (2020). URL https://superfri.org/superfri/article/view/311
Knobloch, M., Saviankou, P., Schlütter, M., Visser, A., Mohr, B.: A picture is worth a thousand numbers – Enhancing Cube’s analysis capabilities with plugins. In: Tools for High Performance Computing 2019 (tbp)
Knüpfer, A., Brunst, H., Doleschal, J., Jurenz, M., Lieber, M., Mickler, H., Müller, M.S., Nagel, W.E.: The Vampir Performance Analysis Tool-Set. In: M. Resch, R. Keller, V. Himmler, B. Krammer, A. Schulz (eds.) Tools for High Performance Computing, pp. 139–155. Springer Berlin / Heidelberg (2008). DOI https://doi.org/10.1007/978-3-540-68564-7_9
Knüpfer, A., Rössel, C., an Mey, D., Biersdorff, S., Diethelm, K., Eschweiler, D., Geimer, M., Gerndt, M., Lorenz, D., Malony, A.D., Nagel, W.E., Oleynik, Y., Philippen, P., Saviankou, P., Schmidl, D., Shende, S.S., Tschüter, R., Wagner, M., Wesarg, B., Wolf, F.: Score-P – A joint performance measurement run-time infrastructure for Periscope, Scalasca, TAU, and Vampir. In: Proc. of the 5th Int’l Workshop on Parallel Tools for High Performance Computing, September 2011, Dresden, pp. 79–91. Springer (2012). DOI https://doi.org/10.1007/978-3-642-31476-6_7
LLNL: Website for XBraid (2018). URL https://www.llnl.gov/casc/xbraid. [Online; accessed July 30, 2018]
Lührs, S., Rohe, D., Schnurpfeil, A., Thust, K., Frings, W.: Flexible and Generic Workflow Management. In: Parallel Computing: On the Road to Exascale, Advances in parallel computing, vol. 27, pp. 431–438. International Conference on Parallel Computing 2015, Edinburgh (United Kingdom), 1 Sep 2015–4 Sep 2015, IOS Press, Amsterdam (2016). DOI https://doi.org/10.3233/978-1-61499-621-7-431. URL http://juser.fz-juelich.de/record/808798
Minion, M., Emmett, M.: Website for libpfasst (2019). URL https://github.com/libpfasst/LibPFASST. [Online; accessed August 13, 2019]
Minion, M.L.: A hybrid parareal spectral deferred corrections method. Communications in Applied Mathematics and Computational Science 5(2), 265–301 (2010). DOI https://doi.org/10.2140/camcos.2010.5.265
Mix, H., Herold, C., Weber, M.: Visualization of Multi-layer I/O Performance in Vampir. In: Parallel and Distributed Processing Symposium Workshop (IPDPSW), 2018 IEEE International (2018)
Ong, B.W., Schroder, J.B.: Applications of time parallelization. Computing and Visualization in Science 23(1), 1–15 (2020)
Ong, B.W., Haynes, R.D., Ladd, K.: Algorithm 965: RIDC Methods: A Family of Parallel Time Integrators. ACM Trans. Math. Softw. 43(1), 8:1–8:13 (2016). DOI https://doi.org/10.1145/2964377
Pillet, V., Labarta, J., Cortes, T., Girona, S.: Paraver: A tool to visualize and analyze parallel code. In: Proceedings of WoTUG-18: transputer and occam developments, vol. 44, pp. 17–31. Citeseer (1995)
Reinders, J.: Vtune performance analyzer essentials. Intel Press (2005)
Ruprecht, D., Speck, R.: Spectral deferred corrections with fast-wave slow-wave splitting. SIAM Journal on Scientific Computing 38(4), A2535–A2557 (2016)
Saviankou, P., Knobloch, M., Visser, A., Mohr, B.: Cube v4: From performance report explorer to performance analysis tool. In: Proceedings of the International Conference on Computational Science, ICCS 2015, Computational Science at the Gates of Nature, Reykjavík, Iceland, 1–3 June, 2015, pp. 1343–1352 (2015). DOI https://doi.org/10.1016/j.procs.2015.05.320
Saviankou, P., Knobloch, M., Visser, A., Mohr, B.: Cube v4: From performance report explorer to performance analysis tool. Procedia Computer Science 51, 1343–1352 (2015)
Sharples, W., Zhukov, I., Geimer, M., Goergen, K., Luehrs, S., Breuer, T., Naz, B., Kulkarni, K., Brdar, S., Kollet, S.: A run control framework to streamline profiling, porting, and tuning simulation runs and provenance tracking of geoscientific applications. Geoscientific Model Development 11(7), 2875–2895 (2018). DOI https://doi.org/10.5194/gmd-11-2875-2018
Shende, S.S., Malony, A.D.: The TAU parallel performance system. The International Journal of High Performance Computing Applications 20(2), 287–311 (2006)
Speck, R.: Algorithm 997: pySDC - Prototyping Spectral Deferred Corrections. ACM Transactions on Mathematical Software 45(3) (2019). DOI https://doi.org/10.1145/3310410
Speck, R.: Parallel-in-time/pysdc: The performance release (2019). DOI https://doi.org/10.5281/zenodo.3407254
Speck, R.: Website for pySDC (2019). URL https://parallel-in-time.org/pySDC/. [Online; accessed August 13, 2019]
Terpstra, D., Jagode, H., You, H., Dongarra, J.: Collecting performance data with papi-c. In: Tools for High Performance Computing 2009, pp. 157–173. Springer (2010)
Treibig, J., Hager, G., Wellein, G.: Likwid: A lightweight performance-oriented tool suite for x86 multicore environments. In: 2010 39th International Conference on Parallel Processing Workshops, pp. 207–216. IEEE (2010)
Weiser, M.: Faster SDC convergence on non-equidistant grids by DIRK sweeps. BIT Numerical Mathematics 55(4), 1219–1241 (2014)
Zhang, J., Du, Q.: Numerical Studies of Discrete Approximations to the Allen-Cahn Equation in the Sharp Interface Limit. SIAM Journal on Scientific Computing 31(4), 3042–3063 (2009). DOI https://doi.org/10.1137/080738398
Zhukov, I., Feld, C., Geimer, M., Knobloch, M., Mohr, B., Saviankou, P.: Scalasca v2: Back to the future. In: Proc. of Tools for High Performance Computing 2014, pp. 1–24. Springer (2015). DOI https://doi.org/10.1007/978-3-319-16012-2_1
Acknowledgements
Parts of this work have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No 676553 and 824080. RS thankfully acknowledges the financial support by the German Federal Ministry of Education and Research through the ParaPhase project within the framework “IKT 2020 - Forschung für Innovationen” (project number 01IH15005A).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Speck, R., Knobloch, M., Lührs, S., Gocht, A. (2021). Using Performance Analysis Tools for a Parallel-in-Time Integrator. In: Ong, B., Schroder, J., Shipton, J., Friedhoff, S. (eds) Parallel-in-Time Integration Methods. PinT 2020. Springer Proceedings in Mathematics & Statistics, vol 356. Springer, Cham. https://doi.org/10.1007/978-3-030-75933-9_3
Download citation
DOI: https://doi.org/10.1007/978-3-030-75933-9_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-75932-2
Online ISBN: 978-3-030-75933-9
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)