Abstract
In this article, we present JUWELS Booster, a recently commissioned high-performance computing system at the Jülich Supercomputing Center. With its system architecture, most importantly its large number of powerful Graphics Processing Units (GPUs) and its fast interconnect via InfiniBand, it is an ideal machine for large-scale Artificial Intelligence (AI) research and applications. We detail its system architecture, parallel, distributed model training, and benchmarks indicating its outstanding performance. We exemplify its potential for research application by presenting large-scale AI research highlights from various scientific fields that require such a facility.
S. Kesselheim, A. Herten, K. Krajsek, J. Ebert, J. Jitsev, M. Cherti, M. Langguth, B. Gong, S. Stadtler, A. Mozaffari, G. Cavallaro, R. Sedona, A. Schug—Equal contribution.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
Notes
- 1.
See e.g. https://github.com/EleutherAI/the-pile.
- 2.
- 3.
PyTorch allows AD for distributing tensors across computational devices based on the remote procedure call (RPC) protocol [9]. However, the RPC framework does not compete with communication frameworks like NCCL or MPI with respect to performance.
- 4.
- 5.
- 6.
- 7.
References
Intel Math Kernel Library. Reference Manual. Intel Corporation (2009)
NVIDIA CUBLAS Library Documentation (2017). https://docs.nvidia.com/cuda/cublas/. Accessed 14 Apr 2021
Pucci, F., Schug, A.: Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction. Methods 162–163, 68–73 (2019). https://doi.org/10.1016/j.ymeth.2019.04.012
Abadi, M., et al.: TensorFlow: Large-Scale Machine Learning on Heterogeneous Systems (2015). http://tensorflow.org/, Software available from tensorflow.org
Agarwal, S., Wang, H., Venkataraman, S., Papailiopoulos, D.: On the utility of gradient compression in distributed training systems. ArXiv abs/2103.00543 (2021)
Amodei, D., Hernandez, D., Sastry, G., Clark, J., Brockman, G., Sutskever, I.: AI and compute. Technical report, OpenAI Blog (2018)
Bauer, P., Thorpe, A., Brunet, G.: Nature. https://doi.org/10.1038/nature14956
Belkin, M., Hsu, D., Ma, S., Mandal, S.: Reconciling modern machine-learning practice and the classical bias-variance trade-off. Proc. Natl. Acad. Sci. U.S.A. 116, 15849–15854 (2019). https://doi.org/10.1073/pnas.1903070116
Birrell, A.D., Nelson, B.J.: Implementing remote procedure calls. ACM Trans. Comput. Syst. 2(1), 39–59 (1984)
Brown, T., et al.: Language models are few-shot learners. In: Larochelle, H., Ranzato, M., Hadsell, R., Balcan, M.F., Lin, H. (eds.) Advances in Neural Information Processing Systems, vol. 33, pp. 1877–1901. Curran Associates, Inc. (2020)
Brown, T.B., et al.: Language models are few-shot learners. arXiv preprint arXiv:2005.14165 (2020)
Canty, M.: Image Analysis, Classification and Change Detection in Remote Sensing: With Algorithms for ENVI/IDL and Python, 3rd edn. Taylor & Francis, New York (2014). ISBN: 9781466570375
Chen, T., Kornblith, S., Swersky, K., Norouzi, M., Hinton, G.: Big self-supervised models are strong semi-supervised learners. arXiv preprint arXiv:2006.10029 (2020)
Cherti, M., Jitsev, J.: Effect of large-scale pre-training on full and few-shot transfer learning for natural and medical images. arXiv preprint arXiv:2106.00116 (2021)
Chetlur, S., et al.: cuDNN: efficient primitives for deep learning (2014)
Cohen, J.P., Morrison, P., Dao, L., Roth, K., Duong, T.Q., Ghassemi, M.: Covid-19 image data collection: Prospective predictions are the future. J. Mach. Learn. Biomed. Imaging (2020)
Cuturello, F., Tiana, G., Bussi, G.: Assessing the accuracy of direct-coupling analysis for RNA contact prediction (2020). https://doi.org/10.1261/rna.074179.119
Dago, A.E., Schug, A., Procaccini, A., Hoch, J.A., Weigt, M., Szurmant, H.: Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc. Natl. Acad. Sci. 109(26), E1733–E1742 (2012)
Deng, J., Dong, W., Socher, R., Li, L., Li, K., Fei-Fei, L.: Imagenet: a large-scale hierarchical image database. In: Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, pp. 248–255, June 2009. https://doi.org/10.1109/CVPR.2009.5206848
Deng, L., Yu, D., Platt, J.: Scalable stacking and learning for building deep architectures. In: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), pp. 2133–2136 (2012). https://doi.org/10.1109/ICASSP.2012.6288333
Dettmers, T.: 8-bit approximations for parallelism in deep learning (2015). arxiv:1511.04561
De Leonardis, E., et al.: Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. Nucl. Acids Res. 43(21), 10444–10455 (2015). https://doi.org/10.1093/nar/gkv932
Ginsburg, B., et al.: Stochastic gradient methods with layer-wise adaptive moments for training of deep networks (2020)
Goyal, P., et al.: Accurate, large minibatch SGD: training Imagenet in 1 hour. CoRR abs/1706.02677 (2017). http://arxiv.org/abs/1706.02677
Goyal, P., et al.: Accurate, large minibatch SGD: training ImageNet in 1 hour (2018)
Götz, M., et al.: HeAT - a distributed and GPU-accelerated tensor framework for data analytics. In: Proceedings of the 19th IEEE International Conference on Big Data, pp. 276–288. IEEE, December 2020
Hernandez, D., Kaplan, J., Henighan, T., McCandlish, S.: Scaling laws for transfer. arXiv preprint arXiv:2102.01293 (2021)
Hersbach, H., et al.: The ERA5 global reanalysis. Q. J. R. Meteorol. Soc. 146(730), 1999–2049 (2020). https://doi.org/10.1002/qj.3803
Ioffe, S., Szegedy, C.: Batch normalization: accelerating deep network training by reducing internal covariate shift. In: Bach, F., Blei, D. (eds.) Proceedings of the 32nd International Conference on Machine Learning. Proceedings of Machine Learning Research, vol. 37, pp. 448–456. PMLR, Lille, France, 7–9 July 2015. http://proceedings.mlr.press/v37/ioffe15.html
Jülich Supercomputing Centre: JUWELS: Modular Tier-0/1 Supercomputer at the Jülich Supercomputing Centre. J. Large-Scale Res. Facil. 5(A171) (2019). http://dx.doi.org/10.17815/jlsrf-5-171
Kalvari, I., et al.: RFAM 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46(D1), D335–D342 (2017). https://doi.org/10.1093/nar/gkx1038
Kaplan, J., et al.: Scaling laws for neural language models. arXiv preprint arXiv:2001.08361 (2020)
Kolesnikov, A., et al.: Big transfer (bit): general visual representation learning. In: Vedaldi, A., Bischof, H., Brox, T., Frahm, J.M. (eds.) Computer Vision - ECCV 2020, pp. 491–507. Springer, Cham (2020)
Krizhevsky, A., Sutskever, I., Hinton, G.E.: ImageNet classification with deep convolutional neural networks. Adv. Neural. Inf. Process. Syst. 25, 1097–1105 (2012)
Kurth, T., et al.: Exascale deep learning for climate analytics. In: SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, pp. 649–660. IEEE (2018)
Laanait, N., et al.: Exascale deep learning for scientific inverse problems. arXiv preprint arXiv:1909.11150 (2019)
Lee, A.X., Zhang, R., Ebert, F., Abbeel, P., Finn, C., Levine, S.: Stochastic adversarial video prediction. arXiv preprint arXiv:1804.01523 (2018)
Lee, S., Purushwalkam, S., Cogswell, M., Crandall, D.J., Batra, D.: Why M heads are better than one: Training a diverse ensemble of deep networks. CoRR abs/1511.06314 (2015). http://arxiv.org/abs/1511.06314
Liu, H., Simonyan, K., Vinyals, O., Fernando, C., Kavukcuoglu, K.: Hierarchical representations for efficient architecture search. arXiv e-prints arXiv:1711.00436, November 2017
Lorenzo, P.R., Nalepa, J., Ramos, L., Ranilla, J.: Hyper-parameter selection in deep neural networks using parallel particle swarm optimization. In: Proceedings of the Genetic and Evolutionary Computation Conference Companion (2017)
Mattson, P., et al.: MLPerf: an industry standard benchmark suite for machine learning performance. IEEE Micro 40(2), 8–16 (2020)
Message Passing Interface Forum: MPI: A Message-Passing Interface Standard, Version 3.1. High Performance Computing Center Stuttgart (HLRS) (2015). https://fs.hlrs.de/projects/par/mpi//mpi31/
Muller, U.A., Gunzinger, A.: Neural net simulation on parallel computers. In: Proceedings of 1994 IEEE International Conference on Neural Networks (ICNN 1994), vol. 6, pp. 3961–3966 (1994). https://doi.org/10.1109/ICNN.1994.374845
Orhan, E., Gupta, V., Lake, B.M.: Self-supervised learning through the eyes of a child. In: Advances in Neural Information Processing Systems, vol. 33 (2020)
Paszke, A., et al.: PyTorch: an imperative style, high-performance deep learning library. In: Advances in Neural Information Processing Systems, vol. 32, pp. 8024–8035. Curran Associates, Inc. (2019). http://papers.neurips.cc/paper/9015-pytorch-an-imperative-style-high-performance-deep-learning-library.pdf
Patton, R.M., et al.: Exascale deep learning to accelerate cancer research. In: 2019 IEEE International Conference on Big Data (Big Data), pp. 1488–1496. IEEE (2019)
Razavian, A.S., Azizpour, H., Sullivan, J., Carlsson, S.: CNN features off-the-shelf: an astounding baseline for recognition. In: Proceedings of IEEE Conference on Computer Vision and Pattern Recognition Workshops, pp. 512–519, June 2014. https://doi.org/10.1109/CVPRW.2014.131
Reichstein, M., Camps-Valls, G., Stevens, B., Jung, M., Denzler, J., Carvalhais, N.: Prabhat: deep learning and process understanding for data-driven Earth system science. Nature (2019). https://doi.org/10.1038/s41586-019-0912-1
Ren, J., et al.: Zero-offload: Democratizing billion-scale model training (2021)
Rocklin, M.: Dask: parallel computation with blocked algorithms and task scheduling. In: Huff, K., Bergstra, J. (eds.) Proceedings of the 14th Python in Science Conference (SciPy 2015), pp. 130–136 (2015)
Russakovsky, O., et al.: Imagenet large scale visual recognition challenge. Int. J. Comput. Vision 115(3), 211–252 (2015)
Schmitt, M., Hughes, L.: Sen12ms
Schug, A., Weigt, M., Onuchic, J.N., Hwa, T., Szurmant, H.: High-resolution protein complexes from integrating genomic information with molecular simulation. Proc. Natl. Acad. Sci. 106(52), 22124–22129 (2009)
Senior, A.W., et al.: Improved protein structure prediction using potentials from deep learning. Nature 577(7792), 706–710 (2020). https://doi.org/10.1038/s41586-019-1923-7
Sergeev, A., Balso, M.D.: Horovod: Fast and Easy Distributed Deep Learning in TensorFlow. arXiv preprint arXiv:1802.05799 (2018)
Shallue, C.J., Lee, J., Antognini, J., Sohl-Dickstein, J., Frostig, R., Dahl, G.E.: Measuring the effects of data parallelism on neural network training. J. Mach. Learn. Res. 20, 1–49 (2019)
Shi, X., et al.: Convolutional lstm network: A machine learning approach for precipitation nowcasting. In: Advances in Neural Information Processing Systems (2015)
Sriram, A., et al.: Covid-19 deterioration prediction via self-supervised representation learning and multi-image prediction. arXiv preprint arXiv:2101.04909 (2021)
Stodden, V., et al.: Enhancing reproducibility for computational methods. Science 354(6317), 1240–1241 (2016)
Subramoney, A., et al.: Igitugraz/l2l: v1.0.0-beta, March 2019. https://doi.org/10.5281/zenodo.2590760
Sumbul, G., Charfuelan, M., Demir, B., Markl, V.: BigEarthNet: a large-scale benchmark archive for remote sensing image understanding. In: Proceedings of the IEEE International Geoscience and Remote Sensing Symposium (IGARSS) (2019). https://doi.org/10.1109/igarss.2019.8900532
Sumbul, G., Kang, J., Kreuziger, T., Marcelino, F., Costa, H., et al.: BigEarthNet dataset with a new class-nomenclature for remote sensing image understanding (2020). http://arxiv.org/abs/2001.06372
Uguzzoni, G., Lovis, S.J., Oteri, F., Schug, A., Szurmant, H., Weigt, M.: Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis. Proc. Natl. Acad. Sci. 114(13), E2662–E2671 (2017)
Vogels, T., Karimireddy, S.P., Jaggi, M.: PowerSGD: practical low-rank gradient compression for distributed optimization. In: Wallach, H., Larochelle, H., Beygelzimer, A., d’ Alché-Buc, F., Fox, E., Garnett, R. (eds.) Advances in Neural Information Processing Systems, vol. 32. Curran Associates, Inc. (2019). https://proceedings.neurips.cc/paper/2019/file/d9fbed9da256e344c1fa46bb46c34c5f-Paper.pdf
Wang, L., Lin, Z.Q., Wong, A.: COVID-net: a tailored deep convolutional neural network design for detection of COVID-19 cases from chest x-ray images. Sci. Rep. 10, 19549 (2020). https://doi.org/10.1038/s41598-020-76550-z
Wehbe, R.M., et al.: DeepCOVID-XR: an artificial intelligence algorithm to detect COVID-19 on chest radiographs trained and tested on a large U.S. clinical data set. Radiology 299, E167–E176 (2021). https://doi.org/10.1148/radiol.2020203511
Weigt, M., White, R.A., Szurmant, H., Hoch, J.A., Hwa, T.: Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Nat. Acad. Sci. 106(1), 67–72 (2009)
Zerihun, M.B., Pucci, F., Peter, E.K., Schug, A.: pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences. Bioinformatics 36(7), 2264–2265 (2020)
Zerihun, M.B., Pucci, F., Schug, A.: Coconet: boosting RNA contact prediction by convolutional neural networks. bioRxiv (2020)
Zhang, D., et al.: The AI index 2021 annual report, Technical report. AI Index Steering Committee, Human-Centered AI Institute, Stanford University, Stanford, CA (2021)
Zhang, S., Choromanska, A.E., LeCun, Y.: Deep learning with elastic averaging SGD. In: Cortes, C., Lawrence, N., Lee, D., Sugiyama, M., Garnett, R. (eds.) Advances in Neural Information Processing Systems, vol. 28. Curran Associates, Inc. (2015). https://proceedings.neurips.cc/paper/2015/file/d18f655c3fce66ca401d5f38b48c89af-Paper.pdf
Acknowledgements
This work was funded by Helmholtz Association’s Initiative and Networking Fund under project number ZT-I-0003 and HelmholtzAI computing resources (HAICORE) Funding has been obtained through grants ERC-2017-ADG 787576 (IntelliAQ) and BMBF 01 IS 18O47A (DeepRain). This work was performed in the CoE RAISE and DEEP-EST projects receiving funding from EU’s Horizon 2020 Research and Innovation Framework Programme under the grant agreement no. 951733 and no. 754304 respectively. We thank ECMWF for providing ERA-5 data. The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this work by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputers JUWELS, JUWELS Booster at Jülich Supercomputing Centre (JSC) and we acknowledge computing resources from the Helmholtz Data Federation. Further computing time was provided on supercomputer JUSUF in frame of offer for epidemiology research on COVID-19 by JSC.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this paper
Cite this paper
Kesselheim, S. et al. (2021). JUWELS Booster – A Supercomputer for Large-Scale AI Research. In: Jagode, H., Anzt, H., Ltaief, H., Luszczek, P. (eds) High Performance Computing. ISC High Performance 2021. Lecture Notes in Computer Science(), vol 12761. Springer, Cham. https://doi.org/10.1007/978-3-030-90539-2_31
Download citation
DOI: https://doi.org/10.1007/978-3-030-90539-2_31
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-90538-5
Online ISBN: 978-3-030-90539-2
eBook Packages: Computer ScienceComputer Science (R0)