Evaluating the Parallel Simulation of Dynamics of Electrons in Molecules on AWS Spot Instances
Resumo
In this paper, we evaluate the cost-effectiveness and performance of simulating the dynamics of electrons in molecules on AWS and investigate the implications of using various types of storage solutions, contrasting the results with those obtained on a traditional HPC cluster. Our findings reveal key insights into the computational efficiency and cost-effectiveness of these diverse platforms, contributing to the critical discourse on how to optimally harness the power of modern computing infrastructures for complex molecular simulations.
Referências
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Buyya, R. et al. (2019). A Manifesto for Future Generation Cloud Computing: Research Directions for the Next Decade. ACM Computing Surveys, 51(5).
Carter, E. A. (2008). Challenges in modeling materials properties without experimental input. Science, 321(5890):800–803.
Ciccotti, G., Dellago, C., Ferrario, M., Hernández, E., and Tuckerman, M. (2022). Molecular simulations: past, present, and future (a topical issue in epjb). The European Physical Journal B, 95.
Dancheva, T., Alonso, U., and Bartoň, M. (2023). Cloud benchmarking and performance analysis of an hpc application in amazon ec2. Cluster Computing, pages 1–18.
De Vivo, M., Masetti, M., Bottegoni, G., and Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9):4035–4061. PMID: 26807648.
Evers, F., Korytár, R., Tewari, S., and van Ruitenbeek, J. M. (2020). Advances and challenges in single-molecule electron transport. Rev. Mod. Phys., 92:035001.
Fernandez, A. (2022). Evaluation of the performance of tightly coupled parallel solvers and mpi communications in iaas from the public cloud. IEEE Transactions on Cloud Computing, 10(4):2613–2622.
Marcus, R. A. (1993). Electron transfer reactions in chemistry. theory and experiment. Rev. Mod. Phys., 65:599–610.
Mell, P. M. and Grance, T. (2011). SP 800-145. The NIST Definition of Cloud Computing. Technical report, National Institute of Standards & Technology, Gaithersburg, MD, USA.
Munhoz, V. and Castro, M. (2022). HPC@Cloud: A provider-agnostic software framework for enabling hpc in public cloud platforms. In Anais do Simpósio em Sistemas Computacionais de Alto Desempenho (WSCAD), pages 157–168, Florianópolis. Brazilian Computer Society.
Munhoz, V., Castro, M., and Mendizabal, O. (2022). Strategies for fault-tolerant tightly-coupled hpc workloads running on low-budget spot cloud infrastructures. In IEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pages 263–272, Bordeaux. IEEE Computer Society.
Netto, M., Calheiros, R., Rodrigues, E., Cunha, R., and Buyya, R. (2018). HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges. ACM Computing Surveys, 51.
Ollitrault, P. J., Miessen, A., and Tavernelli, I. (2021). Molecular quantum dynamics: A quantum computing perspective. Accounts of Chemical Research, 54(23):4229–4238. PMID: 34787398.
Sena, A. C., Boeres, C., Teylo, L., Drummond, L. M. A., and Rebello, V. E. F. (2023). Harnessing Low-Cost Virtual Machines on the Spot, pages 163–189. Springer International Publishing, Cham.
Sharma, P. and Jadhao, V. (2021). Molecular dynamics simulations on cloud computing and machine learning platforms. In IEEE International Conference on Cloud Computing (CLOUD), pages 751–753.
Shu, Y., Zhang, L., Sun, S., and Truhlar, D. G. (2020). Time-derivative couplings for self-consistent electronically nonadiabatic dynamics. Journal of Chemical Theory and Computation, 16(7):4098–4106.
Teylo, L., Arantes, L., Sens, P., and Drummond, L. M. d. A. (2021). Scheduling Bag-of-Tasks in Clouds using Spot and Burstable Virtual Machines. IEEE Transactions on Cloud Computing, pages 1–1.
Torres, A., Prado, L. R., Bortolini, G., and Rego, L. G. C. (2018). Charge transfer driven structural relaxation in a push–pull azobenzene dye–semiconductor complex. The Journal of Physical Chemistry Letters, 9(20):5926–5933.
Wang, C., Liang, Q., and Urgaonkar, B. (2018). An empirical analysis of amazon ec2 spot instance features affecting cost-effective resource procurement. ACM Trans. Model. Perform. Eval. Comput. Syst., 3(2).
Yu, Q., Alonso, A. M., Caminiti, J., Beck, K. M., Sutherland, R. T., Leibfried, D., Rodriguez, K. J., Dhital, M., Hemmerling, B., and Häffner, H. (2022). Feasibility study of quantum computing using trapped electrons. Phys. Rev. A, 105:022420.
Zhou, A. C., Lao, J., Ke, Z., Wang, Y., and Mao, R. (2022). Farspot: Optimizing monetary cost for hpc applications in the cloud spot market. IEEE Transactions on Parallel and Distributed Systems, 33(11):2955–2967.
Brum, R., Teylo, L., Arantes, L., and Sens, P. (2023). Ensuring Application Continuity with Fault Tolerance Techniques, pages 191–212. Springer International Publishing, Cham.
Buyya, R. et al. (2019). A Manifesto for Future Generation Cloud Computing: Research Directions for the Next Decade. ACM Computing Surveys, 51(5).
Carter, E. A. (2008). Challenges in modeling materials properties without experimental input. Science, 321(5890):800–803.
Ciccotti, G., Dellago, C., Ferrario, M., Hernández, E., and Tuckerman, M. (2022). Molecular simulations: past, present, and future (a topical issue in epjb). The European Physical Journal B, 95.
Dancheva, T., Alonso, U., and Bartoň, M. (2023). Cloud benchmarking and performance analysis of an hpc application in amazon ec2. Cluster Computing, pages 1–18.
De Vivo, M., Masetti, M., Bottegoni, G., and Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9):4035–4061. PMID: 26807648.
Evers, F., Korytár, R., Tewari, S., and van Ruitenbeek, J. M. (2020). Advances and challenges in single-molecule electron transport. Rev. Mod. Phys., 92:035001.
Fernandez, A. (2022). Evaluation of the performance of tightly coupled parallel solvers and mpi communications in iaas from the public cloud. IEEE Transactions on Cloud Computing, 10(4):2613–2622.
Marcus, R. A. (1993). Electron transfer reactions in chemistry. theory and experiment. Rev. Mod. Phys., 65:599–610.
Mell, P. M. and Grance, T. (2011). SP 800-145. The NIST Definition of Cloud Computing. Technical report, National Institute of Standards & Technology, Gaithersburg, MD, USA.
Munhoz, V. and Castro, M. (2022). HPC@Cloud: A provider-agnostic software framework for enabling hpc in public cloud platforms. In Anais do Simpósio em Sistemas Computacionais de Alto Desempenho (WSCAD), pages 157–168, Florianópolis. Brazilian Computer Society.
Munhoz, V., Castro, M., and Mendizabal, O. (2022). Strategies for fault-tolerant tightly-coupled hpc workloads running on low-budget spot cloud infrastructures. In IEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pages 263–272, Bordeaux. IEEE Computer Society.
Netto, M., Calheiros, R., Rodrigues, E., Cunha, R., and Buyya, R. (2018). HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges. ACM Computing Surveys, 51.
Ollitrault, P. J., Miessen, A., and Tavernelli, I. (2021). Molecular quantum dynamics: A quantum computing perspective. Accounts of Chemical Research, 54(23):4229–4238. PMID: 34787398.
Sena, A. C., Boeres, C., Teylo, L., Drummond, L. M. A., and Rebello, V. E. F. (2023). Harnessing Low-Cost Virtual Machines on the Spot, pages 163–189. Springer International Publishing, Cham.
Sharma, P. and Jadhao, V. (2021). Molecular dynamics simulations on cloud computing and machine learning platforms. In IEEE International Conference on Cloud Computing (CLOUD), pages 751–753.
Shu, Y., Zhang, L., Sun, S., and Truhlar, D. G. (2020). Time-derivative couplings for self-consistent electronically nonadiabatic dynamics. Journal of Chemical Theory and Computation, 16(7):4098–4106.
Teylo, L., Arantes, L., Sens, P., and Drummond, L. M. d. A. (2021). Scheduling Bag-of-Tasks in Clouds using Spot and Burstable Virtual Machines. IEEE Transactions on Cloud Computing, pages 1–1.
Torres, A., Prado, L. R., Bortolini, G., and Rego, L. G. C. (2018). Charge transfer driven structural relaxation in a push–pull azobenzene dye–semiconductor complex. The Journal of Physical Chemistry Letters, 9(20):5926–5933.
Wang, C., Liang, Q., and Urgaonkar, B. (2018). An empirical analysis of amazon ec2 spot instance features affecting cost-effective resource procurement. ACM Trans. Model. Perform. Eval. Comput. Syst., 3(2).
Yu, Q., Alonso, A. M., Caminiti, J., Beck, K. M., Sutherland, R. T., Leibfried, D., Rodriguez, K. J., Dhital, M., Hemmerling, B., and Häffner, H. (2022). Feasibility study of quantum computing using trapped electrons. Phys. Rev. A, 105:022420.
Zhou, A. C., Lao, J., Ke, Z., Wang, Y., and Mao, R. (2022). Farspot: Optimizing monetary cost for hpc applications in the cloud spot market. IEEE Transactions on Parallel and Distributed Systems, 33(11):2955–2967.
Publicado
17/10/2023
Como Citar
MUNHOZ, Vanderlei; CASTRO, Márcio; REGO, Luis G. C..
Evaluating the Parallel Simulation of Dynamics of Electrons in Molecules on AWS Spot Instances. In: SIMPÓSIO EM SISTEMAS COMPUTACIONAIS DE ALTO DESEMPENHO (SSCAD), 24. , 2023, Porto Alegre/RS.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2023
.
p. 205-216.
DOI: https://doi.org/10.5753/wscad.2023.235765.
