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Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu

Year 2021, Volume: 33 Issue: 4, 609 - 613, 30.12.2021

Büşra Savaş Ezgi Karaca

https://doi.org/10.7240/jeps.920227

Abstract

Yüksek performanslı hesaplama sistemlerinin kullanımının artmasıyla, bu sistemlerde çalıştırılan programların performans optimizasyonu öncelikli hale gelmiştir. Bu duruma istinaden, bu çalışmamızda, yaygın olarak kullanılan moleküler dinamik paketi GROMACS’in, TÜBİTAK ULAKBİM tarafından kullanıma sunulan TRUBA hesaplama kümelerindeki en iyi performans kriterlerini bulmayı hedefledik. Performans tarama çalışmamız sırasında, farklı hesaplama kümelerinde, farklı CPU/GPU çekirdek oranı ve GROMACS versiyonlarını denedik. Bu süreç sonunda en iyi performanslı hesaplama kümesi akya-cuda, en iyi CPU/GPU çekirdek sayı oranı 40/1 ve en hızlı GROMACS versiyonu GROMACS 2020 olarak tespit edilmiştir. Benzer bir çalışma yürütecek araştırmacıların yararlanması adına, performans optimizasyon dosyalarımız ve ayrıntılı sonuçlarımız https://github.com/CSB-KaracaLab/gmx_performance_on_HPC adresinde incelemeye açılmıştır.

Keywords

Moleküler Dinamik Yüksek Başarımlı Hesaplama Kümeleri Optimizasyon GROMACS

Supporting Institution

TÜBİTAK

Project Number

119Z828

Thanks

Bu araştırma TÜBİTAK tarafından 1002 destek programı kapsamında 119Z828 numaralı proje ile desteklenmektedir. Yaptığı çalışmaların sonucu ile bu projenin ortaya çıkmasına yardımcı olan Deniz Doğan’a, desteklerinden dolayı TÜBİTAK’a teşekkür ederiz. Ayrıca bu çalışmadaki hesaplamaların TRUBA kaynaklarında yapılmasına olanak sağlayan TÜBİTAK ULAKBİM’e teşekkür ederiz.

References

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  • [2] Rahman, A. (1964). Correlations in the motion of atoms in liquid argon. Physical Review, 136(2A). https://doi.org/10.1103/PhysRev.136.A405
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  • [12] Kulis, M., & Esteller, M. (2010). DNA Methylation and Cancer. In Advances in Genetics (Vol. 70, Issue C). https://doi.org/10.1016/B978-0-12-380866-0.60002-2
  • [13] Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. In Nature Reviews Genetics (Vol. 11, Issue 3). https://doi.org/10.1038/nrg2719
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  • [16] Norvil, A. B., Petell, C. J., Alabdi, L., Wu, L., Rossie, S., & Gowher, H. (2018). Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry, 57(29). https://doi.org/10.1021/acs.biochem.6b00964
  • [17] TRUBA. https://www.truba.gov.tr/index.php/en/main-page/
  • [18] TRUBA Wiki Sayfası. http://wiki.truba.gov.tr/index.php/Ana_sayfa
  • [19] Ivani, I., Dans, P. D., Noy, A., Pérez, A., Faustino, I., Hospital, A., Walther, J., Andrio, P., Goñi, R., Balaceanu, A., Portella, G., Battistini, F., Gelpí, J. L., González, C., Vendruscolo, M., Laughton, C. A., Harris, S. A., Case, D. A., & Orozco, M. (2015). Parmbsc1: A refined force field for DNA simulations. Nature Methods, 13(1). https://doi.org/10.1038/nmeth.3658

Year 2021, Volume: 33 Issue: 4, 609 - 613, 30.12.2021

Büşra Savaş Ezgi Karaca

https://doi.org/10.7240/jeps.920227

Abstract

Project Number

119Z828

References

  • [1] Alder, B. J., & Wainwright, T. E. (1959). Studies in molecular dynamics. I. General method. The Journal of Chemical Physics, 31(2). https://doi.org/10.1063/1.1730376
  • [2] Rahman, A. (1964). Correlations in the motion of atoms in liquid argon. Physical Review, 136(2A). https://doi.org/10.1103/PhysRev.136.A405
  • [3] Páll, S., Abraham, M. J., Kutzner, C., Hess, B., & Lindahl, E. (2015). Tackling exascale software challenges in molecular dynamics simulations with GROMACS. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8759. https://doi.org/10.1007/978-3-319-15976-8_1
  • [4] Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2. https://doi.org/10.1016/j.softx.2015.06.001
  • [5] Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. In Journal of Computational Chemistry (Vol. 26, Issue 16). https://doi.org/10.1002/jcc.20289
  • [6] Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1–3). https://doi.org/10.1016/0010-4655(95)00041-D
  • [7] Bird, A. (2007). Perceptions of epigenetics. In Nature (Vol. 447, Issue 7143). https://doi.org/10.1038/nature05913
  • [8] Mazzio, E. A., & Soliman, K. F. A. (2012). Basic concepts of epigenetics impact of environmental signals on gene expression. In Epigenetics (Vol. 7, Issue 2). https://doi.org/10.4161/epi.7.2.18764
  • [9] Khavari, D. A., Sen, G. L., & Rinn, J. L. (2010). DNA methylation and epigenetic control of cellular differentiation. In Cell Cycle (Vol. 9, Issue 19). https://doi.org/10.4161/cc.9.19.13385
  • [10] Lee, J. H., Hart, S. R. L., & Skalnik, D. G. (2004). Histone Deacetylase Activity Is Required for Embryonic Stem Cell Differentiation. Genesis, 38(1). https://doi.org/10.1002/gene.10250
  • [11] Weinhold, B. (2006). Epigenetics: the science of change. Environmental Health Perspectives, 114(3). https://doi.org/10.1289/ehp.114-a160
  • [12] Kulis, M., & Esteller, M. (2010). DNA Methylation and Cancer. In Advances in Genetics (Vol. 70, Issue C). https://doi.org/10.1016/B978-0-12-380866-0.60002-2
  • [13] Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. In Nature Reviews Genetics (Vol. 11, Issue 3). https://doi.org/10.1038/nrg2719
  • [14] Chédin, F. (2011). The DNMT3 family of mammalian de novo DNA methyltransferases. In Progress in Molecular Biology and Translational Science (Vol. 101). https://doi.org/10.1016/B978-0-12-387685-0.00007-X
  • [15] Zhang, Z. M., Lu, R., Wang, P., Yu, Y., Chen, D., Gao, L., Liu, S., Ji, D., Rothbart, S. B., Wang, Y., Wang, G. G., & Song, J. (2018). Structural basis for DNMT3A-mediated de novo DNA methylation. Nature, 554(7692). https://doi.org/10.1038/nature25477
  • [16] Norvil, A. B., Petell, C. J., Alabdi, L., Wu, L., Rossie, S., & Gowher, H. (2018). Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry, 57(29). https://doi.org/10.1021/acs.biochem.6b00964
  • [17] TRUBA. https://www.truba.gov.tr/index.php/en/main-page/
  • [18] TRUBA Wiki Sayfası. http://wiki.truba.gov.tr/index.php/Ana_sayfa
  • [19] Ivani, I., Dans, P. D., Noy, A., Pérez, A., Faustino, I., Hospital, A., Walther, J., Andrio, P., Goñi, R., Balaceanu, A., Portella, G., Battistini, F., Gelpí, J. L., González, C., Vendruscolo, M., Laughton, C. A., Harris, S. A., Case, D. A., & Orozco, M. (2015). Parmbsc1: A refined force field for DNA simulations. Nature Methods, 13(1). https://doi.org/10.1038/nmeth.3658
There are 19 citations in total.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Research Articles
Authors

Büşra Savaş 0000-0002-6116-7950

Ezgi Karaca 0000-0002-4926-7991

Project Number 119Z828
Publication Date December 30, 2021
Published in Issue Year 2021 Volume: 33 Issue: 4

Cite

APA Savaş, B., & Karaca, E. (2021). Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu. International Journal of Advances in Engineering and Pure Sciences, 33(4), 609-613. https://doi.org/10.7240/jeps.920227
AMA Savaş B, Karaca E. Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu. JEPS. December 2021;33(4):609-613. doi:10.7240/jeps.920227
Chicago Savaş, Büşra, and Ezgi Karaca. “Türk Ulusal Bilim E-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu”. International Journal of Advances in Engineering and Pure Sciences 33, no. 4 (December 2021): 609-13. https://doi.org/10.7240/jeps.920227.
EndNote Savaş B, Karaca E (December 1, 2021) Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu. International Journal of Advances in Engineering and Pure Sciences 33 4 609–613.
IEEE B. Savaş and E. Karaca, “Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu”, JEPS, vol. 33, no. 4, pp. 609–613, 2021, doi: 10.7240/jeps.920227.
ISNAD Savaş, Büşra - Karaca, Ezgi. “Türk Ulusal Bilim E-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu”. International Journal of Advances in Engineering and Pure Sciences 33/4 (December 2021), 609-613. https://doi.org/10.7240/jeps.920227.
JAMA Savaş B, Karaca E. Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu. JEPS. 2021;33:609–613.
MLA Savaş, Büşra and Ezgi Karaca. “Türk Ulusal Bilim E-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu”. International Journal of Advances in Engineering and Pure Sciences, vol. 33, no. 4, 2021, pp. 609-13, doi:10.7240/jeps.920227.
Vancouver Savaş B, Karaca E. Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu. JEPS. 2021;33(4):609-13.