Grid Computing with Relativistic Quantum Chemistry Software
Case Study of Code Adaptation and Effective Deployment
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Abstract
We describe the adaptation of the scientific software DIRAC for the grid environment and provide the study of the code’s performance. The most effective approach for effective utilizing of the grid computing power is not relying upon program’s specific dependencies installed on grid servers, but rather in precise, local preparation of all necessary static executables and related scripting launchers. Running few functionality and performance tests before carrying out any production calculations with the code is recommended.
Keywords
DIRAC program suite Adaptation for grid computing Relativistic quantum chemistry Effective grid utilization Static executablePreview
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References
- 1.Magoules, F., Pan, J., Tan, K.A., Kumar, A.: Introduction to Grid Computing. Taylor & Francis, New York (2009)MATHGoogle Scholar
- 2.Wang, L., Jie, W., Chen, J.: Grid Computing: Infrastructure, Service, and Applications. Taylor & Francis, New York (2010)Google Scholar
- 3.Wilkinson, B.: Grid Computing: Techniques and Applications. CRC Press, Boca Raton (2011)Google Scholar
- 4.Preve, N.P.: Grid Computing. Springer, Berlin Heidelberg New York (2011)CrossRefGoogle Scholar
- 5.Coveney, P.V.: Scientific grid computing. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 363(1833), 1707 (2005). doi: 10.1098/rsta.2005.1632
- 6.Nishikawa, T., Nagashima, U., Sekiguchi, S.: Computational science ICCS 2003. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J.J., Zomaya, A.Y. (eds.) Lecture Notes in Computer Science no. 2659, pp. 244–253. Springer, Berlin HeidelbergCrossRefGoogle Scholar
- 7.Baldridge, K.K., Greenberg, J.P., Sudholt, W., Mock, S., Altintas, I., Amoreira, C., Potier, Y., Birnbaum, A., Bhatia, K., Taufer, M.: The computational chemistry prototyping environment. Proc. IEEE 93(3), 510 (2005). doi: 10.1109/JPROC.2004.842747 CrossRefGoogle Scholar
- 8.Sudholt, W., Altintas, I., Baldridge, K. In: Alexandrov, V.N., van Albada, G.D., Sloot, P.M.A., Dongarra, J.J. (eds.) Computational science ICCS 2006, vol. 3993, pp. 69–76. Springer, Berlin Heidelberg (2006)Google Scholar
- 9.Costantini, A., Gutierrez, E., Lopez Cacheiro, J., Rodriguez, A., Gervasi, O., Lagana, A.: Int. J. Web Grid Serv. 6(2), 141 (2010). doi: 10.1504/IJWGS.2010.033789 Google Scholar
- 10.Domingo, D., East, J. (eds.) Red hat enterprise linux 6 developer guide - an introduction to application development tools in red hat enterprise linux 6. Red Hat, Inc. and others (2010). Electronic bookGoogle Scholar
- 11.DIRAC: A relativistic ab initio electronic structure program, Release DIRAC12. written by Jensen, H.J.Aa., Bast, R. ,Saue, T. and Visscher, L. with contributions from Bakken, V., Dyall, K.G. , Dubillard, S., Ekström, U., Eliav, E., Enevoldsen, T.,Fleig, T.,Fossgaard, O., Gomes, A.S.P., Helgaker, T., Lærdahl, J.K., Lee, Y.S., Henriksson, J., Iliaš, M., Jacob, Ch.R., Knecht, S., Komorovský, S., Kullie, O., Larsen, C.V., Nataraj, H.S., Norman, P., Olejniczak, G., Olsen, J., Park, Y.C., Pedersen, J.K., Pernpointner, M., Ruud, K., Sałek, P., Schimmelpfennig, B., Sikkema, J., Thorvaldsen, A.J., Thyssen, J., van Stralen, J., Villaume, S., Visser, O., Winther, T., Yamamoto, S. (see http://www.diracprogram.org) (2012)
- 12.Dyall, K.G., Faegri, Jr, K.: Introduction to relativistic quantum chemistry. Oxford University Press, London (2007)Google Scholar
- 13.Reiher, M., Wolf, A.: Relativistic quantum chemistry: The fundamental theory of molecular science. Wiley, New York (2009). http://www.google.sk/books?id=YwSpxCfsNsEC CrossRefGoogle Scholar
- 14.Iliaš, M., Kellö, V., Urban, M.: Relativistic effects in atomic and molecular properties. Acta Phys. Slovaca Rev. Tutorials 60(3), 259 (2010). doi: 10.2478/v10155-010-0003-1 Google Scholar
- 15.Autschbach, J.: Perspective: Relativistic effects J. Chem. Phys. 136(15), 150902 (2012). http://scitation.aip.org/content/aip/journal/jcp/136/15/10.1063/1.3702628 CrossRefGoogle Scholar
- 16.DIRAC- web manual (search for static linking). www.diracprogram.org
- 17.Gomes, A., Merzky, A., Visscher, L.: In: Alexandrov, V., van Albada, G., Sloot, P., Dongarra, J. (eds.) Computational science ICCS, Lecture Notes in Computer Science, vol. 3993, pp. 97–104. Springer, Berlin Heidelberg (2006)Google Scholar
- 18.Intel compilers (Intel Developer Zone). http://software.intel.com/en-us/intel-compilers
- 19.Open MPI: open source high performance computing. http://www.open-mpi.org/
- 20.Python programming language official website. http://www.python.org/
- 21.CMake - cross platform make. http://www.cmake.org/
- 22.CDash - an open source ,web-based testing server. http://www.cdash.org/
- 23.DIRAC - dashboard. https://repo.theochem.kth.se/cdash/index.php?project=DIRAC
- 24.EGEE - VOCE. http://egee.cesnet.cz/en/voce/
- 25.COMPCHEM VO. https://www3.compchem.unipg.it/compchem/
- 26.Laganà, A., Riganelli, A., Gervasi, O.: In: Gavrilova, M., Gervasi, O., Kumar, V., Tan, C., Taniar, D., Lagan, A., Mun, Y., Choo, H. (eds.) Computational science and its applications - ICCSA. Lecture Notes in Computer Science, vol. 3980, pp. 665–674. Springer, Berlin Heidelberg (2006). doi: 10.1007/11751540_70
- 27.Laganà, A., Costantini, A., Gervasi, O., Lago, N., Manuali, C., Rampino, S.: COMPCHEM: progress towards GEMS a Grid Empowered Molecular Simulator and beyond. J. Grid Comput. 8(4), 571 (2010). doi: 10.1007/s10723-010-9164-x CrossRefGoogle Scholar
- 28.SIVVP. http://www.sivvp.sk/home/
- 29.EMI - European Middleware Initiative. http://www.eu-emi.eu/
- 30.JDL - Job description language. http://diracgrid.org/files/docs/UserGuide/GettingStarted/UserJobs/JDLReference/
- 31.Iliaš, M., Saue, T.: An infinite-order two-component relativistic Hamiltonian by a simple one-step transformation. J. Chem. Phys. 126(6), 064102 (2007). doi: 10.1063/1.2436882 CrossRefGoogle Scholar
- 32.Visscher, L., Eliav, E., Kaldor, U.: Formulation and implementation of the relativistic Fock-space coupled cluster method for molecules. J. Chem. Phys. 115(21), 9720 (2001). doi: 10.1063/1.1415746 CrossRefGoogle Scholar
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