GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry
Based on the analysis of modern tools for creating GRID-type information systems that are part of the European EGI “standard” – UMD repository (including new versions of Globus Toolkit, ARC, dCache, etc.), the applying of GRID systems for computational chemistry is briefly discussed. The GRID system...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Yaroslavl State University
2019-09-01
|
| Series: | Моделирование и анализ информационных систем |
| Subjects: | |
| Online Access: | https://www.mais-journal.ru/jour/article/view/1229 |
| _version_ | 1797877935417327616 |
|---|---|
| author | Nikolay A. Anikin Alexander Y. Muskatin Mikhail B. Kuzminsky Alexandr I. Rusakov |
| author_facet | Nikolay A. Anikin Alexander Y. Muskatin Mikhail B. Kuzminsky Alexandr I. Rusakov |
| author_sort | Nikolay A. Anikin |
| collection | DOAJ |
| description | Based on the analysis of modern tools for creating GRID-type information systems that are part of the European EGI “standard” – UMD repository (including new versions of Globus Toolkit, ARC, dCache, etc.), the applying of GRID systems for computational chemistry is briefly discussed. The GRID system created by the authors combines two clusters with Linux CentOS 7 and is based on software from UMD-4. The relevance and effectiveness of batch processing systems (we use Torque 4.2.10) in quantum chemical calculations is increased for mass calculations of docking complexes (including for drug modeling problems), for which an improved semiempirical method with more efficient approximations was proposed, implemented in the Fortran-95 LSSDOCK software package. For such calculations, new approximation methods have been developed, including for DFT functionals, and their software implementation is carried out. Converters of calculation results by LSSDOCK into a natural for GRID XML-based format CML version 3 are developed. Using the CML format based on dCache software, a single tree of a virtual GRID filesystem distributed between heterogeneous nodes is used to store the results of LSSDOCK calculations. |
| first_indexed | 2024-04-10T02:25:51Z |
| format | Article |
| id | doaj.art-3394c853809a467aa402d3e25cdcad5b |
| institution | Directory Open Access Journal |
| issn | 1818-1015 2313-5417 |
| language | English |
| last_indexed | 2024-04-10T02:25:51Z |
| publishDate | 2019-09-01 |
| publisher | Yaroslavl State University |
| record_format | Article |
| series | Моделирование и анализ информационных систем |
| spelling | doaj.art-3394c853809a467aa402d3e25cdcad5b2023-03-13T08:07:30ZengYaroslavl State UniversityМоделирование и анализ информационных систем1818-10152313-54172019-09-0126336036410.18255/1818-1015-2019-3-360-364915GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum ChemistryNikolay A. Anikin0Alexander Y. Muskatin1Mikhail B. Kuzminsky2Alexandr I. Rusakov3Институт органической химии им. Н. Д. Зелинского Российской академии наукИнститут органической химии им. Н. Д. Зелинского Российской академии наукИнститут органической химии им. Н. Д. Зелинского Российской академии наукЯрославский государственный университет им. П. Г. ДемидоваBased on the analysis of modern tools for creating GRID-type information systems that are part of the European EGI “standard” – UMD repository (including new versions of Globus Toolkit, ARC, dCache, etc.), the applying of GRID systems for computational chemistry is briefly discussed. The GRID system created by the authors combines two clusters with Linux CentOS 7 and is based on software from UMD-4. The relevance and effectiveness of batch processing systems (we use Torque 4.2.10) in quantum chemical calculations is increased for mass calculations of docking complexes (including for drug modeling problems), for which an improved semiempirical method with more efficient approximations was proposed, implemented in the Fortran-95 LSSDOCK software package. For such calculations, new approximation methods have been developed, including for DFT functionals, and their software implementation is carried out. Converters of calculation results by LSSDOCK into a natural for GRID XML-based format CML version 3 are developed. Using the CML format based on dCache software, a single tree of a virtual GRID filesystem distributed between heterogeneous nodes is used to store the results of LSSDOCK calculations.https://www.mais-journal.ru/jour/article/view/1229gridumdweb-сервисыраспределенная файловая системаcmlквантовая химиядокинг-комплексы |
| spellingShingle | Nikolay A. Anikin Alexander Y. Muskatin Mikhail B. Kuzminsky Alexandr I. Rusakov GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry Моделирование и анализ информационных систем grid umd web-сервисы распределенная файловая система cml квантовая химия докинг-комплексы |
| title | GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry |
| title_full | GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry |
| title_fullStr | GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry |
| title_full_unstemmed | GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry |
| title_short | GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry |
| title_sort | grid system based on european egi standards for large scale calculations using the original accelerated method of quantum chemistry |
| topic | grid umd web-сервисы распределенная файловая система cml квантовая химия докинг-комплексы |
| url | https://www.mais-journal.ru/jour/article/view/1229 |
| work_keys_str_mv | AT nikolayaanikin gridsystembasedoneuropeanegistandardsforlargescalecalculationsusingtheoriginalacceleratedmethodofquantumchemistry AT alexanderymuskatin gridsystembasedoneuropeanegistandardsforlargescalecalculationsusingtheoriginalacceleratedmethodofquantumchemistry AT mikhailbkuzminsky gridsystembasedoneuropeanegistandardsforlargescalecalculationsusingtheoriginalacceleratedmethodofquantumchemistry AT alexandrirusakov gridsystembasedoneuropeanegistandardsforlargescalecalculationsusingtheoriginalacceleratedmethodofquantumchemistry |