EGI-InSPIRE:Serbia-US-QR12

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Revision as of 01:13, 1 May 2013 by Dusan (talk | contribs) (2.1. User Support achievements)
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Quarterly Report Number NGI Name Partner Name Author
QR12 NGI_AEGIS Institute of Physics Belgrade Dusan Vudragovic


1. MEETINGS AND DISSEMINATION

1.1. CONFERENCES/WORKSHOPS ORGANISED

Date Location Title Participants Outcome (Short report & Indico URL)


1.3. PUBLICATIONS

Publication title Journal / Proceedings title Journal references
Volume number
Issue

Pages from - to
Authors
1.
2.
3.
Et al?
Lattice Dynamics of KNi2Se2 Phys. Rev. B 87 (2013) 144305 1. N. Lazarevic
2. M. M. Radonjic
3. M. Scepanovic
Et al.
Geometric Resonances in Bose-Einstein Condensates with Two- and Three-body Interactions J. Phys. B: At. Mol. Opt. Phys. 46 (2013) 065303; DOI: 10.1088/0953-4075/46/6/065303 1. H. Al-Jibbouri
2. I. Vidanovic
3. A. Balaz
Et al.
Spin Modulation Instabilities and Phase Separation Dynamics in Trapped Two-component Bose Condensates New J. Phys. 15 (2013) 035008; DOI: 10.1088/1367-2630/15/3/035008 1. I. Vidanovic
2. N. J. van Druten
3. M. Haque
A Comparative Study of Electronic Properties of Disordered Conjugated Polymers Phys. Chem. Chem. Phys. 15 (2013) 3542; DOI: 10.1039/C3CP43115K 1. N. Vukmirovic
Monte Carlo Simulations of Crystalline Organic Semiconductors SJEE 10 (2013) 125-134; DOI: 10.2298/SJEE1301125M 1. M. Mladenovic
2. I. E. Stankovic
Efficient Routing on Small Complex Networks Without Buffers Physica A 392 (2013) 2294; DOI: 10.1016/j.physa.2013.01.033 1. J. Smiljanic
2. I. E. Stankovic

2. ACTIVITY REPORT

2.1. User Support achievements

In Q12 NGI_AEGIS User Support team has continued to support Serbian Grid community in the use of already ported Grid applications. Beside of this day-to-day activity, the main focus was on the update of outdated applications available on NGI_AEGIS Grid sites, as well as on installation of new applications.

Together with Serbian chemistry community the following new applications have been deployed to AEGIS01-IPB-SCL Grid site:

  • MEAD, KARLSBERG and OEDocking. MEAD (Macroscopic Electrostatics with Atomic Detail) (http://www.stjuderesearch.org/site/lab/bashford) is a program used for including solvation effects in biological systems such as proteins using an atomic model of the protein.
  • KARLSBERG (http://agknapp.chemie.fu-berlin.de/karlsberg_old/) is a program for Monte-Carlo (MC) calculation of titration patterns of proteins. It will calculate the protonation probabilities for these titratable sites at given pH values.
  • OEDocking (http://www.eyesopen.com/oedocking) is a suite of well-validated molecular docking tools and their associated workflows provided by OpenEye. Each tool is specifically designed to address its own unique application to the docking problem.

NGI_AEGIS User Support team provided support to astrophysics researchers from the Astronomical Observatory Belgrade in preparation of large simulation of early universe on Grid. Smaller simulations were already ported and successfully executed on AEGIS01-IPB-SCL Grid site. Support is also provided to the mathematicians from the Mathematical Institute whose are advised how to use Grid to submit their parallel jobs (hybrid MPI/OpenMP and OpenMP jobs).

NGI_AEGIS Helpdesk (https://helpdesk.aegis.rs/) and NGI_AEGIS website (http://www.aegis.rs/) have been regularly maintained and updated in Q12. We have participated in testing of new GGUS releases and GGUS-NGI_AEGIS Helpdesk interface functionality. EGI AppDB (http://appdb.egi.eu/) has been updated with the new applications.

2.2. Plans

2.3. Issues and mitigation

Issue Description Mitigation Description