Difference between revisions of "EGI-InSPIRE:Serbia-US-QR12"

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[[Category:NGI US QR Reports]]
 
 
<!-- VERY IMPORTANT
 
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This report covers support activities to existing user communities, and belongs to EGI-InSPIRE SA1 (Task SA1.7 - Support Teams). The outreach to new communities activities that NGIs perform under NA2 are gathered through the Virtual Teams. However, there may be outreach activities that do outside of VTs. You can report about these in your 2.2.3 paragraph as well.
 
This report covers support activities to existing user communities, and belongs to EGI-InSPIRE SA1 (Task SA1.7 - Support Teams). The outreach to new communities activities that NGIs perform under NA2 are gathered through the Virtual Teams. However, there may be outreach activities that do outside of VTs. You can report about these in your 2.2.3 paragraph as well.
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!scope="col"|Publication title||Journal / Proceedings title||align="left" |Journal references<br> ''Volume number<br> Issue<br><br>Pages from - to''||align="left" |Authors ''<br>1.<br>2.<br>3.<br>Et al?''
 
!scope="col"|Publication title||Journal / Proceedings title||align="left" |Journal references<br> ''Volume number<br> Issue<br><br>Pages from - to''||align="left" |Authors ''<br>1.<br>2.<br>3.<br>Et al?''
 
|-
 
|-
 +
| Lattice Dynamics of KNi2Se2
 +
| Phys. Rev. B
 +
| 87 (2013) 144305; DOI: [http://dx.doi.org/10.1103/PhysRevB.87.144305 10.1103/PhysRevB.87.144305]
 +
| 1. N. Lazarevic<br>2. M. M. Radonjic<br>3. M. Scepanovic<br>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: [http://dx.doi.org/10.1088/0953-4075/46/6/065303 10.1088/0953-4075/46/6/065303]
 +
| 1. H. Al-Jibbouri<br>2. I. Vidanovic<br>3. A. Balaz<br>Et al.
 +
|-
 +
| Spin Modulation Instabilities and Phase Separation Dynamics in Trapped Two-component Bose Condensates
 +
| New J. Phys.
 +
| 15 (2013) 035008; DOI: [http://dx.doi.org/10.1088/1367-2630/15/3/035008 10.1088/1367-2630/15/3/035008]
 +
| 1. I. Vidanovic<br>2. N. J. van Druten<br>3. M. Haque
 +
|-
 +
| A Comparative Study of Electronic Properties of Disordered Conjugated Polymers
 +
| Phys. Chem. Chem. Phys.
 +
| 15 (2013) 3542; DOI: [http://dx.doi.org/10.1039/C3CP43115K 10.1039/C3CP43115K]
 +
| 1. N. Vukmirovic
 +
|-
 +
| Monte Carlo Simulations of Crystalline Organic Semiconductors
 +
| SJEE
 +
| 10 (2013) 125-134; DOI: [http://dx.doi.org/10.2298/SJEE1301125M 10.2298/SJEE1301125M]
 +
| 1. M. Mladenovic<br>2. I. E. Stankovic
 +
|-
 +
| Efficient Routing on Small Complex Networks Without Buffers
 +
| Physica A
 +
| 392 (2013) 2294; DOI: [http://dx.doi.org/10.1016/j.physa.2013.01.033 10.1016/j.physa.2013.01.033]
 +
| 1. J. Smiljanic<br>2. I. E. Stankovic
 
|}
 
|}
  
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===2.1. User Support achievements===
 
===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===
 
===2.2. Plans===
  
 +
Certification of AEGIS09-FTN-KM Grid site from Kosovska Mitrovica has been successfully finalized in Q12. During the Q13, several applications from the existing NGI_AEGIS Grid software stack will be deployed on this site.
  
 
===2.3. Issues and mitigation===
 
===2.3. Issues and mitigation===

Latest revision as of 11:42, 23 January 2015

EGI Inspire Main page


Inspire reports menu: Home SA1 weekly Reports SA1 Task QR Reports NGI QR Reports NGI QR User support Reports




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; DOI: 10.1103/PhysRevB.87.144305 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

Certification of AEGIS09-FTN-KM Grid site from Kosovska Mitrovica has been successfully finalized in Q12. During the Q13, several applications from the existing NGI_AEGIS Grid software stack will be deployed on this site.

2.3. Issues and mitigation

Issue Description Mitigation Description