Use Cases

1. LAGO

The Latin America Giant Observatory (LAGO - first known as Large Aperture Gamma Ray Observatory, http://labdpr.cab.cnea.gov.ar/lago/colab.php) project is a recent collaboration that counts on Water Cherenkov Detectors in 9 Latin American countries, more than 80 Latin American researchers and a close collaboration with European teams such as IN2P3 in France and INFN in Italy. LAGO use-case success story is based on the DART challenge. The consortium maintains a repository of astrophysics interest that is based on DSpace and uses the Corsika code to study the astroparticle clusters. The LAGO repository has been integrated in the CHAIN-REDS Knowledge Base and the Semantic Search Engine. Al The best strategy for assigning PIDs to the current datasets and to the new data produced as a result of the Corsika executions is currently also being analysed. LAGO will address 3 different phenomena thanks to the CHAIN-REDS DART workflow. More than 21,000 CPU hours have been consumed via the CHAIN-REDS Science Gateway.

2. APHRC

The African Population and Health Research Centre (APHRC) undertakes research in a wide range of topics related to societal health and well-being. APHRC runs around 60 projects, publishes around 60 papers, and trains more than 150 fellows per year. To do so, it counts on 18 donors and 51 partners. This use-case supports data management including assignment of Persistent IDentifiers (PIDs) to the wide plethora of datasets that APHRC manages and curates. This is of utmost importance since these datasets are widely used by almost every country in Africa in order to improve societal health and well-being. APHRC and CHAIN-REDS have first identified which repositories must be catered for and then defined a road-map for making data labelling: the PIDs are being assigned to an entire data set at the top-level. The software being used to document the data is Nesstar (www.nesstar.com).

3. TreeThreader

Knowing the protein structures is essential for a complete understanding of life processes at the molecular level. Threading is the leading method for protein structure prediction, and it is exceedingly time-consuming. The TreeThreader code uses a new practical threading program, which can take pairwise interaction into consideration. TreeThreader can run on a Linux platform and on a volunteer computing e-Infrastructure using the CAS@home BOINC client and consuming around 6 million of CPU hours a year. The code is already available to the desktop computing community, and is now made available on a full-blown e-Infrastructure: virtual machines launched from physical servers belonging to the China ROC and managed with OpenStack. Around 38,600 CPU hours have been consumed on the CHAIN-REDS cloud nodes. For making the use of the new pool of computing resources (BOINC and cloud) easy to use for the scientist, all TreeThreader jobs can be submitted both within China and Europe.

4. GROMACS

Researchers are trying to observe molecular activity of various bio-molecules using molecular dynamics simulation approach. The GROMACS software package is used for molecular dynamics simulation. These kinds of studies present huge computational demand. That is the reason why GROMACS version to be used in this use-case success story is v4.6.5: due to its full-blown MPI capabilities. 14 European, Arab and Indian Grid sites have already been enabled with GROMACS version with 2 flavours: both an installation package and a Science Gateway portlet. In addition, new services related to eTokenServer, GridEngine and wiki pages have been created as well.

5: ABINIT

Due the significant development of the ab-initio calculations especially the Density Functional Theory (DFT) in the fields of quantum chemistry and the physics of materials, the calculations in those areas become vital. Therefore introducing powerful code such as ABINIT within the Grid computing environment facilitates this task for the researchers. To implement this, a team of ABINIT users (mainly from the Arab region) attended the CHAIN-REDS Science Gateway porting school held in Catania in June 2014 and ported to the Grid both sequential and MPI ABINIT versions, the latter of which is v7.6.4 with OpenMPI v1.8.1 enabled. These versions have been installed in 6 European and Arab sites and the required portlet for job submission has been implemented; this activity will be extended to Latin America in the near future.