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A new way to submit high-throughput applications to Grid

Some of the recent bioinformatics applications, particularly the ones where the main goal is the search or the comparison of entire genomes, are highly demanding in terms of computational resources. Due to this reason, Grid technology appears to fit the requirements of such applications since it can provide the needed computational power as well as the storage resources to record the huge amount of data produced.


Grid environment, with its huge amount of storage and CPU power available, proves to be very effective when the applications can be divided in a number, that can even be large, of independent tasks. In this case each independent task can be assigned to one of the many Worker Nodes available over the full grid infrastructure with the effect of reducing the time needed to reach the solution. The drawback is that even simple problems may require the submission of a quite large number of jobs to the Grid. The Job Submission Tool (JST) was developed in order to simplify the submission, management and bookkeeping of large number of jobs required by particular bioinformatics use cases developed inside the LIBI and BioinfoGRID projects. JST has already been used with success to runĀ  a full listĀ  of bioinformatics applications on the INFNgrid and EGEE Grid infrastructures. So far, the job submission to the grid has been performed by teams including the JST developers. The latest evolution in JST development aims to simplify, standardize and automatize the creation of the submission environment in order to give to the JST-non-expert user of the targeted communities the complete control of its jobs submission. This prototype WEB interface to JST has been set up and it is now under evaluation. It represent an important step in order to give-back to application users the complete control over the jobs execution, without requiring any deep knowledge of Grid mechanism.

Another line of development, in strive to reach non-EGI expert user, is the JST as web services RESTfull or SOAP (see http://pos.sissa.it/archive/conferences/162/029/EGICF12-EMITC2_029.pdf). In this approach is possible to call the service as standalone in a browser or within an arbitrary complex orchestration call of different service in a workflow engine. Given the requirement to exchange medium-large sized file the JST web service is coupled with a web dav service that allow machine-machine or machine-human file exchange. This kind of approach was developed in conjunction with CNR-ITB (Saverio Vicario) within the frame of the BioVel project (www.biovel.eu).