Speaker
Dr
Giacinto Donvito
(INFN-BARI)
Description
One of the problems encountered while porting, in the
framework of the BIOINFOGRID EU
project, bioinformatics applications to the GRID, concerns
their input-output.
Many of the widely used tools in bioinformatics, have been
developed when the grid
technology was not yet established, so they make their
input out from the computer
local disk.
To port such an application on the grid, one has to handle
case when the WN local
disk has a local disk not sufficient to contain the job
input output files as well as
cases when the WM is completely disk less.
In such cases it is difficult to change the application
code, which generally was not
developed by the researcher, and sometimes it also difficult
to make use of specific
libraries that could allow the remote file access.
Parrot represents a possible solution to the problem since
it allow the use of a
variety of protocols to map the file-system call, such for
example gridftp and http.
We will report on a development to further improve the
versatility of Parrot and its
usability on the EGEE infrastructure. In particular we have
developed a plugin for
Parrot which uses the GFAL API directly. In this case the
application can run using
only the Logical File Name (LFN) of the required input
output files and does not
have to worry about the details of the underlying storage
system use in the EGEE grid.
Along the same line we have also developed a similar
filesystem which will use GFAL
API and FUSE. As FUSE is the most widely used system to
use remote file services as
a local file on linux. Fuse also has been integrated in
linux kernel and this makes
more easy to implement it on linux environment.
Now we are involved in an intense testing of both the two
implementation.
The most important Grid services involved in this work are
the Storage Services and
the File Catalog Services.
References:
1) Parrot: http://www.cse.nd.edu/~ccl/software/parrot/
2) FUSE: http://fuse.sourceforge.net/
Author
Dr
Giacinto Donvito
(INFN-BARI)
Co-authors
Prof.
Giorgio MAGGI
(INFN-BARI and Politecnico Bari)
Dr
Vihang DUDALKAR
(Università of Bari)