To generate Data/Table(Fact tables/dimension table) in MYSQL DB From difference source like files/different DB - Data Integration tool comes in to picture .
To create Schema on top of Fact tables - Mondrian tool
To handle user/roles on top of created cubes -Meta data editor
To create simple reports on top of small tables - Report Designer
For sequential Execution (at a go) usage of DI jobs/transformation , Reports, Java script - Design Studio
thanks to user surya.thanuri @ forums.pentaho.com
The Data Integration tool is mostly for ETL, it's a separate tool and you can ignore it unless you are doing complex analysis of data from multiple dissimilar data sources. You don't need to 'export' reports to the pentaho server, you can write them directly to a directory then refresh the repository from inside the Pentaho web application. Exporting them is just one workflow technique.
You're going to find that there are about a dozen ways to do any one thing with Pentaho. For instance I use the CDA datasources with my reports vice placing the sql code inside my report. Alternatively you can link up to a Data Integration server to execute the Data Integration scripts to view a result set.
Just to answer your datamart question. In general a datamart should probably be supported by either the Data Integration tool (depending on your situation I don't exactly recommend this) or database functions/replication streams (recommended).
Just to hazard a guess, it sounds like someone tossed you a project saying: We need a BI system, here's the database where the data is stored, here are the reports we're already getting. X looked at Pentaho and liked it. You should use that.
First thing you need to do is understand the shape of the data, volume, tables, interrelations. Figure out what the real questions they want to answer are. Determine whether they need real time reporting, etc..etc. Just getting the datamart together itself, if you even need one, can take quite awhile. I think you may have jumped the gun on Pentaho itself.
thanks to user flamierd @ forums.pentaho.com