Im confused, why wouldnt you just use a single table, with file_num,item_num and num_val as the data? Presuming that we can use four bytes per field we have 12 bytes per record. Thus 1 million records is ~12MB, assuming 100 records per file, we are looking at 120 MB no?
My point here is that unless Im missing something (which i suspect I am) that neither of the ways you describe is how I would solve this problem with an RDBMS engine. BLOBs are a bad idea as they almost always allocate a full page (one cluster iirc) regardless of how big the BLOB is. And using millions of tables just seems bizarre as the overheads of managing the tables will be ridiculous. I suspect, but dont know for sure that Sybase would be very unhappy with a DB with a million tables in it, but i know for sure that it is quite happy to have tables with 120 million records in them.
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