Just out of curiousity, how many fragments are being created for
this large database? mpiformatdb simultaneously opens somewhere
between 4 and 7 files per fragment.
As few as 5, and as high as 64. My observation is that I can crash
the SAN metadata controller with 64 fragments, and that I get
steadily improved performance (in terms of time to complete the
formatdb) as I decrease the number of fragments. The sixteen that
I'm using now is a compromise.
I'll look into the wrapper script idea.
Out of curiosity, has anyone taken one of the many "your very own
relational genbank" implementations and used it to feed the formatdb
process? It seems like it could speed / simplify the process.
-Chris Dwan
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