[Bioclusters] batching of blast searches

Justin Powell bioclusters@bioinformatics.org
Tue, 18 Mar 2003 14:54:36 +0000

On 18 Mar 2003, Joseph Landman wrote:

>   You are fighting the database load (actually an mmap) time, as well as
> the queue latency, against a sequence comparison time, which is
> dominated by the search portin.

I'm not sure I understand how the whole linux page cache and mmap thing
works, but naively I would assume that the VM system knows that the
pages in the cache still contain the mmaped database, and can bring them
in using hardware page mapping rather than any kind of memory to memory
copying? In which case database loading (assuming the whole db fits in
memory) should be insignificant on subsequent runs?

justin powell