[Bioclusters] Daemonizing blast, ie running many sequences through 1 process

[Farul Mohd. Ghazali]

On Fri, 7 Nov 2003 Michael.James@csiro.au wrote:

> We have a problem with 66 nodes becoming NFS bound
>  when blasting many (>10,000) sequences
>  against the same database set.
>
> One approach (which we are trying) is to cache database files locally,
>  so nodes can re-read their files without bottlenecking on NFS.
>
> A totally different approach, with even better performance potential,
>  would be if a blast process could start up, load its database(s)
>  and process multiple queries until told to exit.

Solaris has a CacheFS filesystem used to cache NFS mostly read filesystems
on the local disk for slow connections including PPP. This would be ideal
for your situation, however I don't know if Linux has anything similar.

http://docs.sun.com/db/doc/806-4073/6jd67r9jd?a=view

Of course this requires a local disk. If you're running diskless, it's
going to be a bit more difficult.