RE: [openMosix-general] did anyone compare the efficiecy between mosix cluster and standalone pc

[<mic...@sy...>]

> I would like to solve that tedious bug 
> with complete nt database. Did someone
> else have my same troubles with it?

Yes.  There is a conflict between the openMosix blast patch and the
pre-formatted nt database.  Try downloading nt itself and formatting it with
formatdb yourself.

Also, I don't have the benchmark numbers handy right now, but my initial
tests with and without the openMosix blast patch showed that the patch
caused blast to run about 20% slower (single node to single node
comparison).

So I am not using the blast patch.  I went with an MPI solution and am very
satisfied with it.  Similar to the DFSA solution, I put all the blast
databases on every node and then tell the MPI-farmed process to find the
blast dataset on its local host.

On a related note, when my MPI processors invoke blast, I have been wrapping
it in a "mosrun -0", but after seeing the discussion here on using MPI on
top of (open)Mosix, maybe I shouldn't?  Perhaps openMosix will migrate the
MPI processor if there is a less busy node?  I'll have to try it...

-Michael Peterson


-----Original Message-----
From: ben
To: ope...@li...
Sent: 8/31/02 7:57 AM
Subject: Re: [openMosix-general] did anyone compare the efficiecy between
mosix  cluster and standalone pc

I would like to solve that tedious bug with complete nt database . Did
someone else have my same troubles with it ?
I gave a look to openmosixblastpatch diff file and I saw that the patch
removes trheads and memory mapped i/o from  plain blast
to permit dfsa migration.When this is done blast stores its data into
buffers
rather than into shared memory. As patched blast behaves
nicely with smaller databases but fails with the big one can I infer
that
this might be a buffer lenght / storing / acces problem?
I will try to leave mm-i/o support and see what happens ....