Hi, thank you again for your answer.
> All of
the database fragments are accessible to rank0
If I understood, the mpiBLAST exec NCBI BLAST pass all fragments (as many
together)
just to take statistics values, It is? And it does this for each sequence of
query, ok? (This last one
question is the part that you didn’t understand in last email)
If your
answer will be “YES”, I don’t have more doubts :-).
Regards
Daniel
----- Mensagem original ----
De: Mike Cariaso <[EMAIL PROTECTED]>
Para: [email protected]
Enviadas: Segunda-feira, 26 de Março de 2007 21:39:03
Assunto: Re: [Mpiblast-users] Res: statistics of MPIBlast
>> It is assumed that the rank 0 process has access to the
complete
>> database so that it can calculate the correct effective
lengths for the entire DB
>- How the rank 0 process knows about to complete database,
if it has been fragmented? Or rank 0 process pass just parameters of length
complete DB?
All of the database fragments are accessible to rank0. It is a requirement of
mpiblast that the full database accessible to rank0. It needs this information
to compute the 'effective search space'. This effective search space is what is
passed to the workers. While related, this is different than simply passing the
length of the complete db.
> - What the PATCH does basically on NCBI Toolbox? Conceptually…
You can see the patch here. It is quite small.
http://mpiblast.cvs.sourceforge.net/mpiblast/mpiblast/ncbi_May2006_evalue.patch?revision=1.1&view=markup
The most important part is some extra fields is a key data structure in
blastdef.h. These are used to allow mpiblast to decide when it only has to do
rank0 tasks vs worker tasks, and additional statistics for the complete
database vs an individual fragment. The rest of the changes are related to
honoring those fields, or collecting and using the extra statistics.
>> For some workloads, the search space calculation can be rather
time-consuming
>- About calculate to
effective length. Is it doing to all query sequence? Because this is onerous?
I'm afraid I don't understand this portion. Please explain again? I suspect
this also relates to the 'effective search space'.
--
Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Mpiblast-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mpiblast-users
__________________________________________________
Fale com seus amigos de graça com o novo Yahoo! Messenger
http://br.messenger.yahoo.com/
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Mpiblast-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mpiblast-users
