As best I understand the process. Corrections welcome.
1. the rank0 process will broadcast the input file to all the workers.
2. if you've used a filter_file (-l) rank0 will also broadcast this file to
each worker.
3. The database pieces may still be available on disk from a previous run, and
if so they will not need to be re-copied. If the database pieces are needed
they will be sent to the workers. This can be done via several mechanisms, such
as transfered via mpi, or copied from shared storage, depending on your system
architecture and command line switches.
4. As each worker completes its task, it sends the results back to rank0 via an
mpi_send().
5. it may be necessary to send additional database chunks, depending on the
number of workers, number of db fragments, and previously cached, db fragments.
If so, go back to step 3.
6. when all db fragments have been searched, rank0 produces the output.
There is a bit more communication ( I believe between steps 2&3) to tell the
workers what size the complete database is, this is relevant to computing
E-scores. Aaron put in some optimizations related to this. In some cases it can
be a significant compute on rank0, but only a small amount of info is broadcast
to the workers.
--
Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
----- Original Message ----
From: Ruini Xue <[EMAIL PROTECTED]>
To: [email protected]
Sent: Monday, March 26, 2007 7:08:09 AM
Subject: [Mpiblast-users] file access patterns in mpiBlast
Hello, everyone,
I want to know how mpiblast handle the input and output files. For
example, if I run:
mpirun -np 5 mpiblast -d ecoli.nt -i input -o output -p blastn
5 processes would be started in the cluster, and each one copies small piece of
the database to its local folder. How about the `input' file? Is it distributed
to all workers by rank 0? What about `output'? Does rank 0 collect data from
all workers and write them into output? It's kind of you explain the workflow
of mpiblast, for I am a newbie to it.
Best
Andrew
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