[Bioclusters] Questions on mpiBLAST

Xiaowu Gai xgai at genome.chop.edu
Thu Feb 3 16:34:16 EST 2005

Thanks everyone for the quick and excellent responses.  So, it does not
appear that I did something totally wrong here.   I guess I had expectations
too high to start with, after reading an article saying that mpiBLAST is 170
times faster, and I have never had experience of one blast run taking a time
more than 170 X 1.4 minutes.  I played with larger query data sets:  the
time needed does kinda level off dramatically with a smaller database (the
yeast genome), but was not that obvious for larger data sets like nt/nr or
human genome.  The query sequences are not biased in that they are not
really repetitive sequences.  But Aaron's suggestion of the --disable-mpi-db
might be the key.  I will try it and let everyone know if I do see a



On 2/3/05 3:39 PM, "Aaron Darling" <darling at cs.wisc.edu> wrote:

> I'd like to make a brief addendum to Jason's excellent reply...
> Jason Gans wrote:
>> Hello,
>> There are a number of reasons for the results you show below.
>> 1) Load balancing.
>> The latest version of mpiBLAST uses a master node and
>> a scheduler node. Hence if you run mpiBLAST on 16 nodes, only 14 worker
>> nodes will being performing the actual BLAST search (i.e. the heavy
>> lifting).
>> If you format your database into 16 fragments, 12 worker nodes will be
>> assigned 1 fragment each and 2 worker nodes will get 2 fragments. This
>> is fine
>> for a large query (and may actually improve load balancing) but for a
>> small query
>> the nodes that must search 2 fragments will be the rate limiting step
>> in your calculation.
>> You're better off formatting your database into 14 fragments (so that
>> every worker
>> node searches a single fragment).
> The "scheduler" process performs almost no work, so to really optimize
> performance on a 16 node cluster one could try formatting the database
> into 15 fragments and running 17 processes.  Of course, care must be
> taken that the node which runs two processes is running a scheduler and
> either a worker or output.  The best way I can think of to achieve this
> would be adding the following at line 178 of mpiblast.cpp (version 1.3.0):
> scheduler_process = node_count - 1;
> That will set the last MPI process to be the scheduler.  AFAIK, mpich
> (and possibly other MPI implementations) will wrap around to the first
> node when assigning processes beyond the number of nodes given in the
> mpich configuration.  The net result being that the scheduler process
> and writer process end up on the same cluster node.
>> 2) Run time depends not just on the length of the query, but on the
>> sequence composition of
>> the query as well.
>> A query sequence that is "similar" to a large number of database
>> sequences will take longer to
>> search than a query sequence that is "similar" to a only small number
>> of database sequences.
>> The reason for this is two-fold: (a) The BLAST algorithm only fully
>> aligns two sequences if it first
>> identifies identical sub-sequences of length W or greater. (b) The
>> time that mpiBLAST spends
>> formatting the BLAST output is proportional to the number of database
>> entires that match the
>> query (not the query length).
> One additional factor that can significantly impact the run time is the
> length of DB sequences that your queries hit.  By default, versions
> 1.2.x and 1.3.0 of mpiBLAST transmit the *entire* database sequence over
> the wire, not just the portion of the sequence used in the resulting
> alignment.  Nucleotide databases like nt or the human chromosome DB
> contain sequences several MB in length, which can result in LOTS of
> network traffic.  Long sequences are not usually a problem with protein
> sequence databases.  Fortunately, a workaround exists for blastn
> searches.  The command-line option --disable-mpi-db will prevent workers
> from transmitting sequences over the network.  Instead, the writer
> process reads only the necessary parts of the sequence from the database
> on shared storage (e.g. it reads a small amount of data from NFS instead
> of a large amount of data from worker nodes).
> Summary: to get good performance, always use --disable-mpi-db when
> performing blastn searches on databases with large sequence entries like
> nt and human chromosomes.
> A nice feature for a future mpiBLAST release would be workers
> transmitting only the aligned portion of the bioseq to the writer
> instead of the entire bioseq...
> -Aaron
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