[Bioclusters] Parallel blast SGE

David Adelson bioclusters@bioinformatics.org
Thu, 16 Sep 2004 07:50:36 -0500


This is normal.  As I understand it, it is better to run each segment 
on an individual machine rather than stack them up on half the number 
of machines.  This is because you benefit from increased IO if you 
don't have two searches sharing the same memory, bus, drive, etc...  If 
your cluster had more jobs running on it when the job was generated, 
you would see SGE take advantage of whatever free cpus it could find, 
putting two jobs/machine.  Assuming you have enough RAM on each node, 
the simplest solution to your problem is to format your db into 30 (16 
machines - head node = 15 dual cpu compute elements) chunks rather than 
14.  This will use all of your cluster when the load is low, but the 
trade off is that when the load is high you will probably find your 
searches taking longer because of queueing.  Alternatively, you can 
split your query into two and submit two queries at the same time, 
fulling using the cluster without reformatting your db.

The paradigm for iNquiry is shared computing, for multiple users using 
distributed resource management, this makes for some "inefficiency" if 
only a single user is doing most of the searches.

Dave Adelson
Texas A&M University

On Sep 15, 2004, at 10:15 AM, Juan Perin wrote:

> I am running iNquiry which utilizes Sun Grid Engine for parallel job
> processing.  BTBLASTALL is the wrapper program which takes a given 
> blast job
> from the command line and creates multiple 'blastall' commands to be 
> run on
> individual nodes.  BTBLASTALL determines the number of nodes to use 
> and the
> number of blastall threads to run depending on the number of databases 
> that
> have been created as a result of the parsing algorithm supplied by 
> Bioteam.
> My current run is searching a 1.5 gb FASTA database that was formatted 
> into
> 14 chunks.  BTBLASTALL then created 14 blastall calls which, for some
> reason, was sent each to a single CPU on each of the dual processor 
> Xserve
> G5's.  Therefore, instead of running a single blastall job on a chunk 
> of a
> database on the dual processors devoting two CPU's to a single search 
> and
> fully utilizing our 16 nodes (32 processors), We are running on 14 
> CPU's on
> 7 machines.
> I assumed that adding a '-a' option with perhaps 2 would create more 
> threads
> and force SGE to spread the jobs across more nodes, but this is 
> already done
> automatically in BTBLASTALL.  I then tried -a 4 which seemed to have 
> created
> more threads, and is now running on 8 machines instead of 7.
> My question is::: does anyone know if it would somehow be advantageous 
> to
> add a higher number to the -a option, or if there is some way to 
> configure
> SGE to run on more machines in this instance?  This is the only job 
> running
> on the cluster right now.  So I would like to run it 'all out'.  The 
> search
> is running the 1.5gb database against itself to look for duplications.
> Juan Perin
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters