[Bioclusters] multiple inputs to MPIBLAST

Aaron Darling darling at cs.wisc.edu
Wed Mar 9 17:11:25 EST 2005

Hi Lik

The bad behavior could be due any one of a number of factors (extra 
fragment copies, startup overhead, etc).  In order to pin down what's 
going wrong on your setup it would be helpful to have a debug log as 
generated by adding the --debug command line option.  Debug goes to 
stderr, redirect as appropriate for whatever shell you use.  As the 
mpiblast debug log can get lengthy you may want to send it directly to 
me or post it on a web server somewhere...


Lik Mui wrote:

>Hello, I tried to feed multiple inputs to mpiblast (all in a single FASTA
>file).  I found that when the number of inputs is > 15, mpiblast's
>performance GREATLY deteriotes.  For example, using 1 single head node, I
>get a blastall output in about 20 seconds.  When I feed an input of 20
>input sequences to MPIBLAST on a 24 node cluster, the result takes 3
>minutes to get back.  This is hardly super-linear.
>I am running on a 24 nodes Platform ROCKS cluster with MPICH 1.2.6, and the
>latest MPIBLAST 1.3.0.
>Can anyone explain why this is or how to get around MPIBLAST slowing down
>with multiple inputs.
>Thanks in advanced.
>           Lik Mui
>p.s. because my genome db is about 1 GB, it seems to make sense to process a
>batch of inputs together with a single read of the db.  Hence, I am running
>multiple input files.  If this is not correct reasoning, please comment.
>Bioclusters maillist  -  Bioclusters at bioinformatics.org

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