[Bioclusters] ncbi blast

Susan Chacko bioclusters@bioinformatics.org
Wed, 23 Jun 2004 13:36:49 -0400

On Jun 23, 2004, at 12:22 PM, Joe Landman wrote:

>   Ok.  Which binary are you using?  Did you build it yourself?  Is it  
> one of the
> precompiled ones (including the Scalable Informatics LLC version)?   
> Would you
> mind sharing it?

I'm using NCBI's precompiled binary -- the one from

> What happens if you boot one of the units with a "mem=1024M" option,  
> which
> forces Linux to use only 1 GB ram?  There are some oddities that  
> happen at the 4
> GB region (really 3.8 GB or so depending upon which kernel you are  
> using).

I tried this, and still get the failure. I've also run my test on 1Gb  
and 2Gb nodes with about the same failure rate as on the 4Gb nodes.

>  If I build a static binary of blastall, would you be willing to give  
> it a try?

Yes, I'll definitely try it if you are willing to build a binary.

>> I've also run Blast with the same db+query on an SGI Origin 3400 with
>> no failures, using -a 2, -a 3, -a 4.
> I presume this is with the native MIPSpro compilers (very good  
> compilers BTW)
> and not gcc?

This is NCBI's precompiled binary:

There is limited information about how they compile it, but I'm hoping  
NCBI will provide some answers when they respond to my email.