[Bioclusters] Large memory blast servers

Michael Cariaso bioclusters@bioinformatics.org
Wed, 10 Dec 2003 11:59:56 -0500

Thank you very much. That keyword made it possible to find new info with 

In particular the responses in this usenet thread, are quite helpful

Another promising avenue I've learned about is PAE - Physical Address 

"an Intel-provided memory address extension that enables processors to 
expand the number of bits that can be used to address physical memory 
from 32 bits to 36 bits, through support in the host operating system 
for applications using the Address Windowing Extensions (AWE) API. PAE 
support of up to 64 GB of physical memory for applications running on 
most 32-bit (IA-32) Intel Pentium Pro and later platforms.
Both Linux 2.4+ kernels and newer windows server OSs support PAE.

It seems that a version of BLAST that could address 64G would be a 
significant benefit to the community. Does anyone have any idea what 
would be involved in adding PAE support into NCBI-BLAST?

Mitchell Skinner wrote:

>On Fri, 2003-12-05 at 11:42, Michael Cariaso wrote:
>>a ram cache of the db will be a big help
>>but a linux process can only use 2 or 3GB [1]
>>[1] I've heard 2 & 3 from different responders.No definitive answer yet.
>This depends on your kernel configuration.  For the stock Red Hat 7.3
>kernel, for example, it's 3GB.  I believe the relevant configuration
>option is CONFIG_1GB.
>Bioclusters maillist  -  Bioclusters@bioinformatics.org