Re: [tlug] Making better use of SSDs?

[Nava Whiteford <new@example.com>]

You'll obviously get some benefit from using SSDs for Bioinformatics, but I know of no Bioinformatics tools that currently take advantage of the constant time random access offered by SSDs.

For example, the alignment tools I know of tend to create reference indexes in memory, and align reads sequentially. So your reference genome and reads both get read sequentially.

On Mon, May 28, 2012 at 11:28:42PM +0800, Raymond Wan wrote:
> 
> 
> Hi Satoshi,
> 
> 
> On Monday, May 28, 2012 05:15 PM, satoshi.nagayasu@example.com 
> wrote:
> > I recommend #1 option, and have your own experiments to examine
> > whether SSD benefits your system performance.
> ...
> > Generally speaking, it's safe to say SSD would increase the performance.
> > But practically, you need to determine a type of workload (or a bottleneck
> > of workload) that you're running. And it's really fun! :)
> 
> 
> That is true.  Actually, the software we are considering are 
> neither database systems nor Unix tools like 'sort'.  Sorry 
> for mentioning them in my original post -- they weren't 
> meant to mislead any of you, but to generalize my question.
> 
> The software we are using are actually bioinformatics tools. 
>   While there are many users, the user base is still tiny 
> compared PostgreSQL.  So, there aren't many benchmarks that 
> look into how they perform with combinations of HDDs and SSDs.
> 
> Thanks for your suggestion!
> 
> Ray
> 
> 
> 
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