Re: [tlug] Making better use of SSDs?

[Raymond Wan <rwan.kyoto@example.com>]

Hi Nava,


On Tue, May 29, 2012 at 7:27 AM, Nava Whiteford <new@example.com> wrote:
> 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.


Yes -- if they were handing out SSDs out with tissue packs at the
train station, then no harm in trying them out!  :-)  Especially for
just scratch space.  But, they'll have to be purchased and if they
are, then it's a matter of whether or not they're worth the price.


> 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.


Yes, you're right!  Unlike table access in a database, bioinformatics
software do tend to be sequential.  It isn't like being open-source
would help; the algorithms operate sequentially.

The many reasons by others here against using it as swap space are of
course valid.  Many of them I never thought of.  So, using it as a
disk seems to be the best option and, if so, the benefit is going to
be marginal.

At least, until someone develops bioinformatics software with SSDs in mind...

Ray