[mira_talk] Re: memory usage
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 30 Oct 2012 20:25:21 +0100
On Oct 30, 2012, at 10:16 , Dimitar Kenanov <dimitar@xxxxxxxxxxxxxx> wrote:
> i was reading the manual about memory usage and saw that i can use my swap
> for up to 20% of the needed total memory.
> I have 25M PE Illumina reads. So if MIRA is using about 1.5 Gb RAM per 1M
> reads i need roughly 25*3=75GB RAM. Well i dont have so much :) but i have 64
> and i specially made a swap of 32GB RAM. So i would need additional ~ 11GB
> RAM from the swap which is less then 20% of the total needed.
> Do you think i can try MIRA under that circumstances?
It will be painful, even if the swap is on SSD. If it's on disk, forget it
immediately. However, I think the memory is too tight.
> And one more technical question i think. Surely there is connection between
> the length of the reads and the RAM needed. For example the above estimation
> is for reads which are 100bp (from previous communication). But my reads
> after the trimming are 64bp. How does this relate to the memory consumption?
First: I hope you did not trim via quality values with fastx or similar
programs. You'll get a bias.
Regarding RAM: of course there is a linear effect, but there's also a basic
memory need of >200 bytes per read … even if the read is 0 bytes long.
Regarding memory used by threads: compared to the memory needed by 50m reads,
the additional needs are infinitesimal.
Hope that helps,
Bastien
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