[mira_talk] Re: Out of memory detected : std::bad_alloc

  • From: Gautier SARAH <gautier.sarah@xxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 19 Aug 2010 15:25:24 +0200

Thank You very much for your answer.
I launched the mapping yesterday on a server with 8*24GB and I have no error yet. I thought Mira was only using 4GB of the 32, that's why I did not try that earlier. 

Anyway I will let you know if the mapping go through.

Thanks again

Gautier

Le 17/08/2010 16:28, Bastien Chevreux a écrit :

----- original message --------

I now use Mira since 3 months with 454 data. 1 month ago, I received
Solexa data (around 29M reads). I want to use these solexa reads to
correct/extend my 454 contigs.
I have an Out of Memory error:
[...]
But the strange thing is that if I check, Mira only used 4GB of Memory
on 24GB available

Nope. Your system has 36 GiB. After loading the 29m reads, MIRA already used 32 
GiB, 1 GiB was used by the OS and 3 GiB were free.


What am I doing wrong?

Your machine has a bad set-up: only 4 GiB swap for 36 GiB RAM is not ideal. I'd 
go for a 1:1 setup there. Furthermore, you are operating at the limit of your 
machine there: miramem will tell you that you need around 36 to 40 GiB RAM for 
that project as minimum. Well, looks like you need a bit more than you 
currently have as RAM + swap.

Tip: try mapping 20m reads to see whether you like what MIRA is producing with 
your data.

B.



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