[mira_talk] Re: Out of memory detected : std::bad_alloc
- From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 17 Aug 2010 16:28:10 +0200 (MEST)
----- 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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