[mira_talk] Re: Regarding Time-estimate of mira
- From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 21 Dec 2010 09:51:44 +0530
Thanks Peter and Evan,
I had just 270GB on home and log files generated exceeded this.
So I had to run it on NFS mount (3TB ), for which I got the warning that it
wud reduce the speed by factor of 10.
It has already been 4 days and yet the program is in Pass 1.
I have 454 data with avg size 380, input 8 million reads, how much faster
wd running on home|headnode have been?
If i can get an estimate, we cd consider adding 1 tb to headnode, if that wd
really make it work faster.
As far as I have been observing it, though given an option for 30
processors, it had just used 25 for skim, for rest , it has been using max 1
processor and 25-65 % RAM, if thats the status, How should running on head
node make a difference to speed and if it does by what time can i expect my
assembly to complete.
Regards,
Ganga Jeena
On Mon, Dec 20, 2010 at 10:22 PM, Peter <peter@xxxxxxxxxxxxxxxxxxxxx> wrote:
> Hi all,
>
> Evan - Perhaps you miss-read Ganga's email? Or maybe I am...
>
> If the miramem estimate (about 70GB) is right, he should be fine with
> 512GB of RAM (that's a lot more more than I have access to!).
>
> Based on Evan's time of 7 hours for 8 million Solexa reads, I think
> Ganga should try it overnight and see. If it is still running, I think
> from the log files would be possible to give an estimate of the
> required run time.
>
> Peter
>
> On Mon, Dec 20, 2010 at 4:24 PM, Evan <evan@xxxxxxxxxxx> wrote:
> > Last run I did with 8m solexa 60bp reads on normal took just under 7
> hours
> > with 67+GB of ram and once you run out of ram your computer has to use
> the
> > hard drive which is 1000 times slower.
> >
> > I think its safe to say with your assembly and hardware you would be
> looking
> > at months (?years possibly?)
> >
> > According to this site
> >
> http://www.terryscomputertips.com/computers/speed-of-virtual-memory-versus-ram/
> > it is a difference of 1,300,000 x slower
> >
> >
> > On Mon, Dec 20, 2010 at 1:59 AM, Ganga Jeena <ganga.jeena@xxxxxxxxx>
> wrote:
> >>
> >> I am trying to do assembly of 8 million reads with mira
> >> Configuration of system is as follows:
> >> 512 GB RAM
> >> 8 hexa-core processors
> >>
> >> miramem gives me a memory estimate of 66.6 GB.
> >> How to get the time-estimate for assembly of data on my system.
> >> Regards,
> >> Ganga Jeena
> >>
> >>
> >>
> >
> >
>
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