Hi,
Are you even able to fit a simple animal model?
You need more memory (many many gigabytes - actually a 64 bit processor as
well since on x86 chips, 32 bit processors, a single application is
limited to 3-4GB with some very slow work arounds. This was a topic on
Linux kernal mailing lists http://kt.zork.net/kernel-traffic/.). An out
of memory error will occur when forming the equations.
You should also reduce your pedigree size as most animals don't have
records (30%?). So I would try three to four generations only from the
animals with records. Then it is a matter how good ASREML deals with
memory - 2GB is about 2E9 bytes, assuming 16 bytes (space required by a
double) that leaves space for about 11,180 animals if you had to form the
dense equations. That is assuming my calculations are correct but under X
you will have around 1.5GB free ( use the 'free' and cat /proc/memory
commands).
Or change to a Gibbs sampling model or different model.
Note that you can claim back around 30MB by NOT running X and a
Window manager (change into runlevel 3 - /sbin/telinit 3 AFTER closing
all applications). On my RH7.1 17MB is X and another 10 is KDE.
I, for one, would be very interested in the largest model that you can
run.
Regards
Bruce
On Thu, 30 Aug 2001, Denny Crews wrote:
> ASREML'ers:
>
> I was wondering if anyone has got a good idea of how large a problem ASREML might successfully complete. For example, I have a single trait genetic (variance components) analysis, with n~280,000 and approximately 850,000 animals in a-inverse.
>
> I am running on a Linux (RedHat 7.1) workstation with two Xeon 933 processors, 2GB RDRAM and about 4 GB swap space. Using the above data, the model specifies 2 random effects (direct and maternal genetic) in addition to the residual. Repeated attempts to run this job result in an error message: Too BIG! use -s option. The job was invoked using, for example, the command:
>
> $ asreml -s8 weight
>
> Apparently, ASREML forms and writes ainverse.bin without a problem, so the error occurs either while forming the equations or during iteration. The appropriate .asr file is attached.
>
> Any thoughts or comments would be appreciated.
>
> DENNY
>
>
> *************************************************************
> D. H. "Denny" Crews, Jr.
> Research Scientist and Leader
> Beef Cattle Genetics
> Agriculture and Agri-Food Canada Research Centre
> 5403 1st Avenue South
> Lethbridge, Alberta T1J 4B1 Canada
> 403-317-2288 voice
> 403-382-3156 fax
> dcrews@em.agr.ca
> *************************************************************
> A wise man will hear, and will increase learning,
> and a man of understanding shall attain unto
> wise counsels. Proverbs 1:5
> *************************************************************
>
>
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