[maker-devel] Fwd: 12core speed check

[Ramón Fallon]

Hi!

I've tried again from two different machines, and I can't do a "svn co" nor
"svn update" on the malachite server. Can you verify the server and the svn
service is OK on your side?

Many thanks / Ramón.




On Fri, Mar 15, 2013 at 1:18 PM, Ramón Fallon <ramonfallon at gmail.com> wrote:

> Hi Mark and Carson,
>
> Many thanks for the comments and the speedy replies!
>
> Previously, I never had problem connecting to the svn server on
> malachite.genetics.utah.edu, but this morning, I couldn't connect to
> update to rev 998.
>
> I'l try again later.
>
> Cheers / Ramón.
>
>
> On Thu, Mar 14, 2013 at 6:59 PM, Mark Yandell <myandell at genetics.utah.edu>wrote:
>
>> Thanks Ramon. super interesting analysis!
>>
>>
>> Mark Yandell
>> Professor of Human Genetics
>> H.A. & Edna Benning Presidential Endowed Chair
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> ph:801-587-7707
>>
>> ________________________________________
>> From: maker-devel-bounces at yandell-lab.org [
>> maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [
>> carsonhh at gmail.com]
>> Sent: Thursday, March 14, 2013 11:51 AM
>> To: Ramón Fallon; maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] 12core speed check
>>
>> Could you update to 998.  It was a recent commit to the devel version
>> that caused a weird pause.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Ramón Fallon <ramonfallon at gmail.com<mailto:ramonfallon at gmail.com>>
>> Date: Thursday, 14 March, 2013 11:19 AM
>> To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] 12core speed check
>>
>> Hi,
>>
>> I was trying to tweak some of our machines to maximise Mpich2/Maker (svn
>> rev 997)  throughput and describe one small set of results on this mailing
>> list to allow sharing of experiences.
>>
>> I use the example input dataset "dpp_contig.fasta" with the original
>> sequence repeated 125 times within the same file (under different names of
>> course) to allow for a decent size run. This file totalled 4.019 megabases.
>> I use the dpp_proteins.fasta and  The maker_opts.ctl has "cpus=1" set as
>> the docs recommend for MPI.
>>
>> Hardware is a standalone HP Proliant SL390 with two Intel X5675 @
>> 3.07GHz, totalling 12 cores with 192GB RAM and 1TB disk (local, no NFS)
>> running Ubuntu 10.04 with 2.6.32-41 linux kernel
>>
>> commandline was "mpiexec -n <#cores> maker" within a dedicated directory
>> containing all relevant files.
>>
>>          #cores      time(mins)    Megabases/hr
>>               1           27.00            8.93
>>               2          126.25            1.91
>>               4           42.57            5.66
>>               6           25.42            9.49
>>               8           18.60           12.96
>>              10           16.67           14.47
>>              12           13.98           17.24
>>
>> I attach a png file with graph. The upshot of this particular experiment
>> is that 2 processes show anomalous behaviour and that 6 processors are
>> needed to gain an advantage on the 1 processor run, while 12 processors
>> achieves a speed-up of nearly 2 on the 1 processor version.
>>
>> I am now going to move on to a three node cluster with 2x 8core
>> processors each (so I can go up to 48 processors), so will report back with
>> higher core numbers. Any suggestions on further speed optimizations welcome.
>>
>> Cheers / Ramón.
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
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