[maker-devel] Fwd: 12core speed check

[Carson Holt]

For any users currently using the devel subversion repository.  If you need
to update, please send me an e-mail to get information on how to switch over
to our new server.

Thanks,
Carson


From:  Ramón Fallon <ramonfallon at gmail.com>
Date:  Monday, 18 March, 2013 10:35 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd:  12core speed check

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 <http://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 <tel: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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