[maker-devel] 12core speed check

[Mark Yandell]

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.
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