[maker-devel] 12core speed check

[Carson Holt]

It should use 2 physical cores.   Hyperthreading shouldn't come into play
unless you start more processes than there are physical cores.  I haven't
seen any big performance advantage in most cases with hyperthreading on
linux machines.  I find more often than not it just confuses students into
thinking there are free processors and then starting too many jobs.

--Carson



From:  Olaf Mueller <olaf.mueller at duke.edu>
Date:  Thursday, 14 March, 2013 12:13 PM
To:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] 12core speed check

    
 The X5675 supports hyperthreading. Does i.e. "mpiexec -n 2 maker" use 2
physical cores or 2 threads of the 1st core? If the latter happens it would
be interesting to see your series extended to -n 24.
 
 Cheers
 Olaf
  
 
On 03/14/2013 11:19 AM, Ramón Fallon wrote:
 
 
> 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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> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org
>  
 
 
 
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