[maker-devel] 12core speed check

[Olaf Mueller]

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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