[Beowulf] Re: energy costs and poor grad students

Joe Landman landman at scalableinformatics.com
Thu Jul 10 10:00:24 EDT 2008


Mark Kosmowski wrote:

> 
> I have also decided to upgrade my software to try an eek a little
> speed out of things.  I've done a clean install of OpenSUSE 11.0 using
> KDE 3.5 (I need the GUI for the workstation) and will be installing
> the latest versions of OpenMPI, CPMD, compilers and math libraries.

Great.

> 
> Some people on the CPMD list (my primary code at this point - plane
> wave quantum chemistry) suggest fftw as part of the math library
> solution.  I noticed that only fftw 2.1.5 supports MPI, while the
> latest version of the 3.x series does not.  Eventually I will be
> running large jobs and may need to go back to a cluster, so I'm
> interested in keeping my code MPI-ready and running two processors
> that way.  I will likely use the ACML (AMD math library) for the
> functionality not provided by fftw.  I am uncertain whether I will use
> ifort or gfortran at the moment.  I'd be willing to look at the Sun
> suite.  Other then hopefully a PhD at some point, I am receiving no

Hmmm...  My own tests with the Sun compiler suite about a year to year 
and a half ago suggest it doesn't generate as good code (e.g. fast code) 
as the gnu compilers.  This was true on Solaris 10 and Linux.  Baseline 
RHEL 4 with gcc generated faster code for most of the tests I ran. 
YMMV, but I wouldn't advise going the Sun compiler route unless it 
generates demonstrably better code (and it didn't for me).

> compensation for my research, so ifort is a free option.
> 
> Is fftw 2.1.5 and the latest acml a reasonable combination for speed /
> efficiency or is there a different combination of math libraries that
> stands out for speed?  Is the choice of math library yet another
> instance of the actual application makes a difference on which on is
> fastest?

You may be able to get the Intel MKL on a similar license as the 
compiler, I am not sure.  Check it out.

> 
> Also, is there a recent compiler benchmark somewhere?  The one at
> Polyhedron seems a little dated - the ifort cited is known to have
> issues with the code I use and the Sun compiler is given as 8.x when
> 12.x is available now.  If I break down and decide to run my own
> benchmarks on actual code are there any restrictions on the free
> versions of ifort and Sun to share the results?

I did tests with gcc, ifort, pgi, and the sun compilers on a particular 
code (HMMer) about 2 years ago.  pgi was the best, followed closely by 
ifort and gcc.  Sun trailed badly.  This was with baseline and maximal 
optimization.

HMMer is very different than MD though, so YMMV

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
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