[Beowulf] Re: energy costs and poor grad students

Mark Kosmowski mark.kosmowski at gmail.com
Thu Jul 10 09:29:51 EDT 2008


A couple weeks ago I complained about energy costs with respect to my
personal cluster used for graduate work.  I received a great deal of
excellent advice as well as some offers of compute time when I'm ready
for production runs.  Thank you everyone!

My solution so far has been to consolidate my DIMMs onto one
workstation - I have 14 Gb on it.  During this process I learned which
of my 2 Gb DIMMs was bad.  I'm also in the process of upgrading my
entertainment machine to a 64 bit dual-core Athlon Linux box to be
used as a part-time compute node as needed.  Also, I'm on the lookout
for a couple cheap 2 Gb ECC registered DDR 400 DIMMs to bring the
workstation to a full 16 Gb at some point.  I may also keep an eye out
for multi-core Opterons.

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.

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
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?

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?

Thanks,

Mark E. Kosmowski
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