[gmx-users] pentium III vs Pentium IVs and Intel compiler benchmarks

[mark vaughn]

Greetings,

I was literally filling out a PO for a couple of dual Athlon machines,
but this P4 talk has made me rethink my plans.  I am new to Gromacs and
MD for the most part but I have leaned a great deal from the discussion
in this group.

I am interested in the effect of mechanical forces on lipid membranes
and how those forces affect membrane protein and lipid organization.
With this in mind, I have been trying to understand how to do MD on
systems in which surface tension is controlled.  From the discussions in
this group, I am under the impression that this may be one of those
situations in which double-precision is necessary, or at least
desirable. As I undertand it, the need for double precision arises
primarily to keep the fluctations under control.  Normally, I would have
run some tests before I posted, but since the P4/double precision topic
is hot, I thought I should ask now.

My two questions are:
1) Is double precision necessary/useful in working with membranes that
are "stretched" and/or in which surface tension is controlled?

2) If double precision is required, are the P4 capablities appreciably
better for Gromacs?  I have seen the P4 trounced by Athlon in single
precision benchmarks, but I do not believe I have seen double precision
benchmarks. 

Intel C compiler:
Along with others, I have also been curious about the the Intel compiler
vs gcc, so I ran some simple benchmarks using the cpeptide demo.  For an
old dual PPro machine the Intel compiler made some difference (see
below) for a new dual PIII machine there was little difference. The
results are for a single-precision sumulation using cutoffs (I did not
want to recompile fftw with the icc compiler). Recompiling Gromacs with
icc was trivial (thanks Gromacs team!)

for PPro 192M Ram, 233Mhz 2.4.18SMP kernel (no assembler loops)

About 6% increase in performance for  intel c compiler over gcc 3.0.4
About 14% increase in performance for  intel c compiler over gcc 2.96
About 8% increase in performance for gcc 3.0.4 over gcc 2.96

For PIII 1G Ram, 1000 Mhz, 2.4.8SMP kernel (assembler loops)

About 4% increase in performance for intel c compiler over gcc 2.96

Note: performance means ps simulation/hr cpu time. 

Thanks

Mark Vaughn
Assistant Professor
Chemical Engineering Department
Texas Tech University
PO Box 43121
Lubbock, TX 79409-3121

phone   806-742-5158
fax     806-742-3552
mark.vaughn at ttu.edu