[gmx-users] poor performance of gcc3.1 compiled Gromacs on Athlon

[mark vaughn]

Greetings:

I have been experimenting with a 2-node 4 cpu mini-cluster in
preparation for a larger cluster.  Quick and dirty benchmarks indicate
4-cpu scaling is reasonable, but when Gromaces is compiled using the new
Gnu 3.1 compiler, performance takes a real hit, at least on the d.dppc
benchmark.

For the d.dppc benchmark, Gromacs 3.1.4, system info below. MPI, FFT
were compiled with the same compiler as Gromacs, Lam-MPI version was
6.5.2 from RPM and 6.5.6 from source. Gromacs was configured with
--enable-mpi --enable-float --enable-shared (--enable-shared make failed
with icc  because of an apparent libtool incompatibility). icc used with
-O3 flag. (*) means these were obtained directly from the log file, Real
is in min:sec

compiler                ps/NODE hr(*) ps/day  Real(*)
---------------------------------------------------------               
downloads page rpms 1cpu   3.654       88.7     164:13
gcc 3.1	 1-cpu             2.936       70.5     204:20
icc 6.0  1-cpu             3.771       90.5     159:05

gcc 3.1  2-cpu, smp        7.627      183.0      78:40
icc 6.0  2-cpu  smp       10.471      251.3	 57:18 


I am mystified about this; the reason I used gcc 3.1 to began with was
that on one of the parallel processing software (ATLAS package for
linear algebra)  warned of poor performance from 2.96-3.04 versions and
suggested either pre 2.95 or 3.1. Furthermore, I thought 3.1 was a
release to enhance performance.

Any ideas? Perhaps I am just forgetting something simple. (BTW Eric
Lindahl: I see you posted about the icc/libtool compile problem some
time ago, were you able to resolve it?)

system: Asus A7M266-D dual AMD motherboard,athlon, 2 MP1900+ running at
1600 MHz, 512kDDR266 memory, IBM ATA100 drive, Mandrake 8.2, 2.4.18
kernel, minimal services, no X, private 100Mbit network. 

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