Linux HP Itanium Quadrics

From: Alessandro Cembran (
Date: Fri Nov 10 2006 - 17:04:45 CST


I am running NAMD 2.6 in parallel on this machine:
It's a HP/Linux Itanium2 1.5MHz Madison with QsNetII/Elan-4 Quadrics

Right now I'm running the Linux-ia64 (Itanium) pre-compiled executable
with charmrun:
charmrun namd2 +p16 ++nodelist job.nodelist job.conf > job.out

I compared the test of a 16 processors job on this HP machine with what
I got on a 16-processors node on an Altix machine mounting the same
Itanium 1.5GHz Madison processors. (On Altix I used the Linux-ia64-MPT
(SGI Altix) pre-compiled binary with mpirun).

While the CPU time is similar for both machines (i.e, ~0.3 sec/step),
the Wall time is significantly different: on Altix it is the same as the
CPU time (~0.3 sec/step), while on the HP cluster I get something around
0.42 sec/step. Overall, on the HP the job is ~30% slower.
The AVG LDB on altix is ~32.5, while on HP is ~37

I was wondering if anybody has some clue in this performance difference.
Is this the best that I can get because Altix is a shared-memory system
and the HP cluster instead has an intrinsic slow-down due to the
communication among nodes? Or is there any way I can improve the
performances, by tweaking some MPI variables or by recompiling the code
with specific flags?

Thanks in advance,


Alessandro Cembran,PhD
Post Doctoral Associate
Mailing Address:
Univ. of Minnesota, Dept. of Chemistry
G2, 139 Smith Hall 207 Pleasant St SE
Minneapolis, MN 55455-0431
Univ. of Minnesota, Walter Library
117 Pleasant St SE, Room 473
Phone: +1 612-624-4617

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