Joachim -
My opinion on this may be a little outdated, as I have not recently tried an
AMD Opteron-based system. I wanted to post something nonetheless, to
emphasize that especially with pmemd, you must be sure that the overall
system is well architected for cooling the cpu. PMEMD really drives the
processors to their limits, and this generates a lot of heat. So you must
be sure that whatever system you buy, the cooling is adequate (and an
inadequate system can sit running the OS all day and then get flakey when
you fire up your MD run).
SO, of course your two basic linux choices, presuming we are talking
relatively inexpensive systems, are something in the intel pentium 4 lineage
vs. some sort of amd opteron. The upside for the pentium 4 is that 1) chip
quality and speed are a given, 2) it will be available from a first tier
vendor in a system configuration that optimizes overall system performance,
3) because it is available from a first tier vendor, the system itself
should also be reliable and reasonably quiet (I really like Dell machines in
the US), and 4) while the intel fortran compiler has been problematic, it is
very fast and free for the academic community, and you can bet your bottom
dollar it will not work worse with a pentium than it does with an opteron.
The downside for the pentium 4 is 1) you will pay a little more for it, and
2) it may be a little slower than an opteron. For the opteron, the upside
is price/performance. The downside is 1) there have been heating problems,
at least with some early configurations, and 2) amd chips tend to be
available from 2nd and lower tier vendors, who tend to produce cheaper boxes
of lower quality. I have been through the wars on this one. I like the
little guy and want to give him a chance. I led the charge on athlons in
amber, and still have two. My athlons came from a second (if not third)
tier vendor; the athlon was wonderfully competitive with the early pentium
4's on price and performance. Now the bad news. In the first couple of
years I had to replace 1) a cpu fan, 2) a motherboard, 3) a monitor, and 4)
two system fans on the two systems (fans without ball bearings are cheap and
unreliable). I lost a couple of weeks tracking down flakey machine problems
that were due to flakey memory (inadequate power-on self test and
diagnostics). When the opterons came out, I grimaced and led the charge
again (slow learner), because after all, I am the amber performance guy (or
at least I think so ;-)). The system I got was a dual opteron, hot in all
respects, unbelievably noisy, and from a third tier vendor. I spent 3
months dinking with the hardware (failed hardware raid controller), redhat
for amd 64 vs. redhat 32 bit, and intel fortran compilers (the ifort 8
debacle, circa early 2004). I finally got a solid enough version of the OS
and ifort configured (confirmed elsewhere on other hardware) that I trusted
the hardware (aside from heating), got the hardware to stay up for normal
stuff, and demonstrated to my satisfaction that the machine was
crashing/locking up when I fired up MD using either sander or pmemd
(including old versions of sander compiled with g77). Now, it turns out
that I could run for several hours with sander, and several minutes with
pmemd (more heat). The vendor took the machine and replaced it with a dual
pentium, and that machine is reliable and fast. The vendor also claimed
that it was a memory controller problem, not a heating problem, but never
gave me access to another system to test (though they said they would). It
is also unbelievably noisy and vibrates like a small aircraft on takeoff
(and lives in a separate room).
So my recommendation:
1) Buying a pentium 4 system from a major vendor delivers reasonable
performance for minimal hassle. I would get a dual Xeon (reputed to be a
better performer overall) version of the p4, 3.2 GHz or faster, with the
biggest cache and fastest memory possible from a first tier vendor. If you
plan on expanding, buy fast server-grade network interface cards (the intel
pro/1000 mt server adapter is nice) and make sure you have a faster pci bus
in the box. You can't go wrong doing this. For pmemd/sander, the new intel
64 bit stuff and hyperthreading do not matter. Hyperthreading does not
hurt; you can turn it off. I don't know about the 64 bit extensions, but
presume they did not screw up 32 bit performance.
2) If you like living on the edge, check the reflector for claims of opteron
boxes that work well, and ask folks if they have run pmemd successfully
there. If a vendor has a reliable box that works, this will be your best
price/performance solution, but I cannot make a recommendation based on my
own experience. I am, incidentally, still very excited about the opteron
chip. Cray is using opterons in their new XD1. I helped them get pmemd
running on an XD1, and purportedly it is really fast, though they have not
yet let me get my hands on a box, so I cannot certify any results. I
anticipate having an XD1 available for benchmarking in the next several
months though, and will then be able to point to an opteron-based system
that presumably will be really solid.
If money were no object, right now my favorite system is the sgi altix
running the itanium 2 chip. I believe it currently outperforms anything
else that could conceivably be purchased by a small organization (see the
amber web page benchmarks).
Regards - Bob Duke
----- Original Message -----
From: "Joachim Reichelt" <Reichelt.gbf.de>
To: <amber.scripps.edu>
Sent: Thursday, October 21, 2004 5:34 AM
Subject: AMBER: Wich CPU?
> Dear all,
>
> what type of CPU should I by to get the best (Linux-)System to run
> sander and pmemd?
>
> --
> Mit freundlichen Gruessen Best Regards
>
> Joachim Reichelt
>
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Received on Thu Oct 21 2004 - 14:53:01 PDT
