Re: AMBER: compiler for amber8 on opteron

From: Robert Duke <>
Date: Fri, 18 Mar 2005 08:11:22 -0500

Marc -
I had the same concerns about the intel compiler working well with opterons,
but with the introduction of their 64 bit chips (EM64 stuff, not itanium),
they have ended up producing a compiler that is roughly equivalent to the
pgi compiler in performance, based on some benchmarking I did at Utah on
pmemd. Now, there is another compiler, rather new, that is being very well
received for use on opterons; of the two generic opteron cluster facilities
I have access to, they are both using it as their primary compiler. In my
hands, it was faster and easier to work with. This is the pathscale
compiler, pathf90. I posted a couple of long emails to the reflector, first
about benchmarking pmemd on the utah clusters with pathscale, and then I
released some updated configuration info for a pmemd (new_configure)
utility (the actual config source is available as a link from that included the opteron and also included some
comparison between ifort, pgi, and pathscale. You might want to look on the
reflector and web site for this info. I need to get Dave to post the
benchmarks on the website so everyone can see what the opterons can do. I
did not originally respond to your mail because I have not evolved
configuration support for the entire amber package for the opteron, and I
know the original release there included pgi on the opteron but not ifort
(where you should get the EM64 version) or pathscale. I would suggest you
can adapt from the pmemd config.h to set up the overall config.h, however.
Be aware that there is a sander optimization problem with ifort, whereby the
extra points code does not work properly if you optimize sander to the same
level that pmemd is optimized (one of the reasons I retained separate
configuration for pmemd).
Regards - Bob Duke

----- Original Message -----
From: "Marc Petitmermet" <>
To: <>
Sent: Friday, March 18, 2005 3:22 AM
Subject: Re: AMBER: compiler for amber8 on opteron

>> Performance on Opteron
>> ifort >> pgi >> gcc
> I never thought of the Intel compilers because, well, doesn't Intel
> compilers optimize for Intel CPUs only? You seem to have experience with
> these different compilers, therefore, I will proceed as you suggested.
> Thanks for the advice.
> Regards,
> Marc
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Received on Fri Mar 18 2005 - 13:53:01 PST
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