AMBER Archive (2004)

Subject: Re: AMBER: pmemd machinefiles

From: Robert Duke (
Date: Mon Mar 29 2004 - 08:27:17 CST

Lubos -
In the pmemd 3.1 timeframe, I did not support itanium or opteron machines,
mostly because I did not really have access to them. For the Amber 8
release, I started working on an sgi altix (an itanium 2 smp), titan at ncsc
(an itanium 1 linux cluster), and I also had a dual opteron workstation. I
got all working, but the dual opteron was never particularly stable, and I
either had a bad motherboard, or there were heating problems associated with
running molecular dynamics (I had frequent crashes when running sander 7
compiled with g77, and even more frequent crashes running pmemd compiled
with ifc (which runs about twice as fast) - in both cases I never got
through to even trying to run both processors). I would like to see someone
have success with the opterons, but I am not going to waste more time being
the guinea pig myself, and have sent my dual opteron back to the
manufacturer to be replaced with a dual pentium which I am sure will be
slower, but stable. I will send some machine files for pmemd 3.1 adapted
from the amber 8 pmemd "config_data" files separately in a little bit (I
have had problems with the reflector filtering attachments). These will be
an untested starting point you can use for your systems. Please let me know
how it goes. If anyone else also wants these, let me know.
Regards - Bob
----- Original Message -----
From: "Lubos Vrbka" <>
To: <>
Sent: Monday, March 29, 2004 8:34 AM
Subject: Re: AMBER: pmemd machinefiles

> bob,
> thanks for clarification. just one more question. i plan to try to
> compile and run pmemd on our 64bit machines (both itanium and opteron).
> are there any special changes to makefiles needed? which makefiles
> should i use?
> i was trying to find some info on web, but no luck...
> thanks,
> --
> Lubos
> _@_"
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to