Date: Mon, 29 Mar 2004 13:05:07 -0600
From: Chris Moth
Subject: AMBER: PMEMD and myrinet trouble

At 03:56 PM 3/24/2004, Robert Duke wrote:
>Chris -
>I would first suspect the hardware, based on my past experience with
>myrinet.

Robert:

Thanks for all your round-the-clock help and suggestions with our
PMEMD-on-Myrinet troubles. All is now solved.

I hope our notes below might save time for other groups in future.

As you know, we initially suspected that our bad minimization and MD
trajectory data was a software problem with PMEMD - primarily because
SANDER ran fine on our myrinet
cluster: http://structbio.vanderbilt.edu/comp/hw/piranha/

That said, PMEMD always has run well on all our other platforms.

It turns out that there was a myrinet software problem on our end.

Installing the latest mpich software from
http://www.myri.com/scs/#downloads was the solution. This update is
required for multi-threaded software (which presumably SANDER is not) built
with ifc 7.1.

We've also learned the importance of regression testing with PMEMD in
addition to SANDER as we install upgrades to our platform (hardware, OS, or
drivers).

Small incompatibilities with platform upgrades can cause major trajectory
failures, without warning or error messages!

Again, thanks for all our help double-checking things on your hardware.

Sincerely

Chris Moth