Re: AMBER: parallel AMBER/pmemd installation problem on Opteron

From: Lars Packschies <>
Date: Wed, 23 Feb 2005 17:22:59 +0100

--On Mittwoch, Februar 23, 2005 08:17:54 -0500 Robert Duke
<> wrote:

> Jyh-Shyong -
> I just hit and fixed this one while porting pmemd to a cray with opteron
> cpu's and a pgi compiler. Seems the pgi compiler is extra picky, or
> interprets variable scope nesting restrictions a bit differently. A diff
> file of the fix is:


Oh, wow, thank you, I just stumbled over this problem yesterday, only a few
minutes before Jyh-Shyong posted his report. I could compile pmemd now
(opteron, mpich (Infiniband), pgf90)

I tested Amber8 with all available patches on our opteron cluster (running
Rocks) and everything seems to work fine so far. Pmemd instead justs seems
to hang quite often, tested with the factor ix benchmark.

Interestingly, a pmemd run of factor ix with 4 slots (2 nodes) always hangs
at the same point (if it generates output at all, sometimes it just opens
the filehandle without writing to it)

NSTEP = 400 TIME(PS) = 2543.275 TEMP(K) = 298.80 PRESS =
 Etot = -234217.5764 EKtot = 54870.9021 EPtot =
 BOND = 1149

Several runs with 64 slots stopped earlier, some of them ran just fine...
Seems a bit diffuse.

Is Pmemd known to run less stable compared to sander?

Thanks in advance,


Dr. Lars Packschies, Computing Center, University of Cologne
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 23 2005 - 16:53:00 PST
Custom Search