[gmx-users] GROMACS in parallel on Dual CPU Linux machine

Erik Lindahl lindahl at stanford.edu
Tue May 20 17:40:02 CEST 2003


LAM uses shared memory for the communication within a single SMP host, 
and one of my long-term suspicions (which I haven't been able to 
confirm) is that there is either a bug in LAM or some memory controller 
heating issue that only surfaces for parallel tasks when you run the 
machine quite hot with Gromacs.

It's strange, since Xeon boxes (and some Athlons) work perfectly.



On Tuesday, May 20, 2003, at 08:32  AM, Pratul K. Agarwal wrote:

> A lot of people have responded to my queries. Here is a
> summarized response:
> 1. The motherboard is ASUS A7M266-D and the system runs
>    well without any problems. (I too have had some
>    experience with Tyan Tiger MP S2460 -- they kept dropping
>    like dead flies).
> 2. These boxes are right next to cooling vent and have
>    plenty of ventilation (the nearby temp. is around
>    65F/19C); there is an extra system fan in addition to
>    power supply fan. I am not entirely convinced that
>    this is heating issue. A suggestion has been made that
>    this might be a communication issue. Well since the
>    communication is through the loopback device (or is it
>    not for the same host?), I am not clear what other
>    hardware might be facing heating problems.
> 3. I have been able to run GAMESS, Gaussian98, AMBER (sander
>    v7) in parallel without any problems (numbers do match
>    single CPU runs).
> 4. I found out that I have Registered Non ECC memory. I am
>    wondering if this might have anything to do with it.
> *Most Importantly* I have not been able to reproduce the
> errors yesterday. The systems were rebooted before these
> tests. On the other hand when I noticed these errors
> previously there were other jobs running on the same
> machine. I will keep an eye on the issue and report anything
> new.
> Thanks to all who responded.
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