Re: AMBER: amber8 parallel sander

From: Carlos Simmerling <>
Date: Wed, 12 Jan 2005 09:03:32 -0500

that is a good test to do. the speed is affected by 2 things: how much
the computation
time is reduced for the MD part and how much the communication time
takes for the parallelism.
if the communication time increases by more than the computation time
decreases, the run
will be slower. by doing the tests that you ran, you can find the best
number to use.

yen li wrote:

> Hi,
> Thanks Robert & Carlos for the clearifications.
> I have one more related doubt. I also timed the same simulations for
> the 4 cases: namely 1, 4, 8 & 16 processors. I find that it's the
> fastest for 4 and slower for 1, 8 &16. I can understand for 1 but
> cannot understand it getting slower for increased number of processors.
> All the processors are of the same make(Sun UltraSparc III+), same
> OS(Solaris 8), same amount of RAM(1GB each) and connected over 1GBps
> network.
> Thanks
> */Robert Duke <>/* wrote:
> Yen -
> As Carlos says, this is expected. The reason is that when you
> parallelize the job, the billions of calculations done occur in
> different orders, and this introduces different rounding errors.
> With pmemd, you will even see differences with the same number of
> processors, and this is because there is dynamic load balancing of
> direct force workload (ie., if one processor is taking more time
> to do the direct force calcs, it will be assigned fewer atoms to
> work on). You have to remember that the internal numbers used
> have way more precision than is justified by our knowledge of
> parameters, or for that matter how well the method represents
> reality, and that any one represents one of many possible
> trajectories.
> Regards - Bob Duke
> ----- Original Message -----
> *From:* yen li <>
> *To:* <>
> *Sent:* Wednesday, January 12, 2005 5:57 AM
> *Subject:* AMBER: amber8 parallel sander
> Hello amber
> I am testing the parallel version of amber8. I am running an
> md simulation over a small protein.
> I am testing the calculations on four, eight and sixteen
> processors. My problem is that, initially the energy values in
> the output files are the same, but as the simulation proceeds,
> the values start to diverge making the differences large. Is
> this kind of behaviour ok or do i need to take care of some
> parameters.
> Thanks
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Received on Wed Jan 12 2005 - 14:53:00 PST
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