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Re: AMD vs Intel

From: Jeroen Elassaiss-Schaap <jeroen>
Date: Mon, 18 Nov 2019 23:28:52 +0100

Hi Leonid,

"A while" back we compared model development trajectories and results
between two computational platforms, Itanium and Xeon, see
https://www.page-meeting.org/?abstract=1188. The results roughly were:
1/3 equal, 1/3 rounding differences and 1/3 real different results. From
discussions with the technical knowledgeable people I worked with at the
time, I recall that there are three levels/sources for those differences:

1) computational (hardware) platform

2) compilers (+ optimization settings)

3) libraries (floating point handling does matter)

Assuming you would like to compare the speed of the platforms wrt
NONMEM, my advice would be to test a large series of different models,
from simple ADVAN1 or 2 to complex ODE, ranging from FO to LAPLACIAN INT
NUMERICAL, while keeping compilers and libraries the same. Also small
and large datasets, as in some instances you might be testing only the
L1/L2/L3 cache strategies and Turbo settings. And with and without
parallelization - as that might determine runtime bottlenecks in practice.

Just having a peek at Epyc - seems interesting (noticed results w gcc7.4
compilation). As long as you are able to hold the computation in cache,
a big if for the 64-core, there might be an advantage.

All in all I am not sure that it is worth the trouble. For any given
PK-PD model there is a lot you can tune to gain speed, but the optimal
settings might be very different for the next and overrule any platform
differences.

Hope this helps,

Jeroen

http://pd-value.com
jeroen
  
+31 6 23118438
-- More value out of your data!

On 18/11/19 6:34 pm, Leonid Gibiansky wrote:
> Thanks Bob and Peter!
>
> The model is quite stable, but this is LAPLACIAN, so requires second
> derivatives. At iteration 0, gradients  differ by about 50 to 100%
> between Intel and AMD. This leads to differences in minimization path,
> and slightly different results. Not that different to change the
> recommended dose, but sufficiently different to notice (OF difference
> of 6 points; 50% more model evaluations to get to convergence).
> Thanks
> Leonid
>
>
>
> On 11/18/2019 12:15 PM, Bonate, Peter wrote:
>> Leonid - when you say different.  What do you mean?  Fixed effect and
>> random effects?  Different OFV?
>>
>> We did a poster at AAPS a decade or so ago comparing results across
>> different platforms using the same data and model.  We got different
>> results on the standard errors (which related to matrix inversion and
>> how those are done using software-hardware configurations).  And with
>> overparameterized models we got different error messages - some
>> platforms converged with no problem while some did not converge and
>> gave R matrix singularity.
>>
>> Did your problems go beyond this?
>>
>> pete
>>
>>
>>
>> Peter Bonate, PhD
>> Executive Director
>> Pharmacokinetics, Modeling, and Simulation
>> Astellas
>> 1 Astellas Way, N3.158
>> Northbrook, IL  60062
>> Peter.bonate
>> (224) 205-5855
>>
>>
>>
>> Details are irrelevant in terms of decision making -  Joe Biden.
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: owner-nmusers
>> Behalf Of Leonid Gibiansky
>> Sent: Monday, November 18, 2019 11:05 AM
>> To: nmusers <nmusers
>> Subject: [NMusers] AMD vs Intel
>>
>> Dear All,
>>
>> I am testing the new Epyc processors from AMD (comparing with Intel
>> Xeon), and getting different results. Just wondering whether anybody
>> faced the problem of differences between AMD and Intel processors and
>> knows how to solve it. I am using Intel compiler but ready to switch
>> to gfortran or anything else if this would help to get identical
>> results.
>> There were reports of Intel slowing the AMD execution in the past,
>> but in my tests, speed is comparable but the results differ.
>>
>> Thanks
>> Leonid
>>
>>
>>
>
Received on Mon Nov 18 2019 - 17:28:52 EST

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