NONMEM Users Network Archive

Hosted by Cognigen

Re: AMD vs Intel

From: Leonid Gibiansky <lgibiansky>
Date: Mon, 18 Nov 2019 17:54:53 -0500

Hi Jeroin,

Thanks for your input, very interesting. As far as the goal is
concerned, I am mostly interested to find options that would give
identical results on two platform rather than in speed. So far no luck:
4 combinations of gfortran / Intel compilers on Xeon / AMD processors
give 4 sets of results that are close but not identical.

Related question to the group: have anybody experimented with gfortran
options (rather than using default provided by Nonmem distribution)? Any
recommendations? Same goal: maximum reproducibility across different
OSs, parallelization options, and processor types.

Thanks
Leonid




On 11/18/2019 5:28 PM, Jeroen Elassaiss-Schaap (PD-value B.V.) wrote:
> 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 - 17:54:53 EST

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request@iconplc.com.

Once subscribed, you may contribute to the discussion by emailing: nmusers@globomaxnm.com.