MS-MPI

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 > > > > [email protected] > > > > @PD_value > > > > +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 > > > > > > [email protected] > > > > > > (224) 205-5855 > > > > > > > > > > > > Details are irrelevant in terms of decision making - Joe Biden. > > > > > > > > > > > > -----Original Message----- > > > > > > > > > > > > From: [email protected] < [email protected] > On Behalf Of Leonid Gibiansky > > > > > > > > > > > > Sent: Monday, November 18, 2019 11:05 AM > > > > > > To: nmusers <[email protected]> > > > > > > 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 > > > > Page Title > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- Sam Liao Pharmax Research Inc. 14 Upland, Irvine, CA 92602 Phone: 201-9882043 efax: 720-2946783 www.pharmaxresearch.com