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
jer...@pd-value.com
@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
peter.bon...@astellas.com
(224) 205-5855
Details are irrelevant in terms of decision making - Joe Biden.
-----Original Message-----
From: owner-nmus...@globomaxnm.com <owner-nmus...@globomaxnm.com> On
Behalf Of Leonid Gibiansky
Sent: Monday, November 18, 2019 11:05 AM
To: nmusers <nmusers@globomaxnm.com>
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
